Starting phenix.real_space_refine on Mon Sep 14 07:41:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jm7_22389/09_2026/7jm7_22389_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jm7_22389/09_2026/7jm7_22389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jm7_22389/09_2026/7jm7_22389_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jm7_22389/09_2026/7jm7_22389_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jm7_22389/09_2026/7jm7_22389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jm7_22389/09_2026/7jm7_22389.map" } resolution = 2.82 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= 1.144 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: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 90 5.16 5 Cl 6 4.86 5 C 9322 2.51 5 N 2376 2.21 5 O 2736 1.98 5 H 14054 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28596 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3352 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 10675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 10675 Classifications: {'peptide': 683} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 654} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3352 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 2, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 10675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 10675 Classifications: {'peptide': 683} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 654} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {' CL': 3, ' MG': 1, '0J1': 1, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {' CL': 3, ' MG': 1, '0J1': 1, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 5.16, per 1000 atoms: 0.18 Number of scatterers: 28596 At special positions: 0 Unit cell: (119.877, 84.4106, 136.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 6 17.00 S 90 16.00 P 10 15.00 Mg 2 11.99 O 2736 8.00 N 2376 7.00 C 9322 6.00 H 14054 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 174 " - pdb=" SG CYS D 255 " distance=2.03 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 224 " distance=2.03 Simple disulfide: pdb=" SG CYS D 221 " - pdb=" SG CYS D 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 454 " distance=2.03 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 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG B 502 " - " ASN B 128 " " NAG D 502 " - " ASN D 128 " " NAG F 1 " - " ASN B 184 " " NAG I 1 " - " ASN D 184 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 768.9 milliseconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 69.9% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'B' and resid 81 through 105 removed outlier: 3.971A pdb=" N GLU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 131 Proline residue: B 117 - end of helix Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 169 through 174 removed outlier: 5.766A pdb=" N ALA B 172 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 205 removed outlier: 4.530A pdb=" N GLN B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 247 removed outlier: 5.707A pdb=" N GLU B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ALA B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 271 Processing helix chain 'B' and resid 281 through 310 Proline residue: B 296 - end of helix Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 121 through 170 removed outlier: 4.690A pdb=" N GLU A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 198 Processing helix chain 'A' and resid 199 through 202 Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 223 through 240 Processing helix chain 'A' and resid 247 through 262 removed outlier: 4.188A pdb=" N ILE A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 302 Processing helix chain 'A' and resid 303 through 316 Processing helix chain 'A' and resid 320 through 347 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 374 through 406 removed outlier: 3.551A pdb=" N PHE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 435 Processing helix chain 'A' and resid 461 through 467 Processing helix chain 'A' and resid 469 through 479 Processing helix chain 'A' and resid 486 through 505 Processing helix chain 'A' and resid 513 through 536 removed outlier: 3.531A pdb=" N SER