Starting phenix.real_space_refine on Mon Aug 25 15:53:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ccr_30340/08_2025/7ccr_30340.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ccr_30340/08_2025/7ccr_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_30340/08_2025/7ccr_30340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ccr_30340/08_2025/7ccr_30340.map" model { file = "/net/cci-nas-00/data/ceres_data/7ccr_30340/08_2025/7ccr_30340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ccr_30340/08_2025/7ccr_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-2.0-5787/lib/python3.9/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: 8.19, per 1000 atoms: 0.28 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: 2.64 Conformation dependent library (CDL) restraints added in 739.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 5.43 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: 8.86 Time building geometry restraints manager: 3.57 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' DG T 20 " pdb=" O3' DG T 20 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.35e+00 bond pdb=" C3' DC U 6 " pdb=" O3' DC U 6 " ideal model delta sigma weight residual 1.422 1.360 0.062 3.00e-02 1.11e+03 4.32e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.24e+00 bond pdb=" C3' DC J 6 " pdb=" O3' DC J 6 " ideal model delta sigma weight residual 1.422 1.360 0.062 3.00e-02 1.11e+03 4.23e+00 bond pdb=" CA LYS V 432 " pdb=" C LYS V 432 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.30e-02 5.92e+03 3.59e+00 ... (remaining 31453 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 42531 2.02 - 4.03: 2213 4.03 - 6.05: 156 6.05 - 8.07: 41 8.07 - 10.09: 13 Bond angle restraints: 44954 Sorted by residual: 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 angle pdb=" N LYS K 432 " pdb=" CA LYS K 432 " pdb=" C LYS K 432 " ideal model delta sigma weight residual 111.28 119.12 -7.84 1.09e+00 8.42e-01 5.17e+01 angle pdb=" N LEU V 430 " pdb=" CA LEU V 430 " pdb=" C LEU V 430 " ideal model delta sigma weight residual 111.28 118.24 -6.96 1.09e+00 8.42e-01 4.08e+01 angle pdb=" N LYS K 427 " pdb=" CA LYS K 427 " pdb=" C LYS K 427 " ideal model delta sigma weight residual 110.35 119.03 -8.68 1.36e+00 5.41e-01 4.07e+01 angle pdb=" N LEU K 430 " pdb=" CA LEU K 430 " pdb=" C LEU K 430 " ideal model delta sigma weight residual 111.28 118.22 -6.94 1.09e+00 8.42e-01 4.06e+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 - 0.061: 3815 0.061 - 0.123: 1041 0.123 - 0.184: 172 0.184 - 0.245: 26 0.245 - 0.307: 18 Chirality restraints: 5072 Sorted by residual: 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 2.47 2.16 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C1' DC I -27 " pdb=" O4' DC I -27 " pdb=" C2' DC I -27 " pdb=" N1 DC I -27 " both_signs ideal model delta sigma weight residual False 2.47 2.16 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C1' DT U 13 " pdb=" O4' DT U 13 " pdb=" C2' DT U 13 " pdb=" N1 DT U 13 " both_signs ideal model delta sigma weight residual False 2.47 2.17 0.30 2.00e-01 2.50e+01 2.28e+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: 1.650 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 34.200 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.007 0.066 31458 Z= 0.339 Angle : 0.963 10.085 44954 Z= 0.579 Chirality : 0.058 0.307 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 aren 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 covalent geometry : bond 0.00743 (31458) covalent geometry : angle 0.96329 (44954) hydrogen bonds : bond 0.12669 ( 1820) hydrogen bonds : angle 4.93169 ( 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 : 0.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0653 time to fit residues: 1.7003 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 : 0.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 ASP cc_start: 0.7933 (m-30) cc_final: 0.7542 (m-30) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1011 time to fit residues: 2.5378 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 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 : 0.033 Fit side-chains REVERT: C 64 GLU cc_start: 0.8389 (tt0) cc_final: 0.7167 (mm-30) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0373 time to fit residues: 0.9478 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 : 0.035 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 : 0.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 MET cc_start: 0.9228 (mmm) cc_final: 0.8829 (mmm) REVERT: D 73 ILE cc_start: 0.9340 (mt) cc_final: 0.9101 (tp) REVERT: D 106 LEU cc_start: 0.8732 (tt) cc_final: 0.8469 (pp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1059 time to fit residues: 3.7594 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 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 : 0.036 Fit side-chains revert: symmetry clash REVERT: E 62 ILE cc_start: 0.8743 (mt) cc_final: 0.8425 (mm) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0689 time to fit residues: 2.5184 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 : 0.036 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 : 0.027 Fit side-chains revert: symmetry clash REVERT: F 24 ASP cc_start: 0.8332 (t70) cc_final: 0.7821 (t0) REVERT: F 58 LEU cc_start: 0.9656 (tp) cc_final: 0.9363 (pp) REVERT: F 66 ILE cc_start: 0.9678 (mt) cc_final: 0.9275 (pt) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1057 time to fit residues: 3.9527 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 : 0.027 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: 0.8398 (tt0) cc_final: 0.7875 (mt-10) REVERT: G 95 LYS cc_start: 0.9291 (tttt) cc_final: 0.8834 (pptt) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0597 time to fit residues: 1.9459 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 : 0.034 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 : 0.