Starting phenix.real_space_refine on Fri Jul 3 21:33:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uj4_64213/07_2026/9uj4_64213_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uj4_64213/07_2026/9uj4_64213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uj4_64213/07_2026/9uj4_64213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uj4_64213/07_2026/9uj4_64213.map" model { file = "/net/cci-nas-00/data/ceres_data/9uj4_64213/07_2026/9uj4_64213_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uj4_64213/07_2026/9uj4_64213_neut.cif" } resolution = 2.59 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= -0.001 sd= 0.059 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: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 K 4 8.98 5 P 4 5.49 5 S 80 5.16 5 C 10316 2.51 5 N 2696 2.21 5 O 2860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15968 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2827 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 7, 'TRANS': 341} Chain breaks: 2 Chain: "B" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "H" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2827 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 7, 'TRANS': 341} Chain breaks: 2 Chain: "F" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2827 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 7, 'TRANS': 341} Chain breaks: 2 Chain: "D" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2827 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 7, 'TRANS': 341} Chain breaks: 2 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 54 Ad-hoc single atom residues: {' K': 4} Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain breaks: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "G" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.80, per 1000 atoms: 0.24 Number of scatterers: 15968 At special positions: 0 Unit cell: (114.939, 114.939, 121.176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 8 19.99 K 4 19.00 S 80 16.00 P 4 15.00 O 2860 8.00 N 2696 7.00 C 10316 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: 1.35 Conformation dependent library (CDL) restraints added in 676.4 milliseconds 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 8 sheets defined 78.3% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.921A pdb=" N GLY A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 144 removed outlier: 3.763A pdb=" N THR A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 178 removed outlier: 4.673A pdb=" N ALA A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 196 through 217 Processing helix chain 'A' and resid 226 through 237 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 258 through 285 Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'A' and resid 341 through 359 removed outlier: 3.664A pdb=" N GLY A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 384 removed outlier: 4.223A pdb=" N ALA A 370 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.600A pdb=" N ILE A 394 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 396 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 533 Processing helix chain 'A' and resid 537 through 564 removed outlier: 3.633A pdb=" N VAL A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 21 Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.590A pdb=" N LEU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 66 through 75 removed outlier: 3.678A pdb=" N ARG B 75 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 139 through 149 Processing helix chain 'H' and resid 7 through 21 Processing helix chain 'H' and resid 29 through 41 removed outlier: 3.591A pdb=" N LEU H 40 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 66 through 75 removed outlier: 3.678A pdb=" N ARG H 75 " --> pdb=" O THR H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 92 Processing helix chain 'H' and resid 103 through 113 Processing helix chain 'H' and resid 118 through 128 Processing helix chain 'H' and resid 139 through 149 Processing helix chain 'G' and resid 105 through 116 removed outlier: 3.503A pdb=" N ARG G 109 " --> pdb=" O HIS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 144 removed outlier: 3.763A pdb=" N THR G 144 " --> pdb=" O SER G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 178 removed outlier: 4.674A pdb=" N ALA G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU G 151 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU G 163 " --> pdb=" O MET G 159 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL G 164 " --> pdb=" O GLU G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 186 through 195 Processing helix chain 'G' and resid 196 through 217 Processing helix chain 'G' and resid 226 through 237 Processing helix chain 'G' and resid 238 through 240 No H-bonds generated for 'chain 'G' and resid 238 through 240' Processing helix chain 'G' and resid 245 through 258 Processing helix chain 'G' and resid 258 through 285 Processing helix chain 'G' and resid 298 through 311 Processing helix chain 'G' and resid 322 through 336 Processing helix chain 'G' and resid 341 through 359 removed outlier: 3.665A pdb=" N GLY G 345 " --> pdb=" O ALA G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 366 through 384 removed outlier: 4.223A pdb=" N ALA G 370 " --> pdb=" O ARG G 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 396 removed outlier: 3.600A pdb=" N ILE G 394 " --> pdb=" O THR G 391 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE G 396 " --> pdb=" O LYS G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 507 through 533 Processing helix chain 'G' and resid 537 through 564 removed outlier: 3.632A pdb=" N VAL G 541 " --> pdb=" O ASP G 537 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL G 554 " --> pdb=" O LEU G 550 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP G 564 " --> pdb=" O GLN G 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 21 Processing helix chain 'F' and resid 29 through 41 removed outlier: 3.591A pdb=" N LEU F 40 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 66 through 75 removed outlier: 3.678A pdb=" N ARG F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 92 Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 118 through 128 Processing helix chain 