Starting phenix.real_space_refine on Mon Sep 14 07:52:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ccr_30340/09_2026/7ccr_30340.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ccr_30340/09_2026/7ccr_30340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ccr_30340/09_2026/7ccr_30340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ccr_30340/09_2026/7ccr_30340.map" model { file = "/net/cci-nas-00/data/ceres_data/7ccr_30340/09_2026/7ccr_30340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ccr_30340/09_2026/7ccr_30340.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 588 5.49 5 S 58 5.16 5 C 16892 2.51 5 N 5488 2.21 5 O 6696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29722 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 787 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 789 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2962 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Restraints were copied for chains: L, M, N, O, P, Q, R, S, T, U, V Time building chain proxies: 9.12, per 1000 atoms: 0.31 Number of scatterers: 29722 At special positions: 0 Unit cell: (158, 165, 147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 588 15.00 O 6696 8.00 N 5488 7.00 C 16892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.0 seconds 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 66.6% alpha, 5.1% beta 286 base pairs and 510 stacking pairs defined. Time for finding SS restraints: 4.91 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.744A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.505A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.564A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.787A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.181A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.515A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.577A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.533A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.518A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.228A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 85 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 161 through 176 Processing helix chain 'K' and resid 178 through 198 removed outlier: 4.253A pdb=" N ALA K 182 " --> pdb=" O ASP K 178 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 204 removed outlier: 3.785A pdb=" N PHE K 203 " --> pdb=" O ASP K 200 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG K 204 " --> pdb=" O SER K 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 200 through 204' Processing helix chain 'K' and resid 260 through 266 removed outlier: 3.570A pdb=" N GLN K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 289 removed outlier: 3.841A pdb=" N ASN K 289 " --> pdb=" O LYS K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 335 Processing helix chain 'K' and resid 345 through 354 Processing helix chain 'K' and resid 379 through 389 Processing helix chain 'K' and resid 405 through 424 Processing helix chain 'K' and resid 429 through 433 removed outlier: 3.597A pdb=" N LYS K 432 " --> pdb=" O HIS K 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 449 removed outlier: 3.844A pdb=" N VAL K 438 " --> pdb=" O SER K 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 452 through 458 removed outlier: 3.807A pdb=" N ASP K 456 " --> pdb=" O SER K 453 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG K 457 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS K 458 " --> pdb=" O TRP K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 477 Processing helix chain 'K' and resid 497 through 513 Processing helix chain 'K' and resid 516 through 520 removed outlier: 4.176A pdb=" N ASP K 520 " --> pdb=" O PRO K 517 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 57 removed outlier: 3.744A pdb=" N LYS L 56 " --> pdb=" O ARG L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 79 removed outlier: 3.505A pdb=" N PHE L 78 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 114 Processing helix chain 'L' and resid 120 through 132 Processing helix chain 'M' and resid 30 through 42 Processing helix chain 'M' and resid 49 through 76 removed outlier: 3.564A pdb=" N GLU M 53 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 94 removed outlier: 3.788A pdb=" N VAL M 86 " --> pdb=" O THR M 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 22 Processing helix chain 'N' and resid 26 through 37 Processing helix chain 'N' and resid 45 through 73 removed outlier: 4.182A pdb=" N VAL N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 removed outlier: 3.515A pdb=" N LEU N 83 " --> pdb=" O ILE N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 97 Processing helix chain 'O' and resid 37 through 49 Processing helix chain 'O' and resid 55 through 84 Processing helix chain 'O' and resid 90 through 102 Processing helix chain 'O' and resid 103 through 123 Processing helix chain 'P' and resid 44 through 57 Processing helix chain 'P' and resid 63 through 79 Processing helix chain 'P' and resid 85 through 114 Processing helix chain 'P' and resid 120 through 132 removed outlier: 3.578A pdb=" N ILE P 124 " --> pdb=" O MET P 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 30 through 41 Processing helix chain 'Q' and resid 49 through 76 removed outlier: 3.533A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 94 removed outlier: 3.518A pdb=" N VAL Q 86 " --> pdb=" O THR Q 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 22 Processing helix chain 'R' and resid 26 through 37 Processing helix chain 'R' and resid 45 through 73 removed outlier: 4.228A pdb=" N VAL R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 90 Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'S' and resid 37 through 49 Processing helix chain 'S' and resid 55 through 85 Processing helix chain 'S' and resid 90 through 102 Processing helix chain 'S' and resid 103 through 124 Processing helix chain 'V' and resid 161 through 176 Processing helix chain 'V' and resid 178 through 198 removed outlier: 4.252A pdb=" N ALA V 182 " --> pdb=" O ASP V 178 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY V 184 " --> pdb=" O SER V 180 " (cutoff:3.500A) Processing helix chain 'V' and resid 200 through 204 removed outlier: 3.784A pdb=" N PHE V 203 " --> pdb=" O ASP V 200 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG V 204 " --> pdb=" O SER V 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 200 through 204' Processing helix chain 'V' and resid 260 through 266 removed outlier: 3.570A pdb=" N GLN V 264 " --> pdb=" O ASN V 260 " (cutoff:3.500A) Processing helix chain 'V' and resid 272 through 289 removed outlier: 3.841A pdb=" N ASN V 289 " --> pdb=" O LYS V 285 " (cutoff:3.500A) Processing helix chain 'V' and resid 331 through 335 Processing helix chain 'V' and resid 345 through 354 Processing helix chain 'V' and resid 379 through 389 Processing helix chain 'V' and resid 405 through 424 Processing helix chain 'V' and resid 429 through 433 removed outlier: 3.597A pdb=" N LYS V 432 " --> pdb=" O HIS V 429 " (cutoff:3.500A) Processing helix chain 'V' and resid 434 through 449 removed outlier: 3.843A pdb=" N VAL V 438 " --> pdb=" O SER V 434 " (cutoff:3.500A) Processing helix chain 'V' and resid 452 through 458 removed outlier: 3.808A pdb=" N ASP V 456 " --> pdb=" O SER V 453 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG V 457 " --> pdb=" O GLN V 454 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS V 458 " --> pdb=" O TRP V 455 " (cutoff:3.500A) Processing helix chain 'V' and resid 459 through 477 Processing helix chain 'V' and resid 497 through 513 Processing helix chain 'V' and resid 516 through 520 removed outlier: 4.176A pdb=" N ASP V 520 " --> pdb=" O PRO V 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.048A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 5.952A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.424A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.519A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.524A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.003A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 206 through 208 removed outlier: 5.865A pdb=" N PHE K 230 " --> pdb=" O ALA K 323 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU K 325 " --> pdb=" O PHE K 230 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU K 232 " --> pdb=" O GLU K 325 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N LEU K 322 " --> pdb=" O PRO K 361 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR K 358 " --> pdb=" O SER K 378 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 296 through 298 removed outlier: 3.602A pdb=" N ILE K 297 " --> pdb=" O LEU K 311 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU K 311 " --> pdb=" O ILE K 297 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 83 through 84 removed outlier: 7.048A pdb=" N ARG L 83 " --> pdb=" O VAL M 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 118 through 119 Processing sheet with id=AB6, first strand: chain 'M' and resid 96 through 98 removed outlier: 5.952A pdb=" N THR M 96 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'N' and resid 42 through 43 removed outlier: 7.424A pdb=" N ARG N 42 " --> pdb=" O ILE O 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'N' and resid 77 through 78 Processing sheet with id=AB9, first strand: chain 'N' and resid 101 through 102 removed outlier: 7.519A pdb=" N THR N 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'P' and resid 83 through 84 removed outlier: 6.525A pdb=" N ARG P 83 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'P' and resid 118 through 119 Processing sheet with id=AC3, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.003A pdb=" N ARG R 42 " --> pdb=" O ILE S 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'R' and resid 77 through 78 Processing sheet with id=AC5, first strand: chain 'V' and resid 206 through 208 removed outlier: 5.865A pdb=" N PHE V 230 " --> pdb=" O ALA V 323 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU V 325 " --> pdb=" O PHE V 230 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU V 232 " --> pdb=" O GLU V 325 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N LEU V 322 " --> pdb=" O PRO V 361 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR V 358 " --> pdb=" O SER V 378 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 296 through 298 removed outlier: 3.602A pdb=" N ILE V 297 " --> pdb=" O LEU V 311 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU V 311 " --> pdb=" O ILE V 297 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 728 hydrogen bonds 1448 hydrogen bond angles 0 basepair planarities 286 basepair parallelities 510 stacking parallelities Total time for adding SS restraints: 9.49 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5214 1.33 - 1.45: 10194 1.45 - 1.57: 14790 1.57 - 1.69: 1172 1.69 - 1.81: 88 Bond restraints: 31458 Sorted by residual: bond pdb=" C3' DC U 6 " pdb=" O3' DC U 6 " ideal model delta sigma weight residual 1.435 1.360 0.075 1.30e-02 5.92e+03 3.36e+01 bond pdb=" C3' DC J 6 " pdb=" O3' DC J 6 " ideal model delta sigma weight residual 1.435 1.360 0.075 1.30e-02 5.92e+03 3.30e+01 bond pdb=" C3' DC U 4 " pdb=" O3' DC U 4 " ideal model delta sigma weight residual 1.435 1.366 0.069 1.30e-02 5.92e+03 2.81e+01 bond pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " ideal model delta sigma weight residual 1.435 1.366 0.069 1.30e-02 5.92e+03 2.80e+01 bond pdb=" C3' DC I -9 " pdb=" O3' DC I -9 " ideal model delta sigma weight residual 1.435 1.370 0.065 1.30e-02 5.92e+03 2.46e+01 ... (remaining 31453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 41693 2.02 - 4.03: 3011 4.03 - 6.05: 196 6.05 - 8.07: 41 8.07 - 10.09: 13 Bond angle restraints: 44954 Sorted by residual: angle pdb=" O4' DG U -58 " pdb=" C1' DG U -58 " pdb=" N9 DG U -58 " ideal model delta sigma weight residual 108.00 113.60 -5.60 7.00e-01 2.04e+00 6.41e+01 angle pdb=" O4' DG J -58 " pdb=" C1' DG J -58 " pdb=" N9 DG J -58 " ideal model delta sigma weight residual 108.00 113.55 -5.55 7.00e-01 2.04e+00 6.29e+01 angle pdb=" O4' DA I 17 " pdb=" C1' DA I 17 " pdb=" N9 DA I 17 " ideal model delta sigma weight residual 108.00 102.45 5.55 7.00e-01 2.04e+00 6.29e+01 angle pdb=" O4' DA T 17 " pdb=" C1' DA T 17 " pdb=" N9 DA T 17 " ideal model delta sigma weight residual 108.00 102.49 5.51 7.00e-01 2.04e+00 6.19e+01 angle pdb=" N LYS V 432 " pdb=" CA LYS V 432 " pdb=" C LYS V 432 " ideal model delta sigma weight residual 111.28 119.14 -7.86 1.09e+00 8.42e-01 5.19e+01 ... (remaining 44949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.34: 14566 32.34 - 64.68: 2832 64.68 - 97.02: 74 97.02 - 129.36: 2 129.36 - 161.70: 4 Dihedral angle restraints: 17478 sinusoidal: 11068 harmonic: 6410 Sorted by residual: dihedral pdb=" CA PRO O 103 " pdb=" C PRO O 103 " pdb=" N GLY O 104 " pdb=" CA GLY O 104 " ideal model delta harmonic sigma weight residual -180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 -150.50 -29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA PRO K 361 " pdb=" C PRO K 361 " pdb=" N LYS K 362 " pdb=" CA LYS K 362 " ideal model delta harmonic sigma weight residual 180.00 153.23 26.77 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 17475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3482 0.062 - 0.123: 1223 0.123 - 0.185: 309 0.185 - 0.246: 37 0.246 - 0.308: 21 Chirality restraints: 5072 Sorted by residual: chirality pdb=" C1' DA I 43 " pdb=" O4' DA I 43 " pdb=" C2' DA I 43 " pdb=" N9 DA I 43 " both_signs ideal model delta sigma weight residual False 2.43 2.12 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C1' DA T 43 " pdb=" O4' DA T 43 " pdb=" C2' DA T 43 " pdb=" N9 DA T 43 " both_signs ideal model delta sigma weight residual False 2.43 2.12 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C1' DC T -27 " pdb=" O4' DC T -27 " pdb=" C2' DC T -27 " pdb=" N1 DC T -27 " both_signs ideal model delta sigma weight residual False 2.43 2.16 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 5069 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC U 56 " 0.045 2.00e-02 2.50e+03 3.32e-02 2.48e+01 pdb=" N1 DC U 56 " -0.076 2.00e-02 2.50e+03 pdb=" C2 DC U 56 " 0.040 2.00e-02 2.50e+03 pdb=" O2 DC U 56 " -0.019 2.00e-02 2.50e+03 pdb=" N3 DC U 56 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC U 56 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC U 56 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DC U 56 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC U 56 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 56 " -0.045 2.00e-02 2.50e+03 3.31e-02 2.47e+01 pdb=" N1 DC J 56 " 0.075 2.00e-02 2.50e+03 pdb=" C2 DC J 56 " -0.040 2.00e-02 2.50e+03 pdb=" O2 DC J 56 " 0.019 2.00e-02 2.50e+03 pdb=" N3 DC J 56 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC J 56 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC J 56 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DC J 56 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC J 56 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS V 425 " 0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C LYS V 425 " -0.085 2.00e-02 2.50e+03 pdb=" O LYS V 425 " 0.032 2.00e-02 2.50e+03 pdb=" N ASP V 426 " 0.029 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 4 2.25 - 2.92: 10890 2.92 - 3.58: 46988 3.58 - 4.24: 80363 4.24 - 4.90: 118794 Nonbonded interactions: 257039 Sorted by model distance: nonbonded pdb=" OP1 DA U 57 " pdb=" NZ LYS V 350 " model vdw 1.593 3.120 nonbonded pdb=" OP1 DA J 57 " pdb=" NZ LYS K 350 " model vdw 1.593 3.120 nonbonded pdb=" N2 DG T 21 " pdb=" O2 DC U -21 " model vdw 2.244 2.496 nonbonded pdb=" N2 DG I 21 " pdb=" O2 DC J -21 " model vdw 2.244 2.496 nonbonded pdb=" O LYS K 362 " pdb=" OG1 THR K 374 " model vdw 2.269 3.040 ... (remaining 257034 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = chain 'C' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'U' } ncs_group { reference = chain 'K' selection = chain 'V' } Set up NCS constraints Number of NCS constrained groups: 11 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'M' } pdb_interpretation.ncs_group { reference = chain 'C' selection = chain 'N' } pdb_interpretation.ncs_group { reference = chain 'D' selection = chain 'O' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'P' } pdb_interpretation.ncs_group { reference = chain 'F' selection = chain 'Q' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'R' } pdb_interpretation.ncs_group { reference = chain 'H' selection = chain 'S' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'T' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'U' } pdb_interpretation.ncs_group { reference = chain 'K' selection = chain 'V' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 38.680 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 31458 Z= 0.726 Angle : 1.049 10.085 44954 Z= 0.832 Chirality : 0.067 0.308 5072 Planarity : 0.009 0.065 3660 Dihedral : 24.746 161.695 13330 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.11 % Allowed : 1.37 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.14), residues: 2162 helix: -1.31 (0.11), residues: 1342 sheet: -2.27 (0.44), residues: 90 loop : -2.26 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 53 TYR 0.035 0.004 TYR M 88 PHE 0.027 0.003 PHE V 280 TRP 0.022 0.004 TRP V 343 HIS 0.021 0.003 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00836 / 0.73 (31458) covalent geometry : angle 1.04877 / 0.83 (44954) hydrogen bonds : bond 0.12669 / 8.46 ( 1820) hydrogen bonds : angle 4.93169 / 3.53 ( 4670) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0586 time to fit residues: 1.5340 Evaluate side-chains 9 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.036 Evaluate side-chains 24 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.7929 (m-30) cc_final: 0.7542 (m-30) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0904 time to fit residues: 2.2746 Evaluate side-chains 12 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.025 Evaluate side-chains 22 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.031 Fit side-chains REVERT: C 64 GLU cc_start: 0.8385 (tt0) cc_final: 0.7167 (mm-30) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0340 time to fit residues: 0.8586 Evaluate side-chains 8 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.020 Evaluate side-chains 34 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 MET cc_start: 0.9220 (mmm) cc_final: 0.8819 (mmm) REVERT: D 73 ILE cc_start: 0.9338 (mt) cc_final: 0.9095 (tp) REVERT: D 106 LEU cc_start: 0.8729 (tt) cc_final: 0.8467 (pp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0893 time to fit residues: 3.1834 Evaluate side-chains 16 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.033 Evaluate side-chains 34 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.035 Fit side-chains revert: symmetry clash REVERT: E 62 ILE cc_start: 0.8744 (mt) cc_final: 0.8428 (mm) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0604 time to fit residues: 2.2208 Evaluate side-chains 13 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.040 Evaluate side-chains 36 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.025 Fit side-chains revert: symmetry clash REVERT: F 24 ASP cc_start: 0.8330 (t70) cc_final: 0.7819 (t0) REVERT: F 58 LEU cc_start: 0.9662 (tp) cc_final: 0.9364 (pp) REVERT: F 66 ILE cc_start: 0.9683 (mt) cc_final: 0.9284 (pt) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0935 time to fit residues: 3.5063 Evaluate side-chains 22 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.026 Evaluate side-chains 30 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.032 Fit side-chains REVERT: G 56 GLU cc_start: 0.8405 (tt0) cc_final: 0.7880 (mt-10) REVERT: G 95 LYS cc_start: 0.9290 (tttt) cc_final: 0.8835 (pptt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0565 time to fit residues: 1.8427 Evaluate side-chains 9 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.035 Evaluate side-chains 39 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 68 ASP cc_start: 0.9050 (t0) cc_final: 0.8457 (t0) REVERT: H 71 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8714 (tp30) REVERT: H 72 ARG cc_start: 0.8769 (mtt180) cc_final: 0.8249 (mtt180) REVERT: H 93 GLU cc_start: 0.9002 (mp0) cc_final: 0.8801 (mp0) REVERT: H 100 LEU cc_start: 0.8874 (mt) cc_final: 0.8673 (tt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0978 time to fit residues: 3.9780 Evaluate side-chains 25 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.029 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0457 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0455 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 Evaluate side-chains 38 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 276 MET cc_start: 0.9516 (mmm) cc_final: 0.9128 (tmm) REVERT: K 456 ASP cc_start: 0.8401 (t0) cc_final: 0.8145 (p0) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.1184 time to fit residues: 5.1381 Evaluate side-chains 15 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.2980 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.0570 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN G 110 ASN H 82 HIS H 109 HIS K 192 HIS K 260 ASN ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 466 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.072996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.062668 restraints weight = 7297.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.063117 restraints weight = 6695.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.063483 restraints weight = 6208.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.063842 restraints weight = 5784.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.064075 restraints weight = 5422.242| |-----------------------------------------------------------------------------| r_work (final): 0.3432 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.076592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.064559 restraints weight = 3743.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.066218 restraints weight = 2676.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.067597 restraints weight = 2030.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.068666 restraints weight = 1601.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.069645 restraints weight = 1298.717| |-----------------------------------------------------------------------------| r_work (final): 0.3516 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.062136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.052192 restraints weight = 7013.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.053014 restraints weight = 5347.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.053683 restraints weight = 4379.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.054195 restraints weight = 3743.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.054560 restraints weight = 3299.393| |-----------------------------------------------------------------------------| r_work (final): 0.3196 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.069401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.057076 restraints weight = 6279.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.058267 restraints weight = 4642.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.059108 restraints weight = 3698.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.059825 restraints weight = 3117.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.060337 restraints weight = 2680.381| |-----------------------------------------------------------------------------| r_work (final): 0.3295 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.066928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.055143 restraints weight = 7069.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.056197 restraints weight = 5341.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.057125 restraints weight = 4229.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.057796 restraints weight = 3427.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.058254 restraints weight = 2840.992| |-----------------------------------------------------------------------------| r_work (final): 0.3335 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.064711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.052364 restraints weight = 4178.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.053880 restraints weight = 2682.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.054962 restraints weight = 1963.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.055746 restraints weight = 1551.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.056326 restraints weight = 1302.777| |-----------------------------------------------------------------------------| r_work (final): 0.3308 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.063128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.052508 restraints weight = 5637.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.053872 restraints weight = 3989.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.054991 restraints weight = 2984.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.055751 restraints weight = 2302.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.056441 restraints weight = 1890.435| |-----------------------------------------------------------------------------| r_work (final): 0.3341 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.068038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.055550 restraints weight = 4998.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.056975 restraints weight = 3561.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.058032 restraints weight = 2783.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.058715 restraints weight = 2302.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.058741 restraints weight = 2001.850| |-----------------------------------------------------------------------------| r_work (final): 0.3441 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.106360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.097911 restraints weight = 35776.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.098450 restraints weight = 12704.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.098716 restraints weight = 6902.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.098750 restraints weight = 5715.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.098746 restraints weight = 5433.523| |-----------------------------------------------------------------------------| r_work (final): 0.3904 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.107387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.099354 restraints weight = 35487.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.099996 restraints weight = 11906.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.100649 restraints weight = 6546.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.100750 restraints weight = 5040.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.101042 restraints weight = 4881.183| |-----------------------------------------------------------------------------| r_work (final): 0.3934 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.071206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.060180 restraints weight = 59788.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.060291 restraints weight = 57366.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.060291 restraints weight = 55581.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.060291 restraints weight = 55579.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.060291 restraints weight = 55579.476| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 31458 Z= 0.242 Angle : 0.890 16.586 44954 Z= 0.497 Chirality : 0.055 0.557 5072 Planarity : 0.011 0.163 3660 Dihedral : 29.972 163.986 8852 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.63 % Allowed : 3.27 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.16), residues: 2162 helix: -0.57 (0.12), residues: 1372 sheet: -2.14 (0.45), residues: 88 loop : -2.04 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG B 95 TYR 0.074 0.005 TYR F 98 PHE 0.036 0.002 PHE P 104 TRP 0.010 0.001 TRP K 343 HIS 0.012 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.24 (31458) covalent geometry : angle 0.88955 / 0.50 (44954) hydrogen bonds : bond 0.06889 / 4.45 ( 1820) hydrogen bonds : angle 4.69762 / 3.34 ( 4670) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.028 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 16 average time/residue: 0.0364 time to fit residues: 0.6597 Evaluate side-chains 8 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.032 Evaluate side-chains 18 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.026 Fit side-chains REVERT: M 85 ASP cc_start: 0.7917 (m-30) cc_final: 0.7458 (m-30) REVERT: M 93 GLN cc_start: 0.8895 (pt0) cc_final: 0.8361 (tm-30) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.0736 time to fit residues: 1.4130 Evaluate side-chains 11 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.016 Evaluate side-chains 15 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.031 Fit side-chains REVERT: N 64 GLU cc_start: 0.8263 (tt0) cc_final: 0.7286 (mm-30) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0206 time to fit residues: 0.4044 Evaluate side-chains 4 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.026 Evaluate side-chains 22 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 71 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8466 (mm-30) REVERT: D 106 LEU cc_start: 0.8968 (tt) cc_final: 0.8707 (pp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0556 time to fit residues: 1.3270 Evaluate side-chains 17 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.018 Evaluate side-chains 21 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 54 TYR cc_start: 0.9337 (m-80) cc_final: 0.9113 (m-10) REVERT: P 82 LEU cc_start: 0.7425 (tp) cc_final: 0.7201 (mp) REVERT: P 90 MET cc_start: 0.9393 (mmp) cc_final: 0.9191 (mmp) REVERT: P 94 GLU cc_start: 0.8250 (tt0) cc_final: 0.7654 (pt0) REVERT: P 97 GLU cc_start: 0.9412 (mm-30) cc_final: 0.8934 (mm-30) REVERT: P 105 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8930 (tm-30) outliers start: 2 outliers final: 0 residues processed: 20 average time/residue: 0.0241 time to fit residues: 0.5687 Evaluate side-chains 15 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.032 Evaluate side-chains 27 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 44 LYS cc_start: 0.5944 (OUTLIER) cc_final: 0.5526 (pttp) REVERT: Q 72 TYR cc_start: 0.8485 (m-80) cc_final: 0.8240 (m-80) REVERT: Q 92 ARG cc_start: 0.7350 (mmt180) cc_final: 0.6897 (mtm110) REVERT: Q 100 PHE cc_start: 0.7306 (m-80) cc_final: 0.6880 (m-80) outliers start: 2 outliers final: 0 residues processed: 27 average time/residue: 0.0875 time to fit residues: 2.4794 Evaluate side-chains 17 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.026 Evaluate side-chains 18 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.032 Fit side-chains revert: symmetry clash REVERT: R 95 LYS cc_start: 0.9187 (tttt) cc_final: 0.8763 (pptt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0474 time to fit residues: 0.9565 Evaluate side-chains 9 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.031 Evaluate side-chains 24 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 71 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8862 (tp30) REVERT: H 72 ARG cc_start: 0.9235 (mtt180) cc_final: 0.8845 (mtt180) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0776 time to fit residues: 1.9819 Evaluate side-chains 16 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.030 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.039 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0466 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0420 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.034 Evaluate side-chains 15 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: V 276 MET cc_start: 0.9313 (mmm) cc_final: 0.8992 (tmm) REVERT: V 456 ASP cc_start: 0.8102 (t0) cc_final: 0.7797 (p0) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1212 time to fit residues: 2.1852 Evaluate side-chains 12 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 202 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 252 optimal weight: 0.1980 chunk 258 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 236 optimal weight: 20.0000 chunk 191 optimal weight: 0.0970 chunk 162 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 HIS N 110 ASN P 68 GLN P 93 GLN R 110 ASN V 192 HIS V 260 ASN ** V 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 466 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.070631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.061082 restraints weight = 7459.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.061891 restraints weight = 6374.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.062601 restraints weight = 5499.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.063205 restraints weight = 4774.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.063597 restraints weight = 4193.060| |-----------------------------------------------------------------------------| r_work (final): 0.3451 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.074754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.066137 restraints weight = 4553.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.067471 restraints weight = 3088.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.068519 restraints weight = 2238.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.069285 restraints weight = 1705.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.069852 restraints weight = 1367.114| |-----------------------------------------------------------------------------| r_work (final): 0.3557 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.061814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.051843 restraints weight = 7177.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.052656 restraints weight = 5481.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.053272 restraints weight = 4499.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.053617 restraints weight = 3867.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.053872 restraints weight = 3488.538| |-----------------------------------------------------------------------------| r_work (final): 0.3201 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.072590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.061208 restraints weight = 6074.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.062647 restraints weight = 4099.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.063737 restraints weight = 3001.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.064557 restraints weight = 2338.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.065021 restraints weight = 1915.485| |-----------------------------------------------------------------------------| r_work (final): 0.3385 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.066936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.055345 restraints weight = 6795.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.056371 restraints weight = 5347.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.057203 restraints weight = 4270.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.057843 restraints weight = 3492.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.058413 restraints weight = 2962.599| |-----------------------------------------------------------------------------| r_work (final): 0.3322 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.057440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.049003 restraints weight = 5166.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.050400 restraints weight = 3287.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.051388 restraints weight = 2318.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052099 restraints weight = 1748.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.052602 restraints weight = 1391.347| |-----------------------------------------------------------------------------| r_work (final): 0.3232 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.062413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.051092 restraints weight = 5496.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.052379 restraints weight = 3945.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.053328 restraints weight = 3017.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.054110 restraints weight = 2426.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.054558 restraints weight = 2016.264| |-----------------------------------------------------------------------------| r_work (final): 0.3296 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.067446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.056680 restraints weight = 4837.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.057991 restraints weight = 3196.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.059124 restraints weight = 2413.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.059967 restraints weight = 1922.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.060547 restraints weight = 1591.373| |-----------------------------------------------------------------------------| r_work (final): 0.3469 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.127002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.114374 restraints weight = 16051.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.115551 restraints weight = 5591.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.116319 restraints weight = 3405.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.116808 restraints weight = 2555.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.117111 restraints weight = 2158.013| |-----------------------------------------------------------------------------| r_work (final): 0.3735 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.107362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.099410 restraints weight = 36370.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.100068 restraints weight = 12130.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.100623 restraints weight = 6767.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.100989 restraints weight = 5305.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.101002 restraints weight = 4648.817| |-----------------------------------------------------------------------------| r_work (final): 0.3935 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.070485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.059468 restraints weight = 59334.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.059468 restraints weight = 59267.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.059468 restraints weight = 59267.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.059468 restraints weight = 59267.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.059468 restraints weight = 59267.902| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 31458 Z= 0.188 Angle : 0.769 13.642 44954 Z= 0.437 Chirality : 0.050 0.374 5072 Planarity : 0.007 0.079 3660 Dihedral : 30.072 162.667 8852 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.53 % Allowed : 3.90 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.16), residues: 2162 helix: -0.17 (0.13), residues: 1392 sheet: -2.34 (0.45), residues: 88 loop : -2.16 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG Q 95 TYR 0.047 0.003 TYR N 39 PHE 0.029 0.002 PHE P 104 TRP 0.010 0.001 TRP V 375 HIS 0.010 0.001 HIS M 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 (31458) covalent geometry : angle 0.76918 / 0.44 (44954) hydrogen bonds : bond 0.05840 / 3.81 ( 1820) hydrogen bonds : angle 4.39450 / 3.13 ( 4670) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.035 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0366 time to fit residues: 0.5159 Evaluate side-chains 6 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.025 Evaluate side-chains 18 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.026 Fit side-chains revert: symmetry clash REVERT: B 64 ASN cc_start: 0.9481 (m-40) cc_final: 0.9169 (m110) REVERT: B 68 ASP cc_start: 0.8831 (m-30) cc_final: 0.8561 (m-30) REVERT: B 71 THR cc_start: 0.6779 (OUTLIER) cc_final: 0.6574 (m) REVERT: B 85 ASP cc_start: 0.7709 (m-30) cc_final: 0.7269 (m-30) outliers start: 2 outliers final: 0 residues processed: 18 average time/residue: 0.0648 time to fit residues: 1.2583 Evaluate side-chains 13 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.015 Evaluate side-chains 14 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.032 Fit side-chains REVERT: N 38 ASN cc_start: 0.9053 (m110) cc_final: 0.8755 (t0) REVERT: N 64 GLU cc_start: 0.8175 (tt0) cc_final: 0.7187 (mm-30) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0374 time to fit residues: 0.6151 Evaluate side-chains 7 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.031 Evaluate side-chains 21 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 71 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8502 (mm-30) REVERT: D 106 LEU cc_start: 0.9020 (tt) cc_final: 0.8669 (mt) outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.0542 time to fit residues: 1.2252 Evaluate side-chains 16 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.027 Evaluate side-chains 22 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.7721 (tp) cc_final: 0.7504 (mt) REVERT: E 90 MET cc_start: 0.9370 (mmp) cc_final: 0.9069 (mmm) REVERT: E 105 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8947 (tm-30) outliers start: 2 outliers final: 0 residues processed: 21 average time/residue: 0.0269 time to fit residues: 0.6821 Evaluate side-chains 16 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.045 Evaluate side-chains 23 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 68 ASP cc_start: 0.8827 (m-30) cc_final: 0.8379 (m-30) REVERT: Q 72 TYR cc_start: 0.8385 (m-80) cc_final: 0.7853 (m-80) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0502 time to fit residues: 1.2717 Evaluate side-chains 16 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.035 Evaluate side-chains 17 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.031 Fit side-chains REVERT: R 90 ASP cc_start: 0.8168 (t70) cc_final: 0.7851 (t70) REVERT: R 95 LYS cc_start: 0.9125 (tttt) cc_final: 0.8785 (pptt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0309 time to fit residues: 0.6119 Evaluate side-chains 9 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.019 Evaluate side-chains 22 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.019 Fit side-chains revert: symmetry clash REVERT: H 59 MET cc_start: 0.5827 (tpp) cc_final: 0.5414 (tpp) REVERT: H 68 ASP cc_start: 0.9219 (t70) cc_final: 0.8856 (t0) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0655 time to fit residues: 1.5176 Evaluate side-chains 16 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.029 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0269 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.030 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0420 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Evaluate side-chains 13 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 413 MET cc_start: 0.1536 (ptm) cc_final: 0.1242 (ptm) REVERT: V 456 ASP cc_start: 0.7837 (t0) cc_final: 0.7507 (p0) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1037 time to fit residues: 1.6872 Evaluate side-chains 11 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 113 optimal weight: 0.9980 chunk 236 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 chunk 159 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 188 optimal weight: 0.0970 chunk 253 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 68 GLN E 93 GLN ** V 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 466 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.071052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.060885 restraints weight = 7720.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.061432 restraints weight = 6821.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.061789 restraints weight = 6118.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.062280 restraints weight = 5583.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.062558 restraints weight = 5160.541| |-----------------------------------------------------------------------------| r_work (final): 0.3424 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.074394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.065170 restraints weight = 4698.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.066621 restraints weight = 3276.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.067565 restraints weight = 2422.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.068474 restraints weight = 1910.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.068857 restraints weight = 1537.586| |-----------------------------------------------------------------------------| r_work (final): 0.3567 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.061109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.050787 restraints weight = 7506.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051599 restraints weight = 5834.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.052254 restraints weight = 4819.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.052625 restraints weight = 4137.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.053132 restraints weight = 3678.439| |-----------------------------------------------------------------------------| r_work (final): 0.3196 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.071227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.060156 restraints weight = 5948.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.061345 restraints weight = 4299.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.062256 restraints weight = 3344.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.062893 restraints weight = 2733.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.063268 restraints weight = 2332.551| |-----------------------------------------------------------------------------| r_work (final): 0.3350 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.065378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.054402 restraints weight = 6589.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.055343 restraints weight = 5215.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.055971 restraints weight = 4222.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.056754 restraints weight = 3549.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.057294 restraints weight = 2984.017| |-----------------------------------------------------------------------------| r_work (final): 0.3305 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.060696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.048386 restraints weight = 4360.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.049798 restraints weight = 2879.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050829 restraints weight = 2148.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.051576 restraints weight = 1725.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.052125 restraints weight = 1454.934| |-----------------------------------------------------------------------------| r_work (final): 0.3306 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.061960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.051011 restraints weight = 5448.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.052298 restraints weight = 4002.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053337 restraints weight = 3085.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.054171 restraints weight = 2477.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.054757 restraints weight = 2051.133| |-----------------------------------------------------------------------------| r_work (final): 0.3273 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.065397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.054622 restraints weight = 5657.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.055874 restraints weight = 4118.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.056783 restraints weight = 3231.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.057459 restraints weight = 2669.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.057992 restraints weight = 2300.212| |-----------------------------------------------------------------------------| r_work (final): 0.3352 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.106234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.097627 restraints weight = 35832.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.097910 restraints weight = 13399.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.098234 restraints weight = 7165.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.098234 restraints weight = 5669.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.098234 restraints weight = 5667.604| |-----------------------------------------------------------------------------| r_work (final): 0.3903 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.107117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.100044 restraints weight = 35945.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.100150 restraints weight = 13992.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.100340 restraints weight = 6369.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.100478 restraints weight = 4968.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.100498 restraints weight = 4543.211| |-----------------------------------------------------------------------------| r_work (final): 0.3929 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.071021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.063143 restraints weight = 57394.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.063235 restraints weight = 54331.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.063450 restraints weight = 52568.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.063505 restraints weight = 50841.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.063505 restraints weight = 49430.655| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6162 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 31458 Z= 0.182 Angle : 0.756 12.198 44954 Z= 0.428 Chirality : 0.049 0.320 5072 Planarity : 0.007 0.117 3660 Dihedral : 30.038 163.252 8852 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.21 % Allowed : 3.90 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.17), residues: 2162 helix: -0.01 (0.13), residues: 1378 sheet: -2.43 (0.46), residues: 88 loop : -2.19 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG M 95 TYR 0.038 0.003 TYR B 51 PHE 0.037 0.002 PHE B 61 TRP 0.009 0.001 TRP V 375 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (31458) covalent geometry : angle 0.75617 / 0.43 (44954) hydrogen bonds : bond 0.05524 / 3.57 ( 1820) hydrogen bonds : angle 4.41254 / 3.14 ( 4670) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.027 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0324 time to fit residues: 0.3801 Evaluate side-chains 4 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.019 Evaluate side-chains 15 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 ASN cc_start: 0.9409 (m-40) cc_final: 0.9116 (m-40) REVERT: B 68 ASP cc_start: 0.8877 (m-30) cc_final: 0.8483 (m-30) REVERT: B 85 ASP cc_start: 0.7774 (m-30) cc_final: 0.7113 (m-30) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0725 time to fit residues: 1.1563 Evaluate side-chains 10 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.026 Evaluate side-chains 13 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.019 Fit side-chains REVERT: N 38 ASN cc_start: 0.9015 (m110) cc_final: 0.8691 (t0) REVERT: N 64 GLU cc_start: 0.8261 (tt0) cc_final: 0.7237 (mm-30) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0140 time to fit residues: 0.2479 Evaluate side-chains 9 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.026 Evaluate side-chains 17 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.017 Fit side-chains revert: symmetry clash REVERT: D 71 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8513 (mm-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0383 time to fit residues: 0.7263 Evaluate side-chains 14 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.030 Evaluate side-chains 18 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.036 Fit side-chains revert: symmetry clash REVERT: P 54 TYR cc_start: 0.9385 (m-80) cc_final: 0.8517 (t80) REVERT: P 94 GLU cc_start: 0.8411 (tt0) cc_final: 0.8050 (pt0) REVERT: P 97 GLU cc_start: 0.9421 (mm-30) cc_final: 0.8818 (mm-30) REVERT: P 105 GLU cc_start: 0.9273 (tm-30) cc_final: 0.8956 (tm-30) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.0297 time to fit residues: 0.6153 Evaluate side-chains 14 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.027 Evaluate side-chains 25 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 70 VAL cc_start: 0.9247 (m) cc_final: 0.8995 (p) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0662 time to fit residues: 1.7505 Evaluate side-chains 19 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.016 Evaluate side-chains 16 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.021 Fit side-chains revert: symmetry clash REVERT: R 95 LYS cc_start: 0.9117 (tttt) cc_final: 0.8760 (pptt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0677 time to fit residues: 1.1786 Evaluate side-chains 12 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.031 Evaluate side-chains 23 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.029 Fit side-chains revert: symmetry clash REVERT: H 59 MET cc_start: 0.5487 (tpp) cc_final: 0.5185 (tpp) outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.0678 time to fit residues: 1.6586 Evaluate side-chains 15 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.017 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0257 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.027 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0248 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.019 Evaluate side-chains 12 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 413 MET cc_start: 0.0815 (ptm) cc_final: 0.0593 (ptm) REVERT: V 456 ASP cc_start: 0.7240 (t0) cc_final: 0.6920 (p0) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0918 time to fit residues: 1.3991 Evaluate side-chains 10 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 32 optimal weight: 1.9990 chunk 215 optimal weight: 20.0000 chunk 5 optimal weight: 0.1980 chunk 163 optimal weight: 0.9980 chunk 235 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 264 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** N 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 GLN P 93 GLN ** V 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 466 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.072674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.063633 restraints weight = 7816.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.064007 restraints weight = 7012.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.064540 restraints weight = 6394.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.064921 restraints weight = 5906.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.065115 restraints weight = 5529.241| |-----------------------------------------------------------------------------| r_work (final): 0.3497 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.074870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.063618 restraints weight = 4551.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.064901 restraints weight = 3601.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.065874 restraints weight = 2935.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.066791 restraints weight = 2450.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.067512 restraints weight = 2087.782| |-----------------------------------------------------------------------------| r_work (final): 0.3481 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.060976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.050730 restraints weight = 7347.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.051549 restraints weight = 5755.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.052040 restraints weight = 4767.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.052626 restraints weight = 4171.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.052969 restraints weight = 3680.797| |-----------------------------------------------------------------------------| r_work (final): 0.3202 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.068991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.057834 restraints weight = 5475.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.058873 restraints weight = 3986.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.059655 restraints weight = 3143.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.060345 restraints weight = 2612.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.060905 restraints weight = 2227.850| |-----------------------------------------------------------------------------| r_work (final): 0.3299 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.067463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.055781 restraints weight = 7401.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.056861 restraints weight = 5606.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.057584 restraints weight = 4426.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.058045 restraints weight = 3667.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.058599 restraints weight = 3153.357| |-----------------------------------------------------------------------------| r_work (final): 0.3316 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.059123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.047449 restraints weight = 4429.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.049014 restraints weight = 2756.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.050119 restraints weight = 1980.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.050887 restraints weight = 1547.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.051462 restraints weight = 1288.304| |-----------------------------------------------------------------------------| r_work (final): 0.3109 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.062479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.051632 restraints weight = 5375.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.052963 restraints weight = 3943.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.054024 restraints weight = 3025.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.054825 restraints weight = 2421.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.055401 restraints weight = 2030.481| |-----------------------------------------------------------------------------| r_work (final): 0.3278 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.064760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.053499 restraints weight = 5931.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.054674 restraints weight = 4426.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.055581 restraints weight = 3535.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.056240 restraints weight = 2950.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.056812 restraints weight = 2555.729| |-----------------------------------------------------------------------------| r_work (final): 0.3348 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.104060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.095648 restraints weight = 38722.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.096638 restraints weight = 11624.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.096949 restraints weight = 6319.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.097029 restraints weight = 4774.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.097029 restraints weight = 4493.865| |-----------------------------------------------------------------------------| r_work (final): 0.3861 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.107768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.100095 restraints weight = 36417.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.100626 restraints weight = 12145.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.100911 restraints weight = 6457.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.100958 restraints weight = 5138.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.101222 restraints weight = 4892.072| |-----------------------------------------------------------------------------| r_work (final): 0.3948 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.070944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.062202 restraints weight = 59017.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.062328 restraints weight = 56800.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.062454 restraints weight = 55244.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.062454 restraints weight = 53938.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.062454 restraints weight = 53937.637| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 31458 Z= 0.167 Angle : 0.737 12.656 44954 Z= 0.417 Chirality : 0.049 0.593 5072 Planarity : 0.006 0.062 3660 Dihedral : 30.006 163.534 8852 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.17), residues: 2162 helix: 0.07 (0.13), residues: 1362 sheet: -2.56 (0.46), residues: 88 loop : -2.00 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG Q 95 TYR 0.043 0.003 TYR L 99 PHE 0.027 0.002 PHE S 65 TRP 0.007 0.001 TRP V 375 HIS 0.010 0.001 HIS M 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (31458) covalent geometry : angle 0.73714 / 0.42 (44954) hydrogen bonds : bond 0.05361 / 3.47 ( 1820) hydrogen bonds : angle 4.39327 / 3.12 ( 4670) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.035 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0550 time to fit residues: 0.5779 Evaluate side-chains 5 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.036 Evaluate side-chains 12 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.028 Fit side-chains REVERT: M 68 ASP cc_start: 0.8772 (m-30) cc_final: 0.8344 (m-30) REVERT: M 85 ASP cc_start: 0.7912 (m-30) cc_final: 0.7530 (m-30) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0270 time to fit residues: 0.3979 Evaluate side-chains 10 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.026 Evaluate side-chains 13 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.034 Fit side-chains REVERT: N 38 ASN cc_start: 0.8855 (m110) cc_final: 0.8503 (t0) REVERT: N 64 GLU cc_start: 0.8292 (tt0) cc_final: 0.7264 (mm-30) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0165 time to fit residues: 0.2993 Evaluate side-chains 8 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.036 Evaluate side-chains 14 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.029 Fit side-chains REVERT: O 71 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8571 (mm-30) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0401 time to fit residues: 0.6499 Evaluate side-chains 11 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.029 Evaluate side-chains 18 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.035 Fit side-chains revert: symmetry clash REVERT: E 54 TYR cc_start: 0.9125 (m-80) cc_final: 0.8187 (t80) REVERT: E 97 GLU cc_start: 0.9518 (mm-30) cc_final: 0.8857 (mm-30) REVERT: E 105 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8886 (tm-30) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0315 time to fit residues: 0.6803 Evaluate side-chains 15 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.024 Evaluate side-chains 25 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 68 ASP cc_start: 0.8883 (m-30) cc_final: 0.8659 (m-30) REVERT: Q 70 VAL cc_start: 0.9315 (m) cc_final: 0.8972 (p) REVERT: Q 72 TYR cc_start: 0.7492 (t80) cc_final: 0.6984 (t80) REVERT: Q 84 MET cc_start: 0.9257 (ptp) cc_final: 0.8908 (ppp) REVERT: Q 93 GLN cc_start: 0.9370 (tm-30) cc_final: 0.9144 (tm-30) REVERT: Q 95 ARG cc_start: 0.5597 (tpm170) cc_final: 0.4856 (mtt180) REVERT: Q 96 THR cc_start: 0.6628 (p) cc_final: 0.5895 (p) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0632 time to fit residues: 1.6641 Evaluate side-chains 21 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.016 Evaluate side-chains 16 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.019 Fit side-chains REVERT: R 23 LEU cc_start: 0.7990 (mm) cc_final: 0.7157 (mm) REVERT: R 95 LYS cc_start: 0.9138 (tttt) cc_final: 0.8812 (pptt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0322 time to fit residues: 0.5974 Evaluate side-chains 11 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.029 Evaluate side-chains 19 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 59 MET cc_start: 0.4643 (tpp) cc_final: 0.4059 (tpp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0574 time to fit residues: 1.1762 Evaluate side-chains 14 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.030 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0413 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0430 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.034 Evaluate side-chains 13 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 413 MET cc_start: 0.0976 (ptm) cc_final: 0.0664 (ptm) REVERT: V 456 ASP cc_start: 0.7491 (t0) cc_final: 0.7136 (p0) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0767 time to fit residues: 1.2705 Evaluate side-chains 11 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 89 optimal weight: 20.0000 chunk 198 optimal weight: 1.9990 chunk 243 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 218 optimal weight: 40.0000 chunk 117 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 93 GLN O 95 GLN ** V 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 466 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.069574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.060283 restraints weight = 8214.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.060948 restraints weight = 7101.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.061559 restraints weight = 6269.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.062131 restraints weight = 5613.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.062509 restraints weight = 5065.538| |-----------------------------------------------------------------------------| r_work (final): 0.3436 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.070599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.062081 restraints weight = 5040.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.063382 restraints weight = 3503.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.064351 restraints weight = 2595.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.065137 restraints weight = 2014.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.065706 restraints weight = 1620.665| |-----------------------------------------------------------------------------| r_work (final): 0.3505 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.060004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.050323 restraints weight = 7616.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.051056 restraints weight = 5964.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.051657 restraints weight = 4982.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.052008 restraints weight = 4319.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.052250 restraints weight = 3912.370| |-----------------------------------------------------------------------------| r_work (final): 0.3199 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.066329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.055460 restraints weight = 5699.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.056524 restraints weight = 4071.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.057275 restraints weight = 3113.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057905 restraints weight = 2529.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.058227 restraints weight = 2142.345| |-----------------------------------------------------------------------------| r_work (final): 0.3278 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.061782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.051772 restraints weight = 6964.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.052733 restraints weight = 5403.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.053397 restraints weight = 4325.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.054073 restraints weight = 3609.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.054590 restraints weight = 3021.745| |-----------------------------------------------------------------------------| r_work (final): 0.3291 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.056442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.048384 restraints weight = 5140.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.049618 restraints weight = 3181.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050502 restraints weight = 2226.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.051010 restraints weight = 1694.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.051530 restraints weight = 1403.912| |-----------------------------------------------------------------------------| r_work (final): 0.3101 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.059785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.049431 restraints weight = 5735.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.050527 restraints weight = 4178.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.051437 restraints weight = 3239.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.052138 restraints weight = 2615.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.052691 restraints weight = 2184.782| |-----------------------------------------------------------------------------| r_work (final): 0.3233 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.063820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.052413 restraints weight = 5880.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.053218 restraints weight = 4766.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.053690 restraints weight = 4036.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.054237 restraints weight = 3602.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.054481 restraints weight = 3246.041| |-----------------------------------------------------------------------------| r_work (final): 0.3237 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.101618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.093269 restraints weight = 36870.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.094176 restraints weight = 12725.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.094379 restraints weight = 6714.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.094538 restraints weight = 5638.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.094538 restraints weight = 4745.065| |-----------------------------------------------------------------------------| r_work (final): 0.3838 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.104461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.096781 restraints weight = 37158.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.097315 restraints weight = 11937.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.097769 restraints weight = 6551.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.098210 restraints weight = 5253.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.098231 restraints weight = 4556.491| |-----------------------------------------------------------------------------| r_work (final): 0.3912 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.070003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.062163 restraints weight = 56916.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.062261 restraints weight = 54370.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.062450 restraints weight = 52630.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.062518 restraints weight = 51005.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.062562 restraints weight = 49911.620| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31458 Z= 0.207 Angle : 0.739 9.840 44954 Z= 0.419 Chirality : 0.047 0.376 5072 Planarity : 0.006 0.053 3660 Dihedral : 30.213 168.572 8852 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.17), residues: 2162 helix: 0.37 (0.13), residues: 1366 sheet: -2.76 (0.47), residues: 88 loop : -1.75 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 95 TYR 0.037 0.003 TYR D 121 PHE 0.018 0.002 PHE H 65 TRP 0.007 0.001 TRP K 343 HIS 0.015 0.002 HIS M 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.21 (31458) covalent geometry : angle 0.73895 / 0.42 (44954) hydrogen bonds : bond 0.09515 / 6.37 ( 1820) hydrogen bonds : angle 4.32613 / 3.09 ( 4670) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.025 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0473 time to fit residues: 0.3889 Evaluate side-chains 4 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.020 Evaluate side-chains 14 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.025 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.9206 (m-30) cc_final: 0.8825 (m-30) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0702 time to fit residues: 1.0592 Evaluate side-chains 12 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.025 Evaluate side-chains 11 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.031 Fit side-chains REVERT: N 38 ASN cc_start: 0.8663 (m110) cc_final: 0.8358 (t0) REVERT: N 64 GLU cc_start: 0.8422 (tt0) cc_final: 0.7411 (mm-30) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0218 time to fit residues: 0.3246 Evaluate side-chains 5 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.031 Evaluate side-chains 15 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 62 MET cc_start: 0.8756 (mmp) cc_final: 0.8487 (mmm) REVERT: O 71 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8516 (mm-30) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0391 time to fit residues: 0.6692 Evaluate side-chains 12 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.029 Evaluate side-chains 16 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.028 Fit side-chains revert: symmetry clash REVERT: P 54 TYR cc_start: 0.9186 (m-80) cc_final: 0.8276 (t80) REVERT: P 90 MET cc_start: 0.9405 (mmp) cc_final: 0.9180 (mmm) REVERT: P 97 GLU cc_start: 0.9480 (mm-30) cc_final: 0.8889 (mm-30) REVERT: P 105 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8940 (tm-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0301 time to fit residues: 0.5832 Evaluate side-chains 15 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.037 Evaluate side-chains 25 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 61 PHE cc_start: 0.9428 (t80) cc_final: 0.9156 (t80) REVERT: Q 70 VAL cc_start: 0.9400 (m) cc_final: 0.9046 (p) REVERT: Q 72 TYR cc_start: 0.7712 (t80) cc_final: 0.7350 (t80) REVERT: Q 84 MET cc_start: 0.9178 (ptp) cc_final: 0.8766 (ppp) REVERT: Q 95 ARG cc_start: 0.6384 (tpm170) cc_final: 0.6032 (ttt180) REVERT: Q 96 THR cc_start: 0.5616 (p) cc_final: 0.5400 (p) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0707 time to fit residues: 1.8730 Evaluate side-chains 20 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.026 Evaluate side-chains 15 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.033 Fit side-chains revert: symmetry clash REVERT: R 95 LYS cc_start: 0.9209 (tttt) cc_final: 0.8834 (pttp) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0409 time to fit residues: 0.7131 Evaluate side-chains 8 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.033 Evaluate side-chains 18 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0571 time to fit residues: 1.1196 Evaluate side-chains 13 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.027 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0608 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0286 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 Evaluate side-chains 12 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: V 413 MET cc_start: 0.0829 (ptm) cc_final: 0.0540 (ptm) REVERT: V 456 ASP cc_start: 0.7253 (t0) cc_final: 0.6887 (p0) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0943 time to fit residues: 1.4057 Evaluate side-chains 9 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 40 optimal weight: 4.9990 chunk 245 optimal weight: 0.0970 chunk 253 optimal weight: 0.0980 chunk 178 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 102 optimal weight: 40.0000 chunk 229 optimal weight: 30.0000 chunk 185 optimal weight: 20.0000 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 68 GLN P 93 GLN V 466 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.069573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.060682 restraints weight = 8406.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.061349 restraints weight = 7224.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.061787 restraints weight = 6335.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.062294 restraints weight = 5750.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.062698 restraints weight = 5229.215| |-----------------------------------------------------------------------------| r_work (final): 0.3447 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.071723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.063305 restraints weight = 5089.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.064683 restraints weight = 3490.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.065733 restraints weight = 2566.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.066626 restraints weight = 1978.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.067205 restraints weight = 1539.520| |-----------------------------------------------------------------------------| r_work (final): 0.3511 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.061408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.052346 restraints weight = 7126.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.053077 restraints weight = 5673.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.053587 restraints weight = 4721.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.053893 restraints weight = 4144.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.054191 restraints weight = 3739.400| |-----------------------------------------------------------------------------| r_work (final): 0.3240 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.067993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.056713 restraints weight = 5297.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.057737 restraints weight = 3845.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.058603 restraints weight = 2973.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.059243 restraints weight = 2418.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.059602 restraints weight = 2048.401| |-----------------------------------------------------------------------------| r_work (final): 0.3337 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.064403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.053457 restraints weight = 6795.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.054337 restraints weight = 5340.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.055093 restraints weight = 4334.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.055697 restraints weight = 3591.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.056208 restraints weight = 3066.462| |-----------------------------------------------------------------------------| r_work (final): 0.3285 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.056975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.049032 restraints weight = 5176.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.050308 restraints weight = 3219.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.051196 restraints weight = 2258.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.051843 restraints weight = 1715.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.052330 restraints weight = 1383.290| |-----------------------------------------------------------------------------| r_work (final): 0.3117 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.059910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.049450 restraints weight = 5749.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.050680 restraints weight = 4085.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.051640 restraints weight = 3100.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.052249 restraints weight = 2461.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.052886 restraints weight = 2077.879| |-----------------------------------------------------------------------------| r_work (final): 0.3236 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.064340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.053536 restraints weight = 5687.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.054492 restraints weight = 4455.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.055094 restraints weight = 3679.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.055830 restraints weight = 3173.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.056384 restraints weight = 2784.955| |-----------------------------------------------------------------------------| r_work (final): 0.3302 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.102121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.093068 restraints weight = 36370.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.093986 restraints weight = 11918.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.094197 restraints weight = 6788.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.094859 restraints weight = 5771.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.094892 restraints weight = 4869.064| |-----------------------------------------------------------------------------| r_work (final): 0.3852 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.104764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.097219 restraints weight = 36760.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.097713 restraints weight = 12130.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.097851 restraints weight = 6548.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.098073 restraints weight = 5504.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.098073 restraints weight = 4948.914| |-----------------------------------------------------------------------------| r_work (final): 0.3915 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.070509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.064304 restraints weight = 633746.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.064308 restraints weight = 602006.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.064265 restraints weight = 590946.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.064232 restraints weight = 576940.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.064244 restraints weight = 557316.633| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31458 Z= 0.174 Angle : 0.724 15.697 44954 Z= 0.404 Chirality : 0.045 0.300 5072 Planarity : 0.008 0.269 3660 Dihedral : 30.353 169.637 8852 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.17), residues: 2162 helix: 0.45 (0.13), residues: 1374 sheet: -2.71 (0.47), residues: 88 loop : -1.71 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 92 TYR 0.035 0.003 TYR L 99 PHE 0.032 0.002 PHE M 61 TRP 0.006 0.001 TRP V 375 HIS 0.012 0.001 HIS M 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (31458) covalent geometry : angle 0.72410 / 0.40 (44954) hydrogen bonds : bond 0.05961 / 3.91 ( 1820) hydrogen bonds : angle 4.24906 / 3.02 ( 4670) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.031 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0492 time to fit residues: 0.4155 Evaluate side-chains 4 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.033 Evaluate side-chains 14 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.025 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.9090 (m-30) cc_final: 0.8683 (m-30) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0464 time to fit residues: 0.7181 Evaluate side-chains 10 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.025 Evaluate side-chains 12 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.032 Fit side-chains REVERT: N 38 ASN cc_start: 0.8445 (m110) cc_final: 0.8165 (t0) REVERT: N 64 GLU cc_start: 0.8382 (tt0) cc_final: 0.7361 (mm-30) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0205 time to fit residues: 0.3335 Evaluate side-chains 6 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.031 Evaluate side-chains 14 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.028 Fit side-chains REVERT: O 62 MET cc_start: 0.8725 (mmp) cc_final: 0.8505 (mmm) REVERT: O 71 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8502 (mm-30) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0399 time to fit residues: 0.6355 Evaluate side-chains 11 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.030 Evaluate side-chains 16 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.022 Fit side-chains revert: symmetry clash REVERT: P 54 TYR cc_start: 0.9256 (m-80) cc_final: 0.8350 (t80) REVERT: P 90 MET cc_start: 0.9448 (mmp) cc_final: 0.9196 (mmm) REVERT: P 97 GLU cc_start: 0.9505 (mm-30) cc_final: 0.8926 (mm-30) REVERT: P 105 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8925 (tm-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0316 time to fit residues: 0.6104 Evaluate side-chains 15 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.045 Evaluate side-chains 27 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 70 VAL cc_start: 0.9411 (m) cc_final: 0.9089 (p) REVERT: Q 84 MET cc_start: 0.9055 (ptp) cc_final: 0.8751 (ppp) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0752 time to fit residues: 2.1360 Evaluate side-chains 18 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.026 Evaluate side-chains 17 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.032 Fit side-chains REVERT: R 23 LEU cc_start: 0.7818 (mm) cc_final: 0.7107 (mm) REVERT: R 56 GLU cc_start: 0.8313 (pt0) cc_final: 0.7974 (mt-10) REVERT: R 90 ASP cc_start: 0.8300 (t70) cc_final: 0.7977 (t70) REVERT: R 95 LYS cc_start: 0.9168 (tttt) cc_final: 0.8773 (pttp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0384 time to fit residues: 0.7599 Evaluate side-chains 10 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.019 Evaluate side-chains 16 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.017 Fit side-chains REVERT: S 59 MET cc_start: 0.3849 (tpp) cc_final: 0.3332 (tpp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0453 time to fit residues: 0.8095 Evaluate side-chains 12 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.030 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0409 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.033 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0404 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.021 Evaluate side-chains 13 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: K 311 LEU cc_start: 0.8682 (tt) cc_final: 0.8405 (mm) REVERT: K 413 MET cc_start: 0.1476 (ptm) cc_final: 0.1178 (ptm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0710 time to fit residues: 1.2587 Evaluate side-chains 9 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 115 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 266 optimal weight: 8.9990 chunk 119 optimal weight: 0.0020 chunk 203 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 181 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 183 optimal weight: 0.0970 chunk 92 optimal weight: 40.0000 overall best weight: 1.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 466 ASN N 38 ASN ** Q 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.071301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.061897 restraints weight = 7807.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.062431 restraints weight = 6950.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.062825 restraints weight = 6308.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.063149 restraints weight = 5812.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.063530 restraints weight = 5432.342| |-----------------------------------------------------------------------------| r_work (final): 0.3473 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.072446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.063704 restraints weight = 4704.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.065146 restraints weight = 3277.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.066230 restraints weight = 2407.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.067112 restraints weight = 1848.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.067589 restraints weight = 1448.491| |-----------------------------------------------------------------------------| r_work (final): 0.3540 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.061066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.051248 restraints weight = 7081.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.051985 restraints weight = 5590.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.052584 restraints weight = 4663.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.052598 restraints weight = 4074.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.052598 restraints weight = 4051.419| |-----------------------------------------------------------------------------| r_work (final): 0.3198 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.069863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.058338 restraints weight = 5917.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.059462 restraints weight = 4169.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.060337 restraints weight = 3181.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.061046 restraints weight = 2561.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.061432 restraints weight = 2160.665| |-----------------------------------------------------------------------------| r_work (final): 0.3330 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.063760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.052964 restraints weight = 6709.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.053954 restraints weight = 5134.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.054804 restraints weight = 4075.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.055346 restraints weight = 3319.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.055886 restraints weight = 2811.370| |-----------------------------------------------------------------------------| r_work (final): 0.3289 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.058318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048389 restraints weight = 4732.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.049676 restraints weight = 3174.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.050601 restraints weight = 2366.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.051233 restraints weight = 1897.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.051754 restraints weight = 1617.202| |-----------------------------------------------------------------------------| r_work (final): 0.3106 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.061419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.050692 restraints weight = 5466.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.051920 restraints weight = 3811.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.052786 restraints weight = 2830.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.053589 restraints weight = 2226.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.054024 restraints weight = 1815.482| |-----------------------------------------------------------------------------| r_work (final): 0.3290 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.061019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.051281 restraints weight = 5560.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.052085 restraints weight = 4431.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.052697 restraints weight = 3712.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.053178 restraints weight = 3221.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.053413 restraints weight = 2877.952| |-----------------------------------------------------------------------------| r_work (final): 0.3222 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.104154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.094879 restraints weight = 38395.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.095324 restraints weight = 13113.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.095600 restraints weight = 7390.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.096012 restraints weight = 6156.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.096010 restraints weight = 5481.556| |-----------------------------------------------------------------------------| r_work (final): 0.3883 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.105257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.098677 restraints weight = 36849.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.098928 restraints weight = 15060.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.098906 restraints weight = 11194.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.098910 restraints weight = 8522.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.098783 restraints weight = 6856.151| |-----------------------------------------------------------------------------| r_work (final): 0.3918 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.070763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.064156 restraints weight = 619139.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.064120 restraints weight = 593937.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.064099 restraints weight = 568510.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.064103 restraints weight = 581454.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.064044 restraints weight = 539639.300| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6487 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 31458 Z= 0.160 Angle : 0.695 10.693 44954 Z= 0.391 Chirality : 0.045 0.302 5072 Planarity : 0.005 0.044 3660 Dihedral : 30.257 172.349 8852 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.17), residues: 2162 helix: 0.49 (0.13), residues: 1368 sheet: -2.61 (0.47), residues: 88 loop : -1.62 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG M 95 TYR 0.044 0.003 TYR O 121 PHE 0.025 0.002 PHE F 61 TRP 0.007 0.001 TRP V 455 HIS 0.009 0.001 HIS M 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (31458) covalent geometry : angle 0.69520 / 0.39 (44954) hydrogen bonds : bond 0.05172 / 3.33 ( 1820) hydrogen bonds : angle 4.15028 / 2.96 ( 4670) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.035 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0689 time to fit residues: 0.4885 Evaluate side-chains 4 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.020 Evaluate side-chains 14 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.019 Fit side-chains REVERT: B 68 ASP cc_start: 0.8990 (m-30) cc_final: 0.8591 (m-30) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0260 time to fit residues: 0.4454 Evaluate side-chains 11 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.015 Evaluate side-chains 11 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.020 Fit side-chains REVERT: N 38 ASN cc_start: 0.8427 (m-40) cc_final: 0.8155 (t0) REVERT: N 64 GLU cc_start: 0.8431 (tt0) cc_final: 0.7374 (mm-30) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0214 time to fit residues: 0.3095 Evaluate side-chains 6 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.031 Evaluate side-chains 16 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 71 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8472 (mm-30) REVERT: O 121 TYR cc_start: 0.6301 (m-80) cc_final: 0.6079 (m-80) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0391 time to fit residues: 0.7189 Evaluate side-chains 13 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.031 Evaluate side-chains 17 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.023 Fit side-chains revert: symmetry clash REVERT: P 54 TYR cc_start: 0.9198 (m-80) cc_final: 0.8392 (t80) REVERT: P 90 MET cc_start: 0.9432 (mmp) cc_final: 0.9192 (mmm) REVERT: P 97 GLU cc_start: 0.9497 (mm-30) cc_final: 0.8911 (mm-30) REVERT: P 105 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8880 (tm-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0432 time to fit residues: 0.8430 Evaluate side-chains 15 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.026 Evaluate side-chains 26 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 70 VAL cc_start: 0.9411 (m) cc_final: 0.9107 (p) REVERT: Q 84 MET cc_start: 0.9051 (ptp) cc_final: 0.8759 (ppp) REVERT: Q 95 ARG cc_start: 0.6171 (tpm170) cc_final: 0.5962 (mtt180) REVERT: Q 96 THR cc_start: 0.5057 (p) cc_final: 0.4661 (p) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0523 time to fit residues: 1.4368 Evaluate side-chains 19 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.044 Evaluate side-chains 20 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.030 Fit side-chains REVERT: G 23 LEU cc_start: 0.7837 (mm) cc_final: 0.7403 (mm) REVERT: G 56 GLU cc_start: 0.8074 (pt0) cc_final: 0.7752 (mt-10) REVERT: G 95 LYS cc_start: 0.9199 (tttt) cc_final: 0.8811 (pttp) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0333 time to fit residues: 0.7808 Evaluate side-chains 12 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.034 Evaluate side-chains 18 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 59 MET cc_start: 0.3884 (tpp) cc_final: 0.3177 (tpp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0653 time to fit residues: 1.2757 Evaluate side-chains 15 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.031 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0434 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.033 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0432 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.033 Evaluate side-chains 13 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: K 311 LEU cc_start: 0.9369 (tt) cc_final: 0.9112 (mm) REVERT: K 413 MET cc_start: 0.1352 (ptm) cc_final: 0.0956 (ptm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0672 time to fit residues: 1.1598 Evaluate side-chains 10 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 262 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 115 optimal weight: 0.0010 chunk 165 optimal weight: 0.0050 chunk 148 optimal weight: 0.8980 chunk 145 optimal weight: 0.0770 chunk 207 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 9 optimal weight: 40.0000 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 466 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.075137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.062934 restraints weight = 11273.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.063514 restraints weight = 10083.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.064003 restraints weight = 9074.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.064385 restraints weight = 8235.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.064855 restraints weight = 7591.899| |-----------------------------------------------------------------------------| r_work (final): 0.3543 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.071662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.062945 restraints weight = 4835.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.064339 restraints weight = 3360.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.065467 restraints weight = 2481.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.066200 restraints weight = 1904.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.066939 restraints weight = 1539.255| |-----------------------------------------------------------------------------| r_work (final): 0.3540 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.060500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.051313 restraints weight = 7086.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.052076 restraints weight = 5551.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.052694 restraints weight = 4580.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.053057 restraints weight = 3946.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.053433 restraints weight = 3519.871| |-----------------------------------------------------------------------------| r_work (final): 0.3218 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.069437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.057695 restraints weight = 5278.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.058809 restraints weight = 3835.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.059549 restraints weight = 2951.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.060323 restraints weight = 2430.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.060885 restraints weight = 2045.726| |-----------------------------------------------------------------------------| r_work (final): 0.3326 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.064602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.053709 restraints weight = 6671.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.054700 restraints weight = 5114.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.055477 restraints weight = 4078.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.056011 restraints weight = 3336.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.056496 restraints weight = 2836.946| |-----------------------------------------------------------------------------| r_work (final): 0.3298 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.059494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.050599 restraints weight = 5145.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.051938 restraints weight = 3356.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.052829 restraints weight = 2417.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.053476 restraints weight = 1888.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.053988 restraints weight = 1563.577| |-----------------------------------------------------------------------------| r_work (final): 0.3145 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.061749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.050880 restraints weight = 5473.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.052115 restraints weight = 3853.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.053087 restraints weight = 2884.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.053789 restraints weight = 2255.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.054135 restraints weight = 1855.871| |-----------------------------------------------------------------------------| r_work (final): 0.3291 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.062061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.052358 restraints weight = 5672.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.053358 restraints weight = 4150.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.054117 restraints weight = 3293.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.054569 restraints weight = 2776.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.054883 restraints weight = 2468.576| |-----------------------------------------------------------------------------| r_work (final): 0.3273 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.104343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.095341 restraints weight = 38415.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.095684 restraints weight = 13781.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.095924 restraints weight = 7310.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.095924 restraints weight = 6088.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.095924 restraints weight = 6088.170| |-----------------------------------------------------------------------------| r_work (final): 0.3879 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.105584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.097647 restraints weight = 36766.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.098183 restraints weight = 12989.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.098619 restraints weight = 7565.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.098649 restraints weight = 5768.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.098649 restraints weight = 5580.271| |-----------------------------------------------------------------------------| r_work (final): 0.3919 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.070332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.061160 restraints weight = 58397.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.061163 restraints weight = 56753.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.061173 restraints weight = 56687.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.061173 restraints weight = 56497.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.061173 restraints weight = 56495.419| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 31458 Z= 0.150 Angle : 0.678 8.159 44954 Z= 0.383 Chirality : 0.045 0.300 5072 Planarity : 0.005 0.050 3660 Dihedral : 30.154 173.496 8852 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.17), residues: 2162 helix: 0.59 (0.13), residues: 1376 sheet: -2.58 (0.47), residues: 88 loop : -1.53 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 95 TYR 0.036 0.002 TYR D 121 PHE 0.017 0.001 PHE S 65 TRP 0.005 0.001 TRP K 375 HIS 0.008 0.001 HIS M 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (31458) covalent geometry : angle 0.67847 / 0.38 (44954) hydrogen bonds : bond 0.05021 / 3.22 ( 1820) hydrogen bonds : angle 4.09518 / 2.92 ( 4670) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.029 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0533 time to fit residues: 0.4254 Evaluate side-chains 3 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.031 Evaluate side-chains 13 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.024 Fit side-chains revert: symmetry clash REVERT: B 68 ASP cc_start: 0.8956 (m-30) cc_final: 0.8583 (m-30) REVERT: B 85 ASP cc_start: 0.7670 (m-30) cc_final: 0.7330 (m-30) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0571 time to fit residues: 0.8179 Evaluate side-chains 10 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.024 Evaluate side-chains 12 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.030 Fit side-chains REVERT: N 38 ASN cc_start: 0.8359 (m-40) cc_final: 0.8072 (t0) REVERT: N 64 GLU cc_start: 0.8410 (tt0) cc_final: 0.7336 (mm-30) REVERT: N 90 ASP cc_start: 0.8351 (t0) cc_final: 0.8121 (t70) REVERT: N 111 ILE cc_start: 0.7211 (mm) cc_final: 0.7000 (mm) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0167 time to fit residues: 0.2691 Evaluate side-chains 7 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.019 Evaluate side-chains 17 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.029 Fit side-chains revert: symmetry clash REVERT: O 62 MET cc_start: 0.8685 (mmp) cc_final: 0.8432 (mmp) REVERT: O 71 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8480 (mm-30) REVERT: O 121 TYR cc_start: 0.6228 (m-80) cc_final: 0.6017 (m-80) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0398 time to fit residues: 0.7748 Evaluate side-chains 13 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.029 Evaluate side-chains 16 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.034 Fit side-chains revert: symmetry clash REVERT: P 54 TYR cc_start: 0.9288 (m-80) cc_final: 0.8433 (t80) REVERT: P 90 MET cc_start: 0.9480 (mmp) cc_final: 0.9213 (mmm) REVERT: P 97 GLU cc_start: 0.9511 (mm-30) cc_final: 0.8917 (mm-30) REVERT: P 105 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8967 (tm-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0332 time to fit residues: 0.6357 Evaluate side-chains 15 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.036 Evaluate side-chains 26 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 44 LYS cc_start: 0.7362 (pttm) cc_final: 0.6269 (mttt) REVERT: Q 68 ASP cc_start: 0.9213 (m-30) cc_final: 0.8993 (m-30) REVERT: Q 84 MET cc_start: 0.9087 (ptp) cc_final: 0.8786 (ppp) REVERT: Q 96 THR cc_start: 0.4829 (p) cc_final: 0.4587 (p) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.0735 time to fit residues: 2.0063 Evaluate side-chains 20 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.032 Evaluate side-chains 17 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.024 Fit side-chains REVERT: G 23 LEU cc_start: 0.7777 (mm) cc_final: 0.7379 (mm) REVERT: G 56 GLU cc_start: 0.7950 (pt0) cc_final: 0.7539 (mt-10) REVERT: G 95 LYS cc_start: 0.9174 (tttt) cc_final: 0.8789 (pttp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0608 time to fit residues: 1.1285 Evaluate side-chains 10 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.031 Evaluate side-chains 18 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.030 Fit side-chains revert: symmetry clash REVERT: H 59 MET cc_start: 0.3807 (tpp) cc_final: 0.3187 (tpp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0650 time to fit residues: 1.2728 Evaluate side-chains 12 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.030 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0260 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.036 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0417 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 Evaluate side-chains 13 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 311 LEU cc_start: 0.9040 (tt) cc_final: 0.8826 (mm) REVERT: V 413 MET cc_start: 0.0944 (ptm) cc_final: 0.0618 (ptm) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0949 time to fit residues: 1.5939 Evaluate side-chains 11 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 172 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 159 optimal weight: 0.0970 chunk 218 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 466 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.073967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.062379 restraints weight = 10777.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.063050 restraints weight = 9103.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.063658 restraints weight = 7867.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.064207 restraints weight = 6899.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.064207 restraints weight = 6111.253| |-----------------------------------------------------------------------------| r_work (final): 0.3867 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.070935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.062402 restraints weight = 4798.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.063831 restraints weight = 3344.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.064937 restraints weight = 2480.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.065819 restraints weight = 1907.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.066373 restraints weight = 1518.793| |-----------------------------------------------------------------------------| r_work (final): 0.3530 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.060128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.050521 restraints weight = 7504.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.051308 restraints weight = 5839.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.051940 restraints weight = 4783.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.052395 restraints weight = 4090.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.052778 restraints weight = 3630.753| |-----------------------------------------------------------------------------| r_work (final): 0.3206 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.069377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.058027 restraints weight = 5781.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.059083 restraints weight = 4117.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.059968 restraints weight = 3171.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.060747 restraints weight = 2573.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.061221 restraints weight = 2153.927| |-----------------------------------------------------------------------------| r_work (final): 0.3335 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.063317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.052435 restraints weight = 7022.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.053406 restraints weight = 5396.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.054249 restraints weight = 4294.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.054426 restraints weight = 3503.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.055125 restraints weight = 3310.642| |-----------------------------------------------------------------------------| r_work (final): 0.3280 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.060083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.048230 restraints weight = 4523.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.049797 restraints weight = 2651.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.050801 restraints weight = 1870.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.051425 restraints weight = 1462.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051951 restraints weight = 1243.908| |-----------------------------------------------------------------------------| r_work (final): 0.3254 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.060850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.050500 restraints weight = 5780.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.051759 restraints weight = 4051.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.052603 restraints weight = 2999.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.053267 restraints weight = 2359.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.053600 restraints weight = 1954.431| |-----------------------------------------------------------------------------| r_work (final): 0.3280 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.061067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.051594 restraints weight = 5744.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.052448 restraints weight = 4491.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.052996 restraints weight = 3695.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.053557 restraints weight = 3214.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.053922 restraints weight = 2839.022| |-----------------------------------------------------------------------------| r_work (final): 0.3239 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.103840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.094570 restraints weight = 36962.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.094914 restraints weight = 13183.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.095176 restraints weight = 7497.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.095176 restraints weight = 6290.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.095176 restraints weight = 6290.111| |-----------------------------------------------------------------------------| r_work (final): 0.3871 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.105099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.097105 restraints weight = 37916.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.097724 restraints weight = 13039.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.098322 restraints weight = 7215.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 72)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.098793 restraints weight = 5487.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.098793 restraints weight = 4694.210| |-----------------------------------------------------------------------------| r_work (final): 0.3922 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.069999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.062033 restraints weight = 58269.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.062160 restraints weight = 55919.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.062212 restraints weight = 54255.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.062378 restraints weight = 53159.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.062414 restraints weight = 52051.108| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 31458 Z= 0.164 Angle : 0.690 11.657 44954 Z= 0.388 Chirality : 0.045 0.317 5072 Planarity : 0.006 0.156 3660 Dihedral : 30.161 175.151 8852 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.17), residues: 2162 helix: 0.72 (0.13), residues: 1378 sheet: -2.35 (0.56), residues: 68 loop : -1.42 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 99 TYR 0.036 0.003 TYR D 121 PHE 0.024 0.001 PHE S 65 TRP 0.007 0.001 TRP K 455 HIS 0.009 0.001 HIS M 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (31458) covalent geometry : angle 0.68963 / 0.39 (44954) hydrogen bonds : bond 0.05799 / 3.77 ( 1820) hydrogen bonds : angle 4.06268 / 2.91 ( 4670) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0269 time to fit residues: 0.2327 Evaluate side-chains 5 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.032 Evaluate side-chains 12 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.026 Fit side-chains REVERT: B 68 ASP cc_start: 0.8940 (m-30) cc_final: 0.8580 (m-30) REVERT: B 85 ASP cc_start: 0.7662 (m-30) cc_final: 0.7301 (m-30) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0251 time to fit residues: 0.3733 Evaluate side-chains 9 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.017 Evaluate side-chains 12 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.034 Fit side-chains REVERT: N 38 ASN cc_start: 0.8354 (m-40) cc_final: 0.8070 (t0) REVERT: N 64 GLU cc_start: 0.8431 (tt0) cc_final: 0.7402 (mm-30) REVERT: N 111 ILE cc_start: 0.7146 (mm) cc_final: 0.6915 (mm) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0230 time to fit residues: 0.3655 Evaluate side-chains 5 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.033 Evaluate side-chains 15 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.029 Fit side-chains revert: symmetry clash REVERT: O 62 MET cc_start: 0.8704 (mmp) cc_final: 0.8442 (mmm) REVERT: O 71 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8466 (mm-30) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0397 time to fit residues: 0.6863 Evaluate side-chains 12 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.030 Evaluate side-chains 17 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.033 Fit side-chains revert: symmetry clash REVERT: P 54 TYR cc_start: 0.9286 (m-80) cc_final: 0.8420 (t80) REVERT: P 90 MET cc_start: 0.9405 (mmp) cc_final: 0.9192 (mmm) REVERT: P 97 GLU cc_start: 0.9532 (mm-30) cc_final: 0.9003 (mm-30) REVERT: P 105 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8986 (tm-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0270 time to fit residues: 0.5622 Evaluate side-chains 16 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.038 Evaluate side-chains 25 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 44 LYS cc_start: 0.8290 (pttm) cc_final: 0.7806 (mttt) REVERT: Q 84 MET cc_start: 0.9098 (ptp) cc_final: 0.8858 (ppp) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0718 time to fit residues: 1.9114 Evaluate side-chains 20 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.028 Evaluate side-chains 16 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.021 Fit side-chains REVERT: G 23 LEU cc_start: 0.7854 (mm) cc_final: 0.7429 (mm) REVERT: G 56 GLU cc_start: 0.7999 (pt0) cc_final: 0.7623 (mt-10) REVERT: G 95 LYS cc_start: 0.9186 (tttt) cc_final: 0.8778 (pttp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0334 time to fit residues: 0.6142 Evaluate side-chains 9 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.032 Evaluate side-chains 16 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.031 Fit side-chains REVERT: H 59 MET cc_start: 0.4050 (tpp) cc_final: 0.3415 (tpp) REVERT: H 67 ASN cc_start: 0.9381 (m110) cc_final: 0.9131 (p0) REVERT: H 69 ILE cc_start: 0.9372 (pt) cc_final: 0.9132 (mt) REVERT: H 100 LEU cc_start: 0.9508 (tp) cc_final: 0.9230 (pp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0602 time to fit residues: 1.0526 Evaluate side-chains 13 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.031 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0438 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.031 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0395 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.032 Evaluate side-chains 12 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 311 LEU cc_start: 0.8906 (tt) cc_final: 0.8684 (mm) REVERT: V 413 MET cc_start: 0.0690 (ptm) cc_final: 0.0395 (ptm) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0792 time to fit residues: 1.2517 Evaluate side-chains 11 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 177 optimal weight: 0.0270 chunk 91 optimal weight: 30.0000 chunk 200 optimal weight: 0.9980 chunk 238 optimal weight: 0.6980 chunk 266 optimal weight: 8.9990 chunk 124 optimal weight: 0.0170 chunk 209 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 267 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** V 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 466 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.070101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.061115 restraints weight = 7903.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.061668 restraints weight = 7023.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.062138 restraints weight = 6272.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.062457 restraints weight = 5686.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.062786 restraints weight = 5218.038| |-----------------------------------------------------------------------------| r_work (final): 0.3466 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.071053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.060931 restraints weight = 4574.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.062171 restraints weight = 3493.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.063117 restraints weight = 2752.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.063969 restraints weight = 2255.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.064306 restraints weight = 1900.146| |-----------------------------------------------------------------------------| r_work (final): 0.3421 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.060227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.050691 restraints weight = 7724.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.051534 restraints weight = 5917.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.052219 restraints weight = 4778.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.052743 restraints weight = 4028.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.053021 restraints weight = 3505.878| |-----------------------------------------------------------------------------| r_work (final): 0.3204 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.069904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.058559 restraints weight = 5708.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.059748 restraints weight = 4057.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.060571 restraints weight = 3086.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.061256 restraints weight = 2499.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.061909 restraints weight = 2112.135| |-----------------------------------------------------------------------------| r_work (final): 0.3316 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.063557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.052932 restraints weight = 6740.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.053943 restraints weight = 5088.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.054679 restraints weight = 4028.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.055257 restraints weight = 3304.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.055767 restraints weight = 2795.536| |-----------------------------------------------------------------------------| r_work (final): 0.3284 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.057284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.047373 restraints weight = 4317.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.048752 restraints weight = 2613.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.049635 restraints weight = 1878.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.050209 restraints weight = 1490.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.050647 restraints weight = 1270.533| |-----------------------------------------------------------------------------| r_work (final): 0.3140 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.061231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.050995 restraints weight = 5536.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.052162 restraints weight = 3845.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.053050 restraints weight = 2857.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.053630 restraints weight = 2227.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.054325 restraints weight = 1861.048| |-----------------------------------------------------------------------------| r_work (final): 0.3295 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.062230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.052793 restraints weight = 5513.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.053558 restraints weight = 4382.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.054138 restraints weight = 3661.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.054682 restraints weight = 3172.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.054934 restraints weight = 2796.923| |-----------------------------------------------------------------------------| r_work (final): 0.3253 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.101660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.093572 restraints weight = 37225.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.093807 restraints weight = 14525.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.094185 restraints weight = 7560.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.094280 restraints weight = 5955.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.094298 restraints weight = 5588.231| |-----------------------------------------------------------------------------| r_work (final): 0.3858 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.103694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.096049 restraints weight = 36763.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.096581 restraints weight = 16933.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.096319 restraints weight = 12823.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.096489 restraints weight = 10232.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.096416 restraints weight = 7523.842| |-----------------------------------------------------------------------------| r_work (final): 0.3900 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.070104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.061425 restraints weight = 589435.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.061129 restraints weight = 614178.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.061078 restraints weight = 610154.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.061039 restraints weight = 592404.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.060976 restraints weight = 577116.243| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31458 Z= 0.151 Angle : 0.679 16.305 44954 Z= 0.382 Chirality : 0.045 0.296 5072 Planarity : 0.006 0.150 3660 Dihedral : 30.176 176.208 8852 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.17), residues: 2162 helix: 0.78 (0.13), residues: 1382 sheet: -2.28 (0.56), residues: 68 loop : -1.33 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG H 72 TYR 0.036 0.002 TYR D 121 PHE 0.029 0.001 PHE S 65 TRP 0.007 0.001 TRP V 455 HIS 0.007 0.001 HIS M 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (31458) covalent geometry : angle 0.67948 / 0.38 (44954) hydrogen bonds : bond 0.04944 / 3.17 ( 1820) hydrogen bonds : angle 3.96651 / 2.84 ( 4670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2817.17 seconds wall clock time: 50 minutes 22.93 seconds (3022.93 seconds total)