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 68 ASP cc_start: 0.9043 (t0) cc_final: 0.8442 (t0) REVERT: H 71 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8713 (tp30) REVERT: H 72 ARG cc_start: 0.8784 (mtt180) cc_final: 0.8246 (mtt180) REVERT: H 100 LEU cc_start: 0.8875 (mt) cc_final: 0.8675 (tt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1058 time to fit residues: 4.2966 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 : 0.038 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 : 0.046 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0544 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: 0.0413 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 : 0.031 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 : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 276 MET cc_start: 0.9517 (mmm) cc_final: 0.9129 (tmm) REVERT: K 456 ASP cc_start: 0.8402 (t0) cc_final: 0.8145 (p0) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.1250 time to fit residues: 5.3874 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 : 0.134 ------------------------------------------------------------------------------- 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: 7.9990 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: 9.9990 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... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 110 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 68 GLN P 93 GLN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 110 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS H 109 HIS Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 192 HIS V 260 ASN ** V 351 GLN ** 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 = 0.3603 r_free = 0.3603 target = 0.071727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.061412 restraints weight = 7418.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.061672 restraints weight = 6850.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.062079 restraints weight = 6401.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.062079 restraints weight = 6049.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.062079 restraints weight = 6049.926| |-----------------------------------------------------------------------------| r_work (final): 0.3411 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.077274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.065136 restraints weight = 3858.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.066455 restraints weight = 2956.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.067564 restraints weight = 2387.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.068483 restraints weight = 1976.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.069282 restraints weight = 1679.251| |-----------------------------------------------------------------------------| r_work (final): 0.3508 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.059754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.049083 restraints weight = 7381.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.049911 restraints weight = 5666.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.050542 restraints weight = 4613.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.050896 restraints weight = 3940.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.051483 restraints weight = 3527.812| |-----------------------------------------------------------------------------| r_work (final): 0.3148 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.069614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.057302 restraints weight = 6406.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.058450 restraints weight = 4665.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.059365 restraints weight = 3631.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.059783 restraints weight = 2978.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.060434 restraints weight = 2611.382| |-----------------------------------------------------------------------------| r_work (final): 0.3302 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.067086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.055382 restraints weight = 6993.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.056385 restraints weight = 5397.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.057137 restraints weight = 4302.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.057831 restraints weight = 3560.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.058232 restraints weight = 2989.981| |-----------------------------------------------------------------------------| r_work (final): 0.3345 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.062910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.053669 restraints weight = 4852.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054939 restraints weight = 3270.