'F' and resid 139 through 149 Processing helix chain 'E' and resid 105 through 116 removed outlier: 3.503A pdb=" N ARG E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 144 removed outlier: 3.763A pdb=" N THR E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 178 removed outlier: 4.674A pdb=" N ALA E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU E 151 " --> pdb=" O GLN E 147 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU E 163 " --> pdb=" O MET E 159 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 186 through 195 Processing helix chain 'E' and resid 196 through 217 Processing helix chain 'E' and resid 226 through 237 Processing helix chain 'E' and resid 238 through 240 No H-bonds generated for 'chain 'E' and resid 238 through 240' Processing helix chain 'E' and resid 245 through 258 Processing helix chain 'E' and resid 258 through 285 Processing helix chain 'E' and resid 298 through 311 Processing helix chain 'E' and resid 322 through 336 Processing helix chain 'E' and resid 341 through 359 removed outlier: 3.664A pdb=" N GLY E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 384 removed outlier: 4.224A pdb=" N ALA E 370 " --> pdb=" O ARG E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 396 removed outlier: 3.600A pdb=" N ILE E 394 " --> pdb=" O THR E 391 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 396 " --> pdb=" O LYS E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 533 Processing helix chain 'E' and resid 537 through 564 removed outlier: 3.633A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL E 554 " --> pdb=" O LEU E 550 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP E 564 " --> pdb=" O GLN E 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 21 Processing helix chain 'D' and resid 29 through 41 removed outlier: 3.590A pdb=" N LEU D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 66 through 75 removed outlier: 3.678A pdb=" N ARG D 75 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 92 Processing helix chain 'D' and resid 103 through 113 Processing helix chain 'D' and resid 118 through 128 Processing helix chain 'D' and resid 139 through 149 Processing helix chain 'C' and resid 105 through 116 removed outlier: 3.503A pdb=" N ARG C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 144 removed outlier: 3.763A pdb=" N THR C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 178 removed outlier: 4.674A pdb=" N ALA C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TRP C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 163 " --> pdb=" O MET C 159 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 186 through 195 Processing helix chain 'C' and resid 196 through 217 Processing helix chain 'C' and resid 226 through 237 Processing helix chain 'C' and resid 238 through 240 No H-bonds generated for 'chain 'C' and resid 238 through 240' Processing helix chain 'C' and resid 245 through 258 Processing helix chain 'C' and resid 258 through 285 Processing helix chain 'C' and resid 298 through 311 Processing helix chain 'C' and resid 322 through 336 Processing helix chain 'C' and resid 341 through 359 removed outlier: 3.665A pdb=" N GLY C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 384 removed outlier: 4.223A pdb=" N ALA C 370 " --> pdb=" O ARG C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.600A pdb=" N ILE C 394 " --> pdb=" O THR C 391 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 396 " --> pdb=" O LYS C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 533 Processing helix chain 'C' and resid 537 through 564 removed outlier: 3.632A pdb=" N VAL C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL C 554 " --> pdb=" O LEU C 550 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'H' and resid 27 through 28 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'F' and resid 27 through 28 Processing sheet with id=AA6, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 27 through 28 Processing sheet with id=AA8, first strand: chain 'D' and resid 100 through 102 1108 hydrogen bonds defined for protein. 3300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4244 1.33 - 1.45: 2976 1.45 - 1.57: 8916 1.57 - 1.69: 8 1.69 - 1.81: 136 Bond restraints: 16280 Sorted by residual: bond pdb=" C31 PC1 G 701 " pdb=" O31 PC1 G 701 " ideal model delta sigma weight residual 1.330 1.452 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C31 PC1 A 705 " pdb=" O31 PC1 A 705 " ideal model delta sigma weight residual 1.330 1.451 -0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C31 PC1 C 701 " pdb=" O31 PC1 C 701 " ideal model delta sigma weight residual 1.330 1.451 -0.121 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C31 PC1 E 701 " pdb=" O31 PC1 E 701 " ideal model delta sigma weight residual 1.330 1.451 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" C21 PC1 A 705 " pdb=" O21 PC1 A 705 " ideal model delta sigma weight residual 1.331 1.445 -0.114 2.00e-02 2.50e+03 3.28e+01 ... (remaining 16275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 21530 1.72 - 3.45: 316 3.45 - 5.17: 86 5.17 - 6.90: 16 6.90 - 8.62: 12 Bond angle restraints: 21960 Sorted by residual: angle pdb=" CA GLU F 8 " pdb=" CB GLU F 8 " pdb=" CG GLU F 8 " ideal model delta sigma weight residual 114.10 120.93 -6.83 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA GLU B 8 " pdb=" CB GLU B 8 " pdb=" CG GLU B 8 " ideal model delta sigma weight residual 114.10 120.91 -6.81 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA GLU H 8 " pdb=" CB GLU H 8 " pdb=" CG GLU H 8 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA GLU D 8 " pdb=" CB GLU D 8 " pdb=" CG GLU D 8 " ideal model delta sigma weight residual 114.10 120.89 -6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" C2 PC1 E 701 " pdb=" O21 PC1 E 701 " pdb=" C21 PC1 E 701 " ideal model delta sigma weight residual 119.24 110.62 8.62 3.00e+00 1.11e-01 8.26e+00 ... (remaining 21955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 8600 16.53 - 33.05: 801 33.05 - 49.58: 187 49.58 - 66.11: 32 66.11 - 82.63: 12 Dihedral angle restraints: 9632 sinusoidal: 3944 harmonic: 5688 Sorted by residual: dihedral pdb=" CB MET B 110 " pdb=" CG MET B 110 " pdb=" SD MET B 110 " pdb=" CE MET B 110 " ideal model delta sinusoidal