A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.553A pdb=" N TYR A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 Processing helix chain 'A' and resid 579 through 598 removed outlier: 3.729A pdb=" N PHE A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 609 Processing helix chain 'A' and resid 619 through 624 removed outlier: 4.030A pdb=" N HIS A 623 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 removed outlier: 3.706A pdb=" N VAL A 630 " --> pdb=" O THR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 681 through 690 Processing helix chain 'A' and resid 707 through 714 removed outlier: 3.832A pdb=" N PHE A 711 " --> pdb=" O ARG A 707 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 714 " --> pdb=" O ASP A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 732 removed outlier: 3.690A pdb=" N GLU A 732 " --> pdb=" O GLN A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 765 Processing helix chain 'A' and resid 783 through 789 removed outlier: 3.506A pdb=" N LEU A 787 " --> pdb=" O THR A 783 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 789 " --> pdb=" O LYS A 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 105 removed outlier: 3.971A pdb=" N GLU D 86 " --> pdb=" O PRO D 82 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 131 Proline residue: D 117 - end of helix Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 153 through 168 Processing helix chain 'D' and resid 169 through 174 removed outlier: 5.767A pdb=" N ALA D 172 " --> pdb=" O ALA D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 205 removed outlier: 4.530A pdb=" N GLN D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 247 removed outlier: 5.706A pdb=" N GLU D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ALA D 227 " --> pdb=" O ASN D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 271 Processing helix chain 'D' and resid 281 through 310 Proline residue: D 296 - end of helix Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 121 through 170 removed outlier: 4.691A pdb=" N GLU C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 198 Processing helix chain 'C' and resid 199 through 202 Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 223 through 240 Processing helix chain 'C' and resid 247 through 262 removed outlier: 4.189A pdb=" N ILE C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 302 Processing helix chain 'C' and resid 303 through 316 Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 374 through 406 removed outlier: 3.552A pdb=" N PHE C 402 " --> pdb=" O TRP C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 435 Processing helix chain 'C' and resid 461 through 467 Processing helix chain 'C' and resid 469 through 479 Processing helix chain 'C' and resid 486 through 505 Processing helix chain 'C' and resid 513 through 536 removed outlier: 3.531A pdb=" N SER C 517 " --> pdb=" O VAL C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 560 removed outlier: 3.553A pdb=" N TYR C 547 " --> pdb=" O ASP C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 575 Processing helix chain 'C' and resid 579 through 598 removed outlier: 3.730A pdb=" N PHE C 597 " --> pdb=" O VAL C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 609 Processing helix chain 'C' and resid 619 through 624 removed outlier: 4.030A pdb=" N HIS C 623 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 631 removed outlier: 3.707A pdb=" N VAL C 630 " --> pdb=" O THR C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 653 Processing helix chain 'C' and resid 681 through 690 Processing helix chain 'C' and resid 707 through 714 removed outlier: 3.833A pdb=" N PHE C 711 " --> pdb=" O ARG C 707 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C 714 " --> pdb=" O ASP C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 732 removed outlier: 3.690A pdb=" N GLU C 732 " --> pdb=" O GLN C 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 765 Processing helix chain 'C' and resid 783 through 789 removed outlier: 3.506A pdb=" N LEU C 787 " --> pdb=" O THR C 783 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C 789 " --> pdb=" O LYS C 785 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 96 removed outlier: 4.016A pdb=" N GLU A 95 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 266 Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 440 Processing sheet with id=AA4, first strand: chain 'A' and resid 638 through 639 removed outlier: 6.223A pdb=" N LEU A 638 " --> pdb=" O VAL A 664 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY A 677 " --> pdb=" O VAL A 663 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 641 through 643 removed outlier: 3.936A pdb=" N GLU A 642 " --> pdb=" O MET A 735 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 747 through 749 Processing sheet with id=AA7, first strand: chain 'C' and resid 95 through 96 removed outlier: 4.016A pdb=" N GLU C 95 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 265 through 266 Processing sheet with id=AA9, first strand: chain 'C' and resid 438 through 440 Processing sheet with id=AB1, first strand: chain 'C' and resid 638 through 639 removed outlier: 6.223A pdb=" N LEU C 638 " --> pdb=" O VAL C 664 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY C 677 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 641 through 643 removed outlier: 3.936A pdb=" N GLU C 642 " --> pdb=" O MET C 735 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 747 through 749 938 hydrogen bonds defined for protein. 2772 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: 6.26 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14034 1.03 - 1.23: 33 1.23 - 1.42: 6099 1.42 - 1.62: 8556 1.62 - 1.82: 142 Bond restraints: 28864 Sorted by residual: bond pdb=" C4 ATP C 901 " pdb=" C5 ATP C 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 6.00e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.79e+01 bond pdb=" C5 ATP C 901 " pdb=" C6 ATP C 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.69e+01 bond pdb=" C5 MAN E 4 " pdb=" O5 MAN E 4 " ideal model delta sigma weight residual 1.418 1.518 -0.100 2.00e-02 2.50e+03 2.49e+01 ... (remaining 28859 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.16: 51852 9.16 - 18.33: 26 18.33 - 27.49: 45 27.49 - 36.66: 21 36.66 - 45.82: 4 Bond angle restraints: 51948 Sorted by residual: angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 121.31 18.56 1.00e+00 1.00e+00 3.45e+02 angle pdb=" PB ATP C 901 " pdb=" O3B ATP C 901 " pdb=" PG ATP C 901 " ideal model delta sigma weight residual 139.87 121.37 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" PA ATP C 901 " pdb=" O3A ATP C 901 " pdb=" PB ATP C 901 " ideal model delta sigma weight residual 136.83 119.92 16.91 1.00e+00 1.00e+00 2.86e+02 angle pdb=" PA ATP A 901 " pdb=" O3A ATP A 901 " pdb=" PB ATP A 901 " ideal model delta sigma weight residual 136.83 119.93 16.90 1.00e+00 1.00e+00 2.86e+02 angle pdb="HD21 ASN D 128 " pdb=" ND2 ASN D 128 " pdb="HD22 ASN D 128 " ideal model delta sigma weight residual 120.00 74.18 45.82 3.00e+00 1.11e-01 2.33e+02 ... (remaining 51943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 13061 21.16 - 42.32: 753 42.32 - 63.48: 278 63.48 - 84.64: 34 84.64 - 105.80: 14 Dihedral angle restraints: 14140 sinusoidal: 7902 harmonic: 6238 Sorted by residual: dihedral pdb=" CB CYS D 112 " pdb=" SG CYS D 112 " pdb=" SG CYS D 171 " pdb=" CB CYS D 171 " ideal model delta sinusoidal sigma weight residual 93.00 174.76 -81.76 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS B 112 " pdb=" SG CYS B 112 " pdb=" SG CYS B 171 " pdb=" CB CYS B 171 " ideal model delta sinusoidal sigma weight residual 93.00 174.72 -81.72 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS D 174 " pdb=" SG CYS D 174 " pdb=" SG CYS D 255 " pdb=" CB CYS D 255 " ideal model delta sinusoidal sigma weight residual 93.00 172.23 -79.23 1 1.00e+01 1.00e-02 7.81e+01 ... (remaining 14137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.344: 2394 0.344 - 0.688: 6 0.688 - 1.032: 0 1.032 - 1.376: 2 1.376 - 1.719: 10 Chirality restraints: 2412 Sorted by residual: chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-02 2.50e+03 7.30e+02 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-02 2.50e+03 7.27e+02 chirality pdb=" C1 MAN E 5 " pdb=" O6 BMA E 3 " pdb=" C2 MAN E 5 " pdb=" O5 MAN E 5 " both_signs ideal model delta sigma weight residual False 2.40 2.86 -0.46 2.00e-02 2.50e+03 5.28e+02 ... (remaining 2409 not shown) Planarity restraints: 4190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 271 " -0.229 9.50e-02 