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.055913 restraints weight = 2333.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.056426 restraints weight = 1788.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057104 restraints weight = 1484.563| |-----------------------------------------------------------------------------| r_work (final): 0.3321 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.062267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.050789 restraints weight = 5425.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.052243 restraints weight = 3861.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.053349 restraints weight = 2894.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.054203 restraints weight = 2284.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.054869 restraints weight = 1872.234| |-----------------------------------------------------------------------------| r_work (final): 0.3296 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.069362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.057654 restraints weight = 4814.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.059278 restraints weight = 3293.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.060512 restraints weight = 2478.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.061498 restraints weight = 1994.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.062199 restraints weight = 1664.633| |-----------------------------------------------------------------------------| r_work (final): 0.3501 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.106191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.097408 restraints weight = 35590.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.097668 restraints weight = 14739.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.097927 restraints weight = 7392.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.098182 restraints weight = 6036.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.098182 restraints weight = 5460.157| |-----------------------------------------------------------------------------| r_work (final): 0.3908 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.107904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.100403 restraints weight = 35187.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.100786 restraints weight = 12605.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.101101 restraints weight = 6805.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.101415 restraints weight = 5331.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.101440 restraints weight = 4813.044| |-----------------------------------------------------------------------------| r_work (final): 0.3948 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.071131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.060368 restraints weight = 59900.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.060369 restraints weight = 58053.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.060374 restraints weight = 58036.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.060374 restraints weight = 57919.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.060374 restraints weight = 57919.378| |-----------------------------------------------------------------------------| r_work (final): 0.3961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 31458 Z= 0.207 Angle : 0.728 11.554 44954 Z= 0.414 Chirality : 0.040 0.345 5072 Planarity : 0.007 0.092 3660 Dihedral : 29.821 161.259 8852 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.63 % Allowed : 2.74 % Favored : 96.63 % 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 aren not related in a simple way. whole: -1.16 (0.16), residues: 2162 helix: -0.07 (0.12), residues: 1388 sheet: -2.00 (0.45), residues: 88 loop : -1.88 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 40 TYR 0.057 0.003 TYR F 98 PHE 0.019 0.002 PHE V 280 TRP 0.012 0.002 TRP V 375 HIS 0.011 0.002 HIS M 75 Details of bonding type rmsd covalent geometry : bond 0.00462 (31458) covalent geometry : angle 0.72837 (44954) hydrogen bonds : bond 0.05423 ( 1820) hydrogen bonds : angle 4.24958 ( 4670) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4132 Ramachandran restraints generated. 2066 Oldfield, 0 Emsley, 2066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.035 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0539 time to fit residues: 1.0294 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 : 0.033 Evaluate side-chains 21 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.027 Fit side-chains revert: symmetry clash REVERT: M 64 ASN cc_start: 0.9401 (m-40) cc_final: 0.9059 (m110) REVERT: M 85 ASP cc_start: 0.8013 (m-30) cc_final: 0.7275 (m-30) outliers start: 2 outliers final: 0 residues processed: 20 average time/residue: 0.0991 time to fit residues: 2.0814 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 : 0.028 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 : 0.038 Fit side-chains REVERT: C 38 ASN cc_start: 0.8838 (m110) cc_final: 0.8344 (t0) REVERT: C 64 GLU cc_start: 0.8186 (tt0) cc_final: 0.7172 (mm-30) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0426 time to fit residues: 0.7970 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 : 0.035 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 : 0.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8571 (mm-30) REVERT: D 73 ILE cc_start: 0.9367 (mt) cc_final: 0.9136 (tp) outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.0601 time to fit residues: 1.3781 Evaluate side-chains 18 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.031 Evaluate side-chains 21 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.039 Fit side-chains REVERT: P 54 TYR cc_start: 0.9398 (m-80) cc_final: 0.8567 (t80) REVERT: P 90 MET cc_start: 0.9391 (mmp) cc_final: 0.9125 (mmm) REVERT: P 94 GLU cc_start: 0.7967 (tt0) cc_final: 0.7448 (pt0) REVERT: P 97 GLU cc_start: 0.9358 (mm-30) cc_final: 0.8832 (mm-30) REVERT: P 105 GLU cc_start: 0.9293 (tm-30) cc_final: 0.8976 (tm-30) outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.0317 time to fit residues: 0.7945 Evaluate side-chains 12 residues out of total 85 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.036 Evaluate side-chains 29 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 100 PHE cc_start: 0.6878 (m-80) cc_final: 0.6468 (m-80) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.0873 time to fit residues: 2.6587 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 : 0.022 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 : 0.033 Fit side-chains revert: symmetry clash REVERT: R 95 LYS cc_start: 0.9149 (tttt) cc_final: 0.8774 (pptt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0586 time to fit residues: 1.1074 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 Evaluate side-chains 27 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.030 Fit side-chains revert: symmetry clash REVERT: H 59 MET cc_start: 0.5252 (tpp) cc_final: 0.4689 (tpp) REVERT: H 71 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8832 (tp30) REVERT: H 72 ARG cc_start: 0.9138 (mtt180) cc_final: 0.8797 (mtt180) outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.0892 time to fit residues: 2.5428 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 : 0.033 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 : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0426 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: 0.0408 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 17 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: V 413 MET cc_start: 0.1334 (ptm) cc_final: 0.1048 (ptm) REVERT: V 456 ASP cc_start: 0.8091 (t0) cc_final: 0.7787 (p0) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1164 time to fit residues: 2.3858 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 : 0.121 ------------------------------------------------------------------------------- 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: 0.0870 chunk 20 optimal weight: 1.9990 chunk 202 optimal weight: 0.0570 chunk 47 optimal weight: 1.9990 chunk 252 optimal weight: 20.0000 chunk 258 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 236 optimal weight: 40.0000 chunk 191 optimal weight: 0.9980 chunk 162 optimal weight: 0.0060 chunk 105 optimal weight: 9.9990 overall best weight: 0.6294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 109 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 351 GLN ** 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 = 0.3643 r_free = 0.3643 target = 0.072752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.062742 restraints weight = 7837.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.063307 restraints weight = 6832.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.063870 restraints weight = 6117.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.064224 restraints weight = 5525.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.064685 restraints weight = 5086.365| |-----------------------------------------------------------------------------| r_work (final): 0.3487 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.072915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.061938 restraints weight = 4244.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.063272 restraints weight = 3245.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.064401 restraints weight = 2582.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.065327 restraints weight = 2098.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.066076 restraints weight = 1746.976| |-----------------------------------------------------------------------------| r_work (final): 0.3498 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.061829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051518 restraints weight = 7241.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.052212 restraints weight = 5910.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.052764 restraints weight = 5010.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.053121 restraints weight = 4381.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.053540 restraints weight = 3992.728| |-----------------------------------------------------------------------------| r_work (final): 0.3193 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.069805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.057901 restraints weight = 6724.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.059249 restraints weight = 4412.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.060113 restraints weight = 3248.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.060779 restraints weight = 2618.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.061152 restraints weight = 2234.915| |-----------------------------------------------------------------------------| r_work (final): 0.3299 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.066104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.055501 restraints weight = 7066.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.056585 restraints weight = 5235.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.057384 restraints weight = 4078.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.057995 restraints weight = 3274.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.058446 restraints weight = 2702.457| |-----------------------------------------------------------------------------| r_work (final): 0.3309 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.055539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045701 restraints weight = 4861.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047013 restraints weight = 3031.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.047984 restraints weight = 2234.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.048635 restraints weight = 1761.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.049117 restraints weight = 1462.347| |-----------------------------------------------------------------------------| r_work (final): 0.3037 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.062549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.051690 restraints weight = 5583.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.053101 restraints weight = 3948.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.054257 restraints weight = 2951.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.054996 restraints weight = 2303.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.055639 restraints weight = 1886.549| |-----------------------------------------------------------------------------| r_work (final): 0.3317 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.065799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.054385 restraints weight = 5448.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.055576 restraints weight = 4032.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.056456 restraints weight = 3251.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.057127 restraints weight = 2755.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.057679 restraints weight = 2412.683| |-----------------------------------------------------------------------------| r_work (final): 0.3384 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.103782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.096221 restraints weight = 39398.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.096210 restraints weight = 14048.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.096603 restraints weight = 7049.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.096828 restraints weight = 5468.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.096841 restraints weight = 5002.028| |-----------------------------------------------------------------------------| r_work (final): 0.3881 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.108066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.100022 restraints weight = 35298.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.100530 restraints weight = 12420.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.101280 restraints weight = 7128.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.101492 restraints weight = 5377.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.101526 restraints weight = 4700.815| |-----------------------------------------------------------------------------| r_work (final): 0.3950 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.070217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.059426 restraints weight = 58862.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.059783 restraints weight = 54369.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.060099 restraints weight = 51018.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.060362 restraints weight = 48339.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.060591 restraints weight = 46176.180| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.319 31458 Z= 0.391 Angle : 1.002 17.865 44954 Z= 0.553 Chirality : 0.055 0.600 5072 Planarity : 0.012 0.154 3660 Dihedral : 29.845 161.508 8852 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.95 % Allowed : 2.00 % Favored : 97.05 % Cbeta Deviations : 0.29 % 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 aren not related in a simple way. whole: -1.65 (0.16), residues: 2162 helix: -0.45 (0.12), residues: 1370 sheet: -2.05 (0.46), residues: 88 loop : -2.07 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.003 ARG M 92 TYR 0.234 0.009 TYR A 99 PHE 0.188 0.009 PHE L 78 TRP 0.007 0.001 TRP V 375 HIS 0.059 0.005 HIS L 113 Details of bonding type rmsd covalent geometry : bond 0.00913 (31458) covalent geometry : angle 1.00249 (44954) hydrogen bonds : bond 0.05734 ( 1820) hydrogen bonds : angle 4.43313 ( 4670) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.036 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 12 average time/residue: 0.0491 time to fit residues: 0.6874 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 : 0.036 Evaluate side-chains 19 residues out of total 64 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.030 Fit side-chains revert: symmetry clash REVERT: M 64 ASN cc_start: 0.9375 (m-40) cc_final: 0.9101 (m110) REVERT: M 68 ASP cc_start: 0.8770 (m-30) cc_final: 0.8449 (m-30) REVERT: M 85 ASP cc_start: 0.7933 (m-30) cc_final: 0.7470 (m-30) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.0736 time to fit residues: 1.4210 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 : 0.026 Evaluate side-chains 16 residues out of total 81 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.033 Fit side-chains REVERT: N 38 ASN cc_start: 0.8982 (m110) cc_final: 0.8595 (t0) REVERT: N 64 GLU cc_start: 0.8337 (tt0) cc_final: 0.7324 (mm-30) REVERT: N 73 ASN cc_start: 0.9491 (t0) cc_final: 0.9233 (t0) outliers start: 2 outliers final: 0 residues processed: 16 average time/residue: 0.0223 time to fit residues: 0.4626 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 21 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 62 MET cc_start: 0.8374 (mmm) cc_final: 0.7973 (mmm) REVERT: D 71 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8613 (mm-30) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0500 time to fit residues: 1.1081 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 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 Fit side-chains REVERT: E 54 TYR cc_start: 0.9340 (m-80) cc_final: 0.8569 (t80) REVERT: E 90 MET cc_start: 0.9339 (mmp) cc_final: 0.9108 (mmm) REVERT: E 97 GLU cc_start: 0.9452 (mm-30) cc_final: 0.8758 (mm-30) REVERT: E 105 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8893 (tm-30) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0273 time to fit residues: 0.5058 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 : 0.035 Evaluate side-chains 21 residues out of total 65 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 88 TYR cc_start: 0.8831 (m-80) cc_final: 0.8557 (m-80) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0822 time to fit residues: 1.7423 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 : 0.027 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 : 0.033 Fit side-chains revert: symmetry clash REVERT: R 95 LYS cc_start: 0.9143 (tttt) cc_final: 0.8780 (pptt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0440 time to fit residues: 0.7170 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 : 0.033 Evaluate side-chains 23 residues out of total 79 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.030 Fit side-chains revert: symmetry clash REVERT: H 68 ASP cc_start: 0.9105 (t0) cc_final: 0.8778 (t0) REVERT: H 71 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8798 (tp30) REVERT: H 72 ARG cc_start: 0.9137 (mtt180) cc_final: 0.8722 (mtt180) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0789 time to fit residues: 1.9347 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 : 0.033 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: 0.0422 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: 0.0415 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 413 MET cc_start: 0.1058 (ptm) cc_final: 0.0750 (ptm) REVERT: V 456 ASP cc_start: 0.7962 (t0) cc_final: 0.7646 (p0) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0990 time to fit residues: 1.6551 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 : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.1332 > 50: distance: 1 - 2: 11.518 distance: 1 - 3: 15.796 distance: 4 - 5: 56.323 distance: 5 - 6: 45.679 distance: 5 - 8: 19.070 distance: 6 - 7: 43.714 distance: 6 - 13: 28.797 distance: 7 - 43: 20.718 distance: 8 - 9: 57.555 distance: 9 - 10: 38.364 distance: 10 - 11: 15.414 distance: 10 - 12: 23.738 distance: 13 - 14: 30.702 distance: 14 - 15: 57.201 distance: 14 - 17: 18.071 distance: 15 - 16: 36.679 distance: 15 - 21: 31.626 distance: 16 - 55: 51.898 distance: 17 - 18: 22.583 distance: 17 - 19: 20.150 distance: 18 - 20: 42.160 distance: 21 - 22: 24.687 distance: 22 - 23: 23.892 distance: 22 - 25: 31.511 distance: 23 - 24: 18.798 distance: 23 - 32: 16.288 distance: 25 - 26: 55.481 distance: 26 - 27: 36.363 distance: 27 - 28: 12.378 distance: 28 - 29: 56.033 distance: 29 - 30: 30.621 distance: 29 - 31: 30.332 distance: 32 - 33: 12.206 distance: 33 - 34: 32.376 distance: 33 - 36: 30.431 distance: 34 - 35: 54.595 distance: 34 - 43: 36.771 distance: 35 - 73: 41.711 distance: 36 - 37: 53.426 distance: 37 - 38: 43.072 distance: 38 - 39: 28.804 distance: 39 - 40: 29.413 distance: 40 - 41: 27.193 distance: 40 - 42: 18.367 distance: 43 - 44: 54.174 distance: 44 - 45: 25.424 distance: 44 - 47: 43.066 distance: 45 - 46: 21.413 distance: 45 - 55: 20.179 distance: 47 - 48: 47.544 distance: 48 - 49: 23.331 distance: 48 - 50: 47.937 distance: 50 - 52: 42.901 distance: 51 - 53: 39.547 distance: 52 - 53: 8.482 distance: 53 - 54: 39.818 distance: 55 - 56: 35.013 distance: 56 - 57: 56.777 distance: 56 - 59: 18.118 distance: 57 - 58: 45.636 distance: 57 - 64: 57.711 distance: 59 - 60: 18.842 distance: 60 - 61: 34.973 distance: 61 - 62: 38.157 distance: 61 - 63: 14.702 distance: 64 - 65: 68.021 distance: 65 - 66: 56.555 distance: 65 - 68: 43.478 distance: 66 - 67: 61.352 distance: 66 - 73: 67.985 distance: 68 - 69: 52.316 distance: 69 - 70: 45.857 distance: 70 - 71: 69.178 distance: 71 - 72: 60.420 distance: 73 - 74: 41.490 distance: 74 - 75: 26.348 distance: 74 - 77: 47.500 distance: 75 - 76: 26.727 distance: 75 - 79: 24.135 distance: 77 - 78: 40.485 distance: 79 - 80: 28.390 distance: 80 - 81: 14.821 distance: 80 - 83: 28.179 distance: 81 - 82: 30.923 distance: 83 - 84: 41.770