sigma weight residual 60.00 107.98 -47.98 3 1.50e+01 4.44e-03 8.57e+00 dihedral pdb=" CB MET H 110 " pdb=" CG MET H 110 " pdb=" SD MET H 110 " pdb=" CE MET H 110 " ideal model delta sinusoidal sigma weight residual 60.00 107.96 -47.96 3 1.50e+01 4.44e-03 8.57e+00 dihedral pdb=" CB MET F 110 " pdb=" CG MET F 110 " pdb=" SD MET F 110 " pdb=" CE MET F 110 " ideal model delta sinusoidal sigma weight residual 60.00 107.95 -47.95 3 1.50e+01 4.44e-03 8.57e+00 ... (remaining 9629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1518 0.033 - 0.065: 736 0.065 - 0.098: 133 0.098 - 0.131: 45 0.131 - 0.164: 4 Chirality restraints: 2436 Sorted by residual: chirality pdb=" C2 PC1 E 701 " pdb=" C1 PC1 E 701 " pdb=" C3 PC1 E 701 " pdb=" O21 PC1 E 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.65 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" C2 PC1 G 701 " pdb=" C1 PC1 G 701 " pdb=" C3 PC1 G 701 " pdb=" O21 PC1 G 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.65 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" C2 PC1 C 701 " pdb=" C1 PC1 C 701 " pdb=" C3 PC1 C 701 " pdb=" O21 PC1 C 701 " both_signs ideal model delta sigma weight residual False -2.49 -2.65 0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 2433 not shown) Planarity restraints: 2748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 164 " 0.008 2.00e-02 2.50e+03 1.50e-02 2.25e+00 pdb=" C VAL E 164 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL E 164 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL E 165 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 164 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C VAL C 164 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL C 164 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL C 165 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 164 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C VAL G 164 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL G 164 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL G 165 " 0.008 2.00e-02 2.50e+03 ... (remaining 2745 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 5164 2.82 - 3.40: 18053 3.40 - 3.98: 30674 3.98 - 4.56: 44557 4.56 - 5.14: 62569 Nonbonded interactions: 161017 Sorted by model distance: nonbonded pdb=" O LEU E 175 " pdb=" NH1 ARG E 190 " model vdw 2.245 3.120 nonbonded pdb=" O LEU A 175 " pdb=" NH1 ARG A 190 " model vdw 2.245 3.120 nonbonded pdb=" O LEU G 175 " pdb=" NH1 ARG G 190 " model vdw 2.245 3.120 nonbonded pdb=" O LEU C 175 " pdb=" NH1 ARG C 190 " model vdw 2.245 3.120 nonbonded pdb=" NZ LYS C 362 " pdb=" O GLN C 531 " model vdw 2.333 3.120 ... (remaining 161012 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 104 through 564) selection = (chain 'C' and resid 104 through 564) selection = (chain 'E' and resid 104 through 564) selection = (chain 'G' and resid 104 through 564) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 individual isotropic 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: 5.100 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.330 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.005 0.122 16280 Z= 0.217 Angle : 0.620 8.621 21960 Z= 0.333 Chirality : 0.038 0.164 2436 Planarity : 0.003 0.034 2748 Dihedral : 13.725 82.633 5968 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.48 % Allowed : 3.39 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.16), residues: 1940 helix: -1.22 (0.11), residues: 1500 sheet: None (None), residues: 0 loop : -0.96 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 507 TYR 0.013 0.001 TYR F 139 PHE 0.010 0.001 PHE C 332 TRP 0.014 0.002 TRP E 305 HIS 0.003 0.001 HIS C 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.22 (16280) covalent geometry : angle 0.61964 / 0.33 (21960) hydrogen bonds : bond 0.14388 / 9.65 ( 1108) hydrogen bonds : angle 6.54378 / 4.79 ( 3300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 358 time to evaluate : 0.647 Fit side-chains REVERT: A 249 ARG cc_start: 0.7452 (ttm110) cc_final: 0.7219 (ttp-110) REVERT: A 293 ARG cc_start: 0.7796 (mtt90) cc_final: 0.7527 (ptt180) REVERT: A 366 ARG cc_start: 0.7390 (mmt-90) cc_final: 0.7055 (mmp-170) REVERT: A 393 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7541 (mmtt) REVERT: G 249 ARG cc_start: 0.7458 (ttm110) cc_final: 0.7223 (ttp-110) REVERT: G 293 ARG cc_start: 0.7787 (mtt90) cc_final: 0.7515 (ptt180) REVERT: G 366 ARG cc_start: 0.7396 (mmt-90) cc_final: 0.7060 (mmp-170) REVERT: G 393 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7533 (mmtt) REVERT: E 249 ARG cc_start: 0.7479 (ttm110) cc_final: 0.7250 (ttp-110) REVERT: E 293 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7534 (ptt180) REVERT: E 393 LYS cc_start: 0.8187 (mtpt) cc_final: 0.7573 (mmtt) REVERT: C 249 ARG cc_start: 0.7456 (ttm110) cc_final: 0.7227 (ttp-110) REVERT: C 293 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7543 (ptt180) REVERT: C 366 ARG cc_start: 0.7392 (mmt-90) cc_final: 0.7058 (mmp-170) REVERT: C 393 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7532 (mmtt) outliers start: 8 outliers final: 0 residues processed: 363 average time/residue: 0.8286 time to fit residues: 323.9614 Evaluate side-chains 276 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 ASN A 386 ASN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN B 54 ASN B 108 HIS H 54 ASN H 108 HIS H 112 ASN G 365 ASN G 386 ASN ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 560 GLN F 54 ASN F 108 HIS F 112 ASN E 365 ASN E 386 ASN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 GLN D 54 ASN D 108 HIS D 112 ASN C 365 ASN C 386 ASN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.185139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.132034 restraints weight = 16006.828| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.77 r_work: 0.3274 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16280 Z= 0.154 Angle : 0.518 5.140 21960 Z= 0.283 Chirality : 0.039 0.119 2436 Planarity : 0.003 0.039 2748 Dihedral : 8.929 88.537 2344 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 2.36 % Allowed : 10.05 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.18), residues: 1940 helix: 0.42 (0.12), residues: 1512 sheet: None (None), residues: 0 loop : -0.12 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 555 TYR 0.010 0.001 TYR H 139 PHE 0.012 0.001 PHE A 332 TRP 0.012 0.001 TRP E 305 HIS 0.003 0.001 HIS G 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (16280) covalent geometry : angle 0.51843 / 0.28 (21960) hydrogen bonds : bond 0.04972 / 3.31 ( 1108) hydrogen bonds : angle 4.46922 / 3.27 ( 3300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 0.490 Fit side-chains REVERT: A 249 ARG cc_start: 0.7889 (ttm110) cc_final: 0.7285 (ttp-110) REVERT: A 293 ARG cc_start: 0.8388 (mtt90) cc_final: 0.7371 (ptt180) REVERT: A 365 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7709 (m-40) REVERT: A 366 ARG cc_start: 0.7702 (mmt-90) cc_final: 0.7121 (mmp-170) REVERT: B 23 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6808 (p0) REVERT: B 25 ASP cc_start: 0.7680 (m-30) cc_final: 0.7297 (m-30) REVERT: B 83 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7549 (mt-10) REVERT: H 23 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6832 (p0) REVERT: H 25 ASP cc_start: 0.7678 (m-30) cc_final: 0.7301 (m-30) REVERT: H 83 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7541 (mt-10) REVERT: G 249 ARG cc_start: 0.7892 (ttm110) cc_final: 0.7284 (ttp-110) REVERT: G 293 ARG cc_start: 0.8398 (mtt90) cc_final: 0.7378 (ptt180) REVERT: G 365 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7698 (m-40) REVERT: G 366 ARG cc_start: 0.7709 (mmt-90) cc_final: 0.7128 (mmp-170) REVERT: F 23 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6832 (p0) REVERT: F 25 ASP cc_start: 0.7720 (m-30) cc_final: 0.7316 (m-30) REVERT: F 83 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7551 (mt-10) REVERT: E 249 ARG cc_start: 0.7907 (ttm110) cc_final: 0.7299 (ttp-110) REVERT: E 293 ARG cc_start: 0.8402 (mtt90) cc_final: 0.7390 (ptt180) REVERT: D 23 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6819 (p0) REVERT: D 25 ASP cc_start: 0.7667 (m-30) cc_final: 0.7293 (m-30) REVERT: D 83 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7542 (mt-10) REVERT: C 249 ARG cc_start: 0.7882 (ttm110) cc_final: 0.7276 (ttp-110) REVERT: C 293 ARG cc_start: 0.8398 (mtt90) cc_final: 0.7388 (ptt180) REVERT: C 365 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7699 (m-40) REVERT: C 366 ARG cc_start: 0.7697 (mmt-90) cc_final: 0.7122 (mmp-170) REVERT: C 555 ARG cc_start: 0.7414 (mmt90) cc_final: 0.6943 (mtt180) outliers start: 39 outliers final: 10 residues processed: 294 average time/residue: 0.7311 time to fit residues: 232.1847 Evaluate side-chains 271 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 254 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain G residue 365 ASN Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain C residue 365 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 82 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 190 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 159 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 365 ASN ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.185355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.131544 restraints weight = 16217.193| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.78 r_work: 0.3272 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16280 Z= 0.134 Angle : 0.479 5.247 21960 Z= 0.261 Chirality : 0.038 0.123 2436 Planarity : 0.003 0.038 2748 Dihedral : 8.700 88.417 2344 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 3.63 % Allowed : 10.41 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.18), residues: 1940 helix: 1.04 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : 0.14 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 555 TYR 0.009 0.001 TYR H 139 PHE 0.012 0.001 PHE E 332 TRP 0.011 0.001 TRP A 305 HIS 0.003 0.001 HIS C 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (16280) covalent geometry : angle 0.47888 / 0.26 (21960) hydrogen bonds : bond 0.04583 / 3.05 ( 1108) hydrogen bonds : angle 4.17835 / 3.06 ( 3300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 266 time to evaluate : 0.639 Fit side-chains REVERT: A 249 ARG cc_start: 0.7839 (ttm110) cc_final: 0.7227 (ttp-110) REVERT: A 293 ARG cc_start: 0.8377 (mtt90) cc_final: 0.7320 (ptt180) REVERT: A 363 HIS cc_start: 0.7386 (m170) cc_final: 0.6942 (t70) REVERT: A 365 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7682 (m-40) REVERT: A 366 ARG cc_start: 0.7704 (mmt-90) cc_final: 0.7152 (mmp-170) REVERT: B 23 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.6864 (p0) REVERT: B 25 ASP cc_start: 0.7697 (m-30) cc_final: 0.7227 (m-30) REVERT: B 140 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6080 (mp0) REVERT: H 23 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.6908 (p0) REVERT: H 25 ASP cc_start: 0.7706 (m-30) cc_final: 0.7250 (m-30) REVERT: H 140 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6089 (mp0) REVERT: G 249 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7214 (ttp-110) REVERT: G 293 ARG cc_start: 0.8387 (mtt90) cc_final: 0.7328 (ptt180) REVERT: G 363 HIS cc_start: 0.7397 (m170) cc_final: 0.6929 (t70) REVERT: G 365 ASN cc_start: 0.8003 (OUTLIER) cc_final: 0.7697 (m-40) REVERT: G 366 ARG cc_start: 0.7715 (mmt-90) cc_final: 0.7188 (mmp-170) REVERT: F 23 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.6903 (p0) REVERT: F 25 ASP cc_start: 0.7705 (m-30) cc_final: 0.7241 (m-30) REVERT: F 140 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6099 (mp0) REVERT: E 249 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7238 (ttp-110) REVERT: E 293 ARG cc_start: 0.8366 (mtt90) cc_final: 0.7315 (ptt180) REVERT: E 363 HIS cc_start: 0.7395 (m170) cc_final: 0.7084 (t70) REVERT: E 366 ARG cc_start: 0.7730 (mmt180) cc_final: 0.7309 (mmp-170) REVERT: D 23 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.6882 (p0) REVERT: D 25 ASP cc_start: 0.7692 (m-30) cc_final: 0.7235 (m-30) REVERT: D 140 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6093 (mp0) REVERT: C 249 ARG cc_start: 0.7827 (ttm110) cc_final: 0.7211 (ttp-110) REVERT: C 293 ARG cc_start: 0.8377 (mtt90) cc_final: 0.7327 (ptt180) REVERT: C 363 HIS cc_start: 0.7394 (m170) cc_final: 0.6940 (t70) REVERT: C 365 ASN cc_start: 0.8015 (OUTLIER) cc_final: 0.7694 (m-40) REVERT: C 366 ARG cc_start: 0.7735 (mmt-90) cc_final: 0.7174 (mmp-170) REVERT: C 555 ARG cc_start: 0.7430 (mmt90) cc_final: 0.6889 (mtt180) outliers start: 60 outliers final: 14 residues processed: 301 average time/residue: 0.7869 time to fit residues: 256.0186 Evaluate side-chains 276 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 251 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 365 ASN Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 365 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 365 ASN ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 549 HIS ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.184376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.131143 restraints weight = 16057.315| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.83 r_work: 0.3259 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16280 Z= 0.160 Angle : 0.497 5.298 21960 Z= 0.268 Chirality : 0.039 0.123 2436 Planarity : 0.003 0.037 2748 Dihedral : 8.642 88.954 2344 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.21 % Allowed : 12.47 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 1940 helix: 1.21 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : 0.18 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 38 TYR 0.011 0.001 TYR B 139 PHE 0.013 0.001 PHE G 332 TRP 0.013 0.001 TRP C 305 HIS 0.003 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (16280) covalent geometry : angle 0.49739 / 0.27 (21960) hydrogen bonds : bond 0.04626 / 3.07 ( 1108) hydrogen bonds : angle 4.12936 / 3.03 ( 3300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 253 time to evaluate : 0.679 Fit side-chains REVERT: A 249 ARG cc_start: 0.7832 (ttm110) cc_final: 0.7211 (ttp-110) REVERT: A 293 ARG cc_start: 0.8357 (mtt90) cc_final: 0.7300 (ptt180) REVERT: A 363 HIS cc_start: 0.7357 (m170) cc_final: 0.6913 (t-90) REVERT: A 555 ARG cc_start: 0.7569 (mtt90) cc_final: 0.7232 (mtt180) REVERT: B 110 MET cc_start: 0.8389 (mmp) cc_final: 0.8023 (mmt) REVERT: B 140 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6049 (mp0) REVERT: H 110 MET cc_start: 0.8395 (mmp) cc_final: 0.8029 (mmt) REVERT: H 140 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6064 (mp0) REVERT: G 249 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7208 (ttp-110) REVERT: G 293 ARG cc_start: 0.8363 (mtt90) cc_final: 0.7308 (ptt180) REVERT: G 363 HIS cc_start: 0.7338 (m170) cc_final: 0.6911 (t-90) REVERT: G 555 ARG cc_start: 0.7576 (mtt90) cc_final: 0.7288 (mtt180) REVERT: F 23 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.6945 (p0) REVERT: F 25 ASP cc_start: 0.7725 (m-30) cc_final: 0.7260 (m-30) REVERT: F 110 MET cc_start: 0.8386 (mmp) cc_final: 0.8025 (mmt) REVERT: F 140 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6065 (mp0) REVERT: E 249 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7205 (ttp-110) REVERT: E 293 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7294 (ptt180) REVERT: E 363 HIS cc_start: 0.7396 (m170) cc_final: 0.7082 (t70) REVERT: E 555 ARG cc_start: 0.7590 (mtt90) cc_final: 0.7311 (mtt180) REVERT: D 110 MET cc_start: 0.8392 (mmp) cc_final: 0.8023 (mmt) REVERT: D 140 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6069 (mp0) REVERT: C 249 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7199 (ttp-110) REVERT: C 293 ARG cc_start: 0.8337 (mtt90) cc_final: 0.7287 (ptt180) REVERT: C 363 HIS cc_start: 0.7337 (m170) cc_final: 0.6903 (t-90) outliers start: 53 outliers final: 14 residues processed: 281 average time/residue: 0.7580 time to fit residues: 229.9353 Evaluate side-chains 259 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 140 GLU Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain C residue 310 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.0370 chunk 8 optimal weight: 0.8980 chunk 154 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 188 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 152 optimal weight: 0.2980 chunk 116 optimal weight: 2.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 ASN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.186942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134118 restraints weight = 16110.801| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.76 r_work: 0.3311 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16280 Z= 0.112 Angle : 0.447 5.415 21960 Z= 0.242 Chirality : 0.037 0.120 2436 Planarity : 0.003 0.037 2748 Dihedral : 8.308 87.579 2344 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.91 % Allowed : 14.04 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.19), residues: 1940 helix: 1.49 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.52 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 38 TYR 0.008 0.001 TYR B 139 PHE 0.011 0.001 PHE E 332 TRP 0.010 0.001 TRP E 323 HIS 0.003 0.001 HIS A 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (16280) covalent geometry : angle 0.44659 / 0.24 (21960) hydrogen bonds : bond 0.04074 / 2.71 ( 1108) hydrogen bonds : angle 3.93769 / 2.89 ( 3300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 250 time to evaluate : 0.611 Fit side-chains REVERT: A 293 ARG cc_start: 0.8384 (mtt90) cc_final: 0.7351 (ptt180) REVERT: A 363 HIS cc_start: 0.7255 (m170) cc_final: 0.6978 (t70) REVERT: A 385 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7630 (mm-30) REVERT: A 555 ARG cc_start: 0.7602 (mtt90) cc_final: 0.7336 (mtt180) REVERT: G 159 MET cc_start: 0.6728 (mmp) cc_final: 0.5911 (mtp) REVERT: G 293 ARG cc_start: 0.8386 (mtt90) cc_final: 0.7349 (ptt180) REVERT: G 363 HIS cc_start: 0.7241 (m170) cc_final: 0.6992 (t70) REVERT: G 385 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7628 (mm-30) REVERT: G 555 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7360 (mtt180) REVERT: F 73 MET cc_start: 0.7980 (mmm) cc_final: 0.7547 (mmp) REVERT: E 159 MET cc_start: 0.6778 (mmp) cc_final: 0.5953 (mtp) REVERT: E 293 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7389 (ptt180) REVERT: E 363 HIS cc_start: 0.7314 (m170) cc_final: 0.7084 (t70) REVERT: E 385 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7603 (mm-30) REVERT: E 555 ARG cc_start: 0.7663 (mtt90) cc_final: 0.7375 (mtt180) REVERT: C 159 MET cc_start: 0.6775 (mmp) cc_final: 0.5796 (mtp) REVERT: C 293 ARG cc_start: 0.8353 (mtt90) cc_final: 0.7388 (ptt180) REVERT: C 363 HIS cc_start: 0.7246 (m170) cc_final: 0.6995 (t70) REVERT: C 385 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7631 (mm-30) REVERT: C 555 ARG cc_start: 0.7613 (mtt90) cc_final: 0.7324 (mtt180) outliers start: 48 outliers final: 6 residues processed: 274 average time/residue: 0.7174 time to fit residues: 213.4662 Evaluate side-chains 253 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 243 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain G residue 385 GLU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 385 GLU Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 385 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 88 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 181 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 530 GLN ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 GLN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.185532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.131988 restraints weight = 15973.438| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.85 r_work: 0.3273 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16280 Z= 0.145 Angle : 0.482 6.653 21960 Z= 0.260 Chirality : 0.038 0.123 2436 Planarity : 0.003 0.036 2748 Dihedral : 8.262 86.157 2344 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.24 % Allowed : 16.65 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.19), residues: 1940 helix: 1.47 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.56 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.011 0.001 TYR H 139 PHE 0.013 0.001 PHE G 332 TRP 0.012 0.001 TRP C 305 HIS 0.003 0.001 HIS G 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (16280) covalent geometry : angle 0.48163 / 0.26 (21960) hydrogen bonds : bond 0.04354 / 2.89 ( 1108) hydrogen bonds : angle 3.97525 / 2.92 ( 3300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.604 Fit side-chains REVERT: A 159 MET cc_start: 0.6744 (mmp) cc_final: 0.5749 (mtp) REVERT: A 249 ARG cc_start: 0.7821 (ttm110) cc_final: 0.7594 (ttp-110) REVERT: A 293 ARG cc_start: 0.8360 (mtt90) cc_final: 0.7302 (ptt90) REVERT: A 363 HIS cc_start: 0.7299 (m170) cc_final: 0.6976 (t70) REVERT: A 555 ARG cc_start: 0.7575 (mtt90) cc_final: 0.7260 (mtt180) REVERT: B 37 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7580 (mtt) REVERT: B 73 MET cc_start: 0.7978 (mmm) cc_final: 0.7665 (mmp) REVERT: B 110 MET cc_start: 0.8380 (mmp) cc_final: 0.8025 (mmt) REVERT: H 73 MET cc_start: 0.7957 (mmm) cc_final: 0.7645 (mmp) REVERT: H 110 MET cc_start: 0.8383 (mmp) cc_final: 0.8024 (mmt) REVERT: G 159 MET cc_start: 0.6698 (mmp) cc_final: 0.5855 (mtp) REVERT: G 249 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7609 (ttp-110) REVERT: G 293 ARG cc_start: 0.8362 (mtt90) cc_final: 0.7307 (ptt90) REVERT: G 363 HIS cc_start: 0.7285 (m170) cc_final: 0.7011 (t70) REVERT: G 555 ARG cc_start: 0.7628 (mtt90) cc_final: 0.7339 (mtt180) REVERT: F 25 ASP cc_start: 0.7634 (m-30) cc_final: 0.7413 (m-30) REVERT: F 73 MET cc_start: 0.7960 (mmm) cc_final: 0.7485 (mmp) REVERT: F 77 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6724 (mtt) REVERT: F 110 MET cc_start: 0.8375 (mmp) cc_final: 0.8019 (mmt) REVERT: E 159 MET cc_start: 0.6685 (mmp) cc_final: 0.5838 (mtp) REVERT: E 249 ARG cc_start: 0.7817 (ttm110) cc_final: 0.7590 (ttp-110) REVERT: E 293 ARG cc_start: 0.8375 (mtt90) cc_final: 0.7360 (ptt90) REVERT: E 363 HIS cc_start: 0.7375 (m170) cc_final: 0.7045 (t70) REVERT: E 555 ARG cc_start: 0.7639 (mtt90) cc_final: 0.7348 (mtt180) REVERT: D 73 MET cc_start: 0.7971 (mmm) cc_final: 0.7655 (mmp) REVERT: D 110 MET cc_start: 0.8377 (mmp) cc_final: 0.7979 (mmt) REVERT: C 159 MET cc_start: 0.6778 (mmp) cc_final: 0.5919 (mtp) REVERT: C 249 ARG cc_start: 0.7824 (ttm110) cc_final: 0.7596 (ttp-110) REVERT: C 293 ARG cc_start: 0.8370 (mtt90) cc_final: 0.7357 (ptt90) REVERT: C 363 HIS cc_start: 0.7296 (m170) cc_final: 0.6999 (t70) REVERT: C 555 ARG cc_start: 0.7584 (mtt90) cc_final: 0.7293 (mtt180) outliers start: 37 outliers final: 4 residues processed: 250 average time/residue: 0.7811 time to fit residues: 210.8299 Evaluate side-chains 237 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 231 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain F residue 77 MET Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain C residue 310 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 0.3980 chunk 110 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 0.0770 chunk 158 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.186167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.133279 restraints weight = 15935.935| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.76 r_work: 0.3303 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16280 Z= 0.126 Angle : 0.461 5.739 21960 Z= 0.250 Chirality : 0.037 0.122 2436 Planarity : 0.003 0.036 2748 Dihedral : 8.107 84.847 2344 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.42 % Allowed : 16.89 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.19), residues: 1940 helix: 1.57 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.61 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.009 0.001 TYR F 139 PHE 0.013 0.001 PHE E 332 TRP 0.011 0.001 TRP E 305 HIS 0.002 0.001 HIS A 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (16280) covalent geometry : angle 0.46080 / 0.25 (21960) hydrogen bonds : bond 0.04155 / 2.76 ( 1108) hydrogen bonds : angle 3.90163 / 2.86 ( 3300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 0.635 Fit side-chains REVERT: A 159 MET cc_start: 0.6782 (mmp) cc_final: 0.5926 (mtp) REVERT: A 249 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7611 (ttp-110) REVERT: A 293 ARG cc_start: 0.8358 (mtt90) cc_final: 0.7338 (ptt180) REVERT: A 363 HIS cc_start: 0.7263 (m170) cc_final: 0.7001 (t70) REVERT: A 555 ARG cc_start: 0.7614 (mtt90) cc_final: 0.7319 (mtt180) REVERT: B 37 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7589 (mtt) REVERT: B 73 MET cc_start: 0.7972 (mmm) cc_final: 0.7570 (mmp) REVERT: B 110 MET cc_start: 0.8359 (mmp) cc_final: 0.8007 (mmt) REVERT: H 37 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7513 (mtt) REVERT: H 73 MET cc_start: 0.7943 (mmm) cc_final: 0.7552 (mmp) REVERT: G 159 MET cc_start: 0.6685 (mmp) cc_final: 0.5865 (mtp) REVERT: G 249 ARG cc_start: 0.7841 (ttm110) cc_final: 0.7620 (ttp-110) REVERT: G 293 ARG cc_start: 0.8365 (mtt90) cc_final: 0.7345 (ptt90) REVERT: G 363 HIS cc_start: 0.7234 (m170) cc_final: 0.7004 (t70) REVERT: G 555 ARG cc_start: 0.7646 (mtt90) cc_final: 0.7326 (mtt180) REVERT: F 37 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7483 (mtt) REVERT: F 73 MET cc_start: 0.7997 (mmm) cc_final: 0.7560 (mmp) REVERT: F 110 MET cc_start: 0.8360 (mmp) cc_final: 0.8005 (mmt) REVERT: E 159 MET cc_start: 0.6703 (mmp) cc_final: 0.5863 (mtp) REVERT: E 249 ARG cc_start: 0.7825 (ttm110) cc_final: 0.7605 (ttp-110) REVERT: E 293 ARG cc_start: 0.8399 (mtt90) cc_final: 0.7387 (ptt180) REVERT: E 363 HIS cc_start: 0.7417 (m170) cc_final: 0.7145 (t70) REVERT: D 37 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7519 (mtt) REVERT: D 73 MET cc_start: 0.7950 (mmm) cc_final: 0.7555 (mmp) REVERT: C 159 MET cc_start: 0.6831 (mmp) cc_final: 0.5954 (mtp) REVERT: C 249 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7603 (ttp-110) REVERT: C 293 ARG cc_start: 0.8377 (mtt90) cc_final: 0.7388 (ptt180) REVERT: C 363 HIS cc_start: 0.7236 (m170) cc_final: 0.7008 (t70) REVERT: C 555 ARG cc_start: 0.7633 (mtt90) cc_final: 0.7379 (mtt180) outliers start: 40 outliers final: 6 residues processed: 267 average time/residue: 0.7755 time to fit residues: 224.2955 Evaluate side-chains 248 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 238 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 GLN Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain C residue 310 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 68 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 530 GLN ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 GLN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.185234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.131903 restraints weight = 16031.697| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.79 r_work: 0.3288 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16280 Z= 0.152 Angle : 0.489 5.623 21960 Z= 0.263 Chirality : 0.039 0.133 2436 Planarity : 0.003 0.034 2748 Dihedral : 8.093 82.835 2344 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.88 % Allowed : 17.80 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.19), residues: 1940 helix: 1.51 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : 0.59 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.011 0.001 TYR F 139 PHE 0.014 0.001 PHE E 332 TRP 0.013 0.001 TRP A 305 HIS 0.003 0.001 HIS C 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (16280) covalent geometry : angle 0.48904 / 0.26 (21960) hydrogen bonds : bond 0.04392 / 2.91 ( 1108) hydrogen bonds : angle 3.95936 / 2.91 ( 3300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 247 time to evaluate : 0.570 Fit side-chains REVERT: A 159 MET cc_start: 0.6797 (mmp) cc_final: 0.5962 (mtp) REVERT: A 249 ARG cc_start: 0.7847 (ttm110) cc_final: 0.7622 (ttp-110) REVERT: A 293 ARG cc_start: 0.8374 (mtt90) cc_final: 0.7343 (ptt90) REVERT: A 363 HIS cc_start: 0.7291 (m170) cc_final: 0.7045 (t70) REVERT: A 555 ARG cc_start: 0.7628 (mtt90) cc_final: 0.7314 (mtt180) REVERT: B 73 MET cc_start: 0.8007 (mmm) cc_final: 0.7577 (mmp) REVERT: H 73 MET cc_start: 0.8000 (mmm) cc_final: 0.7581 (mmp) REVERT: G 159 MET cc_start: 0.6709 (mmp) cc_final: 0.5898 (mtp) REVERT: G 249 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7625 (ttp-110) REVERT: G 293 ARG cc_start: 0.8373 (mtt90) cc_final: 0.7339 (ptt90) REVERT: G 363 HIS cc_start: 0.7262 (m170) cc_final: 0.7042 (t70) REVERT: G 555 ARG cc_start: 0.7639 (mtt90) cc_final: 0.7341 (mtt180) REVERT: E 159 MET cc_start: 0.6702 (mmp) cc_final: 0.5892 (mtp) REVERT: E 249 ARG cc_start: 0.7843 (ttm110) cc_final: 0.7621 (ttp-110) REVERT: E 293 ARG cc_start: 0.8382 (mtt90) cc_final: 0.7394 (ptt90) REVERT: E 363 HIS cc_start: 0.7411 (m170) cc_final: 0.7170 (t70) REVERT: E 555 ARG cc_start: 0.7526 (mtt90) cc_final: 0.7319 (mtt180) REVERT: D 73 MET cc_start: 0.7992 (mmm) cc_final: 0.7562 (mmp) REVERT: D 110 MET cc_start: 0.8374 (mmp) cc_final: 0.7978 (mmt) REVERT: C 159 MET cc_start: 0.6799 (mmp) cc_final: 0.5987 (mtp) REVERT: C 249 ARG cc_start: 0.7836 (ttm110) cc_final: 0.7612 (ttp-110) REVERT: C 293 ARG cc_start: 0.8390 (mtt90) cc_final: 0.7388 (ptt90) REVERT: C 363 HIS cc_start: 0.7275 (m170) cc_final: 0.7056 (t70) REVERT: C 555 ARG cc_start: 0.7644 (mtt90) cc_final: 0.7343 (mtt180) outliers start: 31 outliers final: 6 residues processed: 261 average time/residue: 0.7744 time to fit residues: 218.8507 Evaluate side-chains 250 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 244 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain C residue 310 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 110 optimal weight: 0.0470 chunk 121 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 530 GLN ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 GLN ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.185762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132609 restraints weight = 15970.967| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.77 r_work: 0.3287 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16280 Z= 0.139 Angle : 0.489 6.553 21960 Z= 0.260 Chirality : 0.039 0.138 2436 Planarity : 0.003 0.035 2748 Dihedral : 7.971 80.933 2344 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.21 % Allowed : 18.46 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.19), residues: 1940 helix: 1.53 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.74 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 38 TYR 0.010 0.001 TYR H 139 PHE 0.014 0.001 PHE A 332 TRP 0.011 0.001 TRP A 305 HIS 0.002 0.001 HIS C 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (16280) covalent geometry : angle 0.48937 / 0.26 (21960) hydrogen bonds : bond 0.04267 / 2.83 ( 1108) hydrogen bonds : angle 3.92875 / 2.89 ( 3300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 244 time to evaluate : 0.483 Fit side-chains REVERT: A 159 MET cc_start: 0.6834 (mmp) cc_final: 0.5959 (mtp) REVERT: A 249 ARG cc_start: 0.7855 (ttm110) cc_final: 0.7633 (ttp-110) REVERT: A 293 ARG cc_start: 0.8369 (mtt90) cc_final: 0.7333 (ptt90) REVERT: A 363 HIS cc_start: 0.7297 (m170) cc_final: 0.7025 (t70) REVERT: A 555 ARG cc_start: 0.7622 (mtt90) cc_final: 0.7261 (mtt180) REVERT: B 37 MET cc_start: 0.7817 (mtt) cc_final: 0.7534 (mtt) REVERT: H 37 MET cc_start: 0.7808 (mtt) cc_final: 0.7516 (mtt) REVERT: H 73 MET cc_start: 0.7990 (mmm) cc_final: 0.7601 (mmp) REVERT: G 159 MET cc_start: 0.6662 (mmp) cc_final: 0.5876 (mtp) REVERT: G 249 ARG cc_start: 0.7863 (ttm110) cc_final: 0.7640 (ttp-110) REVERT: G 293 ARG cc_start: 0.8373 (mtt90) cc_final: 0.7331 (ptt90) REVERT: G 363 HIS cc_start: 0.7285 (m170) cc_final: 0.7031 (t70) REVERT: G 555 ARG cc_start: 0.7621 (mtt90) cc_final: 0.7321 (mtt180) REVERT: F 37 MET cc_start: 0.7803 (mtt) cc_final: 0.7503 (mtt) REVERT: E 159 MET cc_start: 0.6686 (mmp) cc_final: 0.5872 (mtp) REVERT: E 249 ARG cc_start: 0.7847 (ttm110) cc_final: 0.7628 (ttp-110) REVERT: E 293 ARG cc_start: 0.8373 (mtt90) cc_final: 0.7377 (ptt90) REVERT: E 363 HIS cc_start: 0.7398 (m170) cc_final: 0.7134 (t70) REVERT: D 37 MET cc_start: 0.7830 (mtt) cc_final: 0.7556 (mtt) REVERT: D 73 MET cc_start: 0.7998 (mmm) cc_final: 0.7601 (mmp) REVERT: C 159 MET cc_start: 0.6772 (mmp) cc_final: 0.5964 (mtp) REVERT: C 249 ARG cc_start: 0.7852 (ttm110) cc_final: 0.7629 (ttp-110) REVERT: C 293 ARG cc_start: 0.8388 (mtt90) cc_final: 0.7380 (ptt90) REVERT: C 363 HIS cc_start: 0.7276 (m170) cc_final: 0.7018 (t70) REVERT: C 366 ARG cc_start: 0.7873 (mmt180) cc_final: 0.7595 (mmp-170) REVERT: C 555 ARG cc_start: 0.7645 (mtt90) cc_final: 0.7331 (mtt180) outliers start: 20 outliers final: 6 residues processed: 256 average time/residue: 0.7540 time to fit residues: 208.8401 Evaluate side-chains 248 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 242 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain C residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 157 optimal weight: 0.6980 chunk 63 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 40 optimal weight: 0.0470 chunk 72 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 530 GLN ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.187303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.135183 restraints weight = 16071.969| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.88 r_work: 0.3294 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16280 Z= 0.113 Angle : 0.466 7.064 21960 Z= 0.247 Chirality : 0.037 0.155 2436 Planarity : 0.003 0.036 2748 Dihedral : 7.688 77.242 2344 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.09 % Allowed : 18.64 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.19), residues: 1940 helix: 1.64 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.84 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 38 TYR 0.008 0.001 TYR D 139 PHE 0.012 0.001 PHE A 332 TRP 0.010 0.001 TRP A 379 HIS 0.002 0.001 HIS C 509 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (16280) covalent geometry : angle 0.46569 / 0.25 (21960) hydrogen bonds : bond 0.03954 / 2.62 ( 1108) hydrogen bonds : angle 3.84084 / 2.82 ( 3300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 246 time to evaluate : 0.636 Fit side-chains REVERT: A 159 MET cc_start: 0.6848 (mmp) cc_final: 0.5959 (mtp) REVERT: A 293 ARG cc_start: 0.8361 (mtt90) cc_final: 0.7299 (ptt180) REVERT: A 363 HIS cc_start: 0.7237 (m170) cc_final: 0.6977 (t70) REVERT: A 555 ARG cc_start: 0.7629 (mtt90) cc_final: 0.7372 (mtt180) REVERT: B 37 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7466 (mtt) REVERT: B 73 MET cc_start: 0.7950 (mmm) cc_final: 0.7668 (mmp) REVERT: H 37 MET cc_start: 0.7762 (mtt) cc_final: 0.7463 (mtt) REVERT: H 73 MET cc_start: 0.7936 (mmm) cc_final: 0.7607 (mmp) REVERT: G 159 MET cc_start: 0.6704 (mmp) cc_final: 0.5861 (mtp) REVERT: G 293 ARG cc_start: 0.8359 (mtt90) cc_final: 0.7288 (ptt180) REVERT: G 363 HIS cc_start: 0.7194 (m170) cc_final: 0.6914 (t70) REVERT: G 555 ARG cc_start: 0.7611 (mtt90) cc_final: 0.7280 (mtt180) REVERT: F 37 MET cc_start: 0.7762 (mtt) cc_final: 0.7452 (mtt) REVERT: F 73 MET cc_start: 0.7985 (mmm) cc_final: 0.7691 (mmp) REVERT: F 85 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7935 (mm-30) REVERT: E 159 MET cc_start: 0.6679 (mmp) cc_final: 0.5849 (mtp) REVERT: E 293 ARG cc_start: 0.8358 (mtt90) cc_final: 0.7325 (ptt180) REVERT: E 363 HIS cc_start: 0.7336 (m170) cc_final: 0.7094 (t70) REVERT: D 37 MET cc_start: 0.7789 (mtt) cc_final: 0.7488 (mtt) REVERT: D 73 MET cc_start: 0.7955 (mmm) cc_final: 0.7614 (mmp) REVERT: D 85 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7903 (mm-30) REVERT: C 159 MET cc_start: 0.6794 (mmp) cc_final: 0.5915 (mtp) REVERT: C 293 ARG cc_start: 0.8367 (mtt90) cc_final: 0.7325 (ptt180) REVERT: C 363 HIS cc_start: 0.7197 (m170) cc_final: 0.6906 (t70) REVERT: C 366 ARG cc_start: 0.7863 (mmt180) cc_final: 0.7566 (mmp-170) REVERT: C 555 ARG cc_start: 0.7625 (mtt90) cc_final: 0.7300 (mtt180) outliers start: 18 outliers final: 4 residues processed: 254 average time/residue: 0.7775 time to fit residues: 213.5893 Evaluate side-chains 241 residues out of total 1684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 234 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain G residue 310 VAL Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain C residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 54 ASN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.184140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.133144 restraints weight = 15907.364| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.69 r_work: 0.3267 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16280 Z= 0.186 Angle : 0.542 6.934 21960 Z= 0.288 Chirality : 0.041 0.141 2436 Planarity : 0.003 0.034 2748 Dihedral : 7.821 74.649 2344 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.09 % Allowed : 18.83 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 1940 helix: 1.42 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : 0.77 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 38 TYR 0.012 0.002 TYR H 139 PHE 0.014 0.002 PHE A 332 TRP 0.015 0.002 TRP C 305 HIS 0.004 0.001 HIS G 126 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (16280) covalent geometry : angle 0.54209 / 0.29 (21960) hydrogen bonds : bond 0.04629 / 3.06 ( 1108) hydrogen bonds : angle 4.02816 / 2.96 ( 3300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7943.97 seconds wall clock time: 135 minutes 35.27 seconds (8135.27 seconds total)