1.11e+02 9.07e-02 5.94e+01 pdb=" NE ARG D 271 " 0.068 2.00e-02 2.50e+03 pdb=" CZ ARG D 271 " -0.110 2.00e-02 2.50e+03 pdb=" NH1 ARG D 271 " -0.038 2.00e-02 2.50e+03 pdb=" NH2 ARG D 271 " 0.014 2.00e-02 2.50e+03 pdb="HH11 ARG D 271 " 0.016 2.00e-02 2.50e+03 pdb="HH12 ARG D 271 " 0.052 2.00e-02 2.50e+03 pdb="HH21 ARG D 271 " 0.011 2.00e-02 2.50e+03 pdb="HH22 ARG D 271 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 271 " -0.205 9.50e-02 1.11e+02 8.11e-02 4.79e+01 pdb=" NE ARG B 271 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG B 271 " -0.090 2.00e-02 2.50e+03 pdb=" NH1 ARG B 271 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 271 " 0.015 2.00e-02 2.50e+03 pdb="HH11 ARG B 271 " -0.021 2.00e-02 2.50e+03 pdb="HH12 ARG B 271 " 0.021 2.00e-02 2.50e+03 pdb="HH21 ARG B 271 " -0.034 2.00e-02 2.50e+03 pdb="HH22 ARG B 271 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 191 " -0.010 2.00e-02 2.50e+03 2.01e-02 6.07e+00 pdb=" CG ASN B 191 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN B 191 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 191 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 191 " -0.012 2.00e-02 2.50e+03 pdb="HD22 ASN B 191 " -0.002 2.00e-02 2.50e+03 ... (remaining 4187 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1554 2.20 - 2.80: 58216 2.80 - 3.40: 79314 3.40 - 4.00: 102916 4.00 - 4.60: 162102 Nonbonded interactions: 404102 Sorted by model distance: nonbonded pdb=" O MET A 368 " pdb=" HH TYR A 579 " model vdw 1.601 2.450 nonbonded pdb=" O MET C 368 " pdb=" HH TYR C 579 " model vdw 1.602 2.450 nonbonded pdb="HH21 ARG C 640 " pdb=" OG SER C 738 " model vdw 1.626 2.450 nonbonded pdb="HH21 ARG A 640 " pdb=" OG SER A 738 " model vdw 1.627 2.450 nonbonded pdb=" OD1 ASN C 104 " pdb=" H PHE C 107 " model vdw 1.655 2.450 ... (remaining 404097 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' } 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: 3.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.360 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 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 0.100 14838 Z= 0.292 Angle : 1.150 44.613 20196 Z= 0.542 Chirality : 0.122 1.719 2412 Planarity : 0.005 0.121 2474 Dihedral : 15.613 105.803 5832 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.17 % Allowed : 0.39 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.63 (0.20), residues: 1774 helix: 2.14 (0.15), residues: 1138 sheet: None (None), residues: 0 loop : -0.92 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.094 0.002 ARG D 271 TYR 0.010 0.001 TYR D 188 PHE 0.017 0.001 PHE A 273 TRP 0.012 0.001 TRP C 524 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.29 (14810) covalent geometry : angle 0.86390 / 0.48 (20124) SS BOND : bond 0.00164 / 0.12 ( 12) SS BOND : angle 0.95306 / 0.63 ( 24) hydrogen bonds : bond 0.13031 / 8.70 ( 938) hydrogen bonds : angle 6.12460 / 4.51 ( 2772) link_ALPHA1-3 : bond 0.00740 / 0.37 ( 2) link_ALPHA1-3 : angle 25.85031 / 12.34 ( 6) link_ALPHA1-6 : bond 0.00815 / 0.41 ( 2) link_ALPHA1-6 : angle 29.78635 / 14.37 ( 6) link_BETA1-4 : bond 0.01119 / 0.82 ( 8) link_BETA1-4 : angle 8.78533 / 5.60 ( 24) link_NAG-ASN : bond 0.00257 / 0.13 ( 4) link_NAG-ASN : angle 6.32307 / 3.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 248 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 CYS cc_start: 0.5892 (t) cc_final: 0.5623 (t) REVERT: A 373 HIS cc_start: 0.6697 (m-70) cc_final: 0.6454 (m-70) REVERT: A 595 ASP cc_start: 0.7792 (m-30) cc_final: 0.7541 (m-30) REVERT: A 739 GLU cc_start: 0.7155 (pm20) cc_final: 0.6693 (pm20) REVERT: C 98 ASP cc_start: 0.7878 (m-30) cc_final: 0.7463 (m-30) REVERT: C 373 HIS cc_start: 0.6796 (m-70) cc_final: 0.6594 (m-70) REVERT: C 595 ASP cc_start: 0.7949 (m-30) cc_final: 0.7648 (m-30) REVERT: C 739 GLU cc_start: 0.7214 (pm20) cc_final: 0.6967 (pm20) REVERT: C 773 ASP cc_start: 0.6410 (t0) cc_final: 0.6205 (t0) outliers start: 18 outliers final: 2 residues processed: 256 average time/residue: 0.9221 time to fit residues: 270.2777 Evaluate side-chains 209 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain D residue 184 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN D 93 ASN D 191 ASN C 101 ASN 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 = 0.185530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.157300 restraints weight = 41115.037| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.98 r_work: 0.3739 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14838 Z= 0.176 Angle : 0.718 14.188 20196 Z= 0.347 Chirality : 0.121 1.736 2412 Planarity : 0.005 0.051 2474 Dihedral : 13.092 85.382 2666 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.91 % Allowed : 7.63 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 2.00 (0.20), residues: 1774 helix: 2.45 (0.15), residues: 1160 sheet: None (None), residues: 0 loop : -0.95 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 110 TYR 0.013 0.001 TYR A 505 PHE 0.021 0.002 PHE A 392 TRP 0.011 0.001 TRP C 524 HIS 0.005 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (14810) covalent geometry : angle 0.69127 / 0.34 (20124) SS BOND : bond 0.00229 / 0.13 ( 12) SS BOND : angle 1.49701 / 2.06 ( 24) hydrogen bonds : bond 0.05450 / 3.71 ( 938) hydrogen bonds : angle 4.54304 / 3.32 ( 2772) link_ALPHA1-3 : bond 0.00986 / 0.50 ( 2) link_ALPHA1-3 : angle 5.22782 / 2.33 ( 6) link_ALPHA1-6 : bond 0.00982 / 0.49 ( 2) link_ALPHA1-6 : angle 1.73493 / 0.74 ( 6) link_BETA1-4 : bond 0.00338 / 0.17 ( 8) link_BETA1-4 : angle 2.37285 / 1.76 ( 24) link_NAG-ASN : bond 0.00534 / 0.26 ( 4) link_NAG-ASN : angle 6.04591 / 2.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 HIS cc_start: 0.7212 (m-70) cc_final: 0.6852 (m-70) REVERT: A 379 ILE cc_start: 0.8018 (mt) cc_final: 0.7792 (mm) REVERT: A 607 GLN cc_start: 0.7714 (mt0) cc_final: 0.7367 (mt0) REVERT: A 628 ARG cc_start: 0.7249 (ttp-110) cc_final: 0.6985 (ttp-170) REVERT: A 678 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8617 (tt) REVERT: A 739 GLU cc_start: 0.7621 (pm20) cc_final: 0.7089 (pm20) REVERT: A 751 GLU cc_start: 0.7689 (mm-30) cc_final: 0.6804 (mp0) REVERT: C 373 HIS cc_start: 0.7333 (m-70) cc_final: 0.7018 (m-70) REVERT: C 607 GLN cc_start: 0.7824 (mt0) cc_final: 0.7484 (mt0) REVERT: C 739 GLU cc_start: 0.7551 (pm20) cc_final: 0.7203 (pm20) outliers start: 14 outliers final: 8 residues processed: 220 average time/residue: 1.0454 time to fit residues: 260.3416 Evaluate side-chains 218 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 209 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 776 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 23 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.176200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147921 restraints weight = 41836.430| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.93 r_work: 0.3648 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14838 Z= 0.230 Angle : 0.727 14.401 20196 Z= 0.359 Chirality : 0.122 1.738 2412 Planarity : 0.005 0.044 2474 Dihedral : 11.905 87.917 2662 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.04 % Allowed : 8.47 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.56 (0.19), residues: 1774 helix: 2.14 (0.14), residues: 1160 sheet: None (None), residues: 0 loop : -1.21 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 110 TYR 0.015 0.002 TYR C 505 PHE 0.017 0.002 PHE A 392 TRP 0.011 0.002 TRP C 524 HIS 0.005 0.001 HIS C 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 (14810) covalent geometry : angle 0.70416 / 0.35 (20124) SS BOND : bond 0.00624 / 0.25 ( 12) SS BOND : angle 1.52098 / 2.16 ( 24) hydrogen bonds : bond 0.05855 / 4.00 ( 938) hydrogen bonds : angle 4.44871 / 3.25 ( 2772) link_ALPHA1-3 : bond 0.00988 / 0.50 ( 2) link_ALPHA1-3 : angle 3.67663 / 1.66 ( 6) link_ALPHA1-6 : bond 0.00369 / 0.18 ( 2) link_ALPHA1-6 : angle 1.43434 / 0.62 ( 6) link_BETA1-4 : bond 0.00420 / 0.24 ( 8) link_BETA1-4 : angle 2.49041 / 2.06 ( 24) link_NAG-ASN : bond 0.00463 / 0.24 ( 4) link_NAG-ASN : angle 5.77366 / 2.92 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ASP cc_start: 0.7049 (p0) cc_final: 0.6789 (p0) REVERT: B 231 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8650 (mt) REVERT: A 95 GLU cc_start: 0.8141 (tp30) cc_final: 0.7891 (tp30) REVERT: A 373 HIS cc_start: 0.7358 (m-70) cc_final: 0.7040 (m-70) REVERT: A 607 GLN cc_start: 0.7748 (mt0) cc_final: 0.7494 (mt0) REVERT: A 678 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8655 (tt) REVERT: A 739 GLU cc_start: 0.7955 (pm20) cc_final: 0.7424 (pm20) REVERT: A 751 GLU cc_start: 0.7710 (mm-30) cc_final: 0.6844 (mp0) REVERT: D 148 MET cc_start: 0.7390 (ptt) cc_final: 0.7177 (ptt) REVERT: D 262 MET cc_start: 0.8238 (tpt) cc_final: 0.7593 (tpt) REVERT: C 177 LEU cc_start: 0.7748 (mp) cc_final: 0.7541 (mm) REVERT: C 373 HIS cc_start: 0.7336 (m-70) cc_final: 0.7004 (m-70) REVERT: C 595 ASP cc_start: 0.8224 (m-30) cc_final: 0.7794 (m-30) REVERT: C 607 GLN cc_start: 0.7786 (mt0) cc_final: 0.7541 (mt0) REVERT: C 739 GLU cc_start: 0.7871 (pm20) cc_final: 0.7445 (pm20) outliers start: 16 outliers final: 9 residues processed: 242 average time/residue: 1.0778 time to fit residues: 294.1005 Evaluate side-chains 228 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 217 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 776 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 113 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.175904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147766 restraints weight = 41658.770| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.92 r_work: 0.3643 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 0.050 14838 Z= 0.184 Angle : 0.688 14.660 20196 Z= 0.337 Chirality : 0.121 1.728 2412 Planarity : 0.005 0.044 2474 Dihedral : 10.866 86.749 2662 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.37 % Allowed : 9.78 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.62 (0.20), residues: 1774 helix: 2.23 (0.14), residues: 1160 sheet: None (None), residues: 0 loop : -1.29 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 107 TYR 0.013 0.002 TYR A 505 PHE 0.017 0.001 PHE A 392 TRP 0.011 0.001 TRP A 524 HIS 0.005 0.001 HIS C 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (14810) covalent geometry : angle 0.66559 / 0.33 (20124) SS BOND : bond 0.00234 / 0.16 ( 12) SS BOND : angle 1.43704 / 1.56 ( 24) hydrogen bonds : bond 0.05335 / 3.67 ( 938) hydrogen bonds : angle 4.29162 / 3.14 ( 2772) link_ALPHA1-3 : bond 0.00860 / 0.43 ( 2) link_ALPHA1-3 : angle 3.10850 / 1.37 ( 6) link_ALPHA1-6 : bond 0.00330 / 0.16 ( 2) link_ALPHA1-6 : angle 2.14896 / 0.94 ( 6) link_BETA1-4 : bond 0.00257 / 0.19 ( 8) link_BETA1-4 : angle 2.10434 / 1.73 ( 24) link_NAG-ASN : bond 0.00355 / 0.18 ( 4) link_NAG-ASN : angle 5.84116 / 2.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 168 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7490 (tm-30) REVERT: A 373 HIS cc_start: 0.7361 (m-70) cc_final: 0.7048 (m-70) REVERT: A 607 GLN cc_start: 0.7796 (mt0) cc_final: 0.7370 (mt0) REVERT: A 678 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8640 (tt) REVERT: A 739 GLU cc_start: 0.7916 (pm20) cc_final: 0.7460 (pm20) REVERT: A 751 GLU cc_start: 0.7725 (mm-30) cc_final: 0.6847 (mp0) REVERT: D 148 MET cc_start: 0.7501 (ptt) cc_final: 0.7277 (ptt) REVERT: C 238 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8053 (t) REVERT: C 373 HIS cc_start: 0.7271 (m-70) cc_final: 0.6916 (m-70) REVERT: C 607 GLN cc_start: 0.7764 (mt0) cc_final: 0.7341 (mt0) REVERT: C 739 GLU cc_start: 0.7841 (pm20) cc_final: 0.7516 (pm20) outliers start: 21 outliers final: 14 residues processed: 230 average time/residue: 1.1197 time to fit residues: 287.8769 Evaluate side-chains 226 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 776 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 84 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.178912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.151275 restraints weight = 41851.492| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 1.92 r_work: 0.3646 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14838 Z= 0.163 Angle : 0.666 14.820 20196 Z= 0.325 Chirality : 0.121 1.739 2412 Planarity : 0.004 0.043 2474 Dihedral : 10.505 89.331 2662 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.69 % Allowed : 10.89 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.81 (0.20), residues: 1774 helix: 2.38 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.26 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 405 TYR 0.012 0.001 TYR A 505 PHE 0.014 0.001 PHE A 392 TRP 0.011 0.001 TRP A 524 HIS 0.005 0.001 HIS C 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (14810) covalent geometry : angle 0.64280 / 0.32 (20124) SS BOND : bond 0.00215 / 0.16 ( 12) SS BOND : angle 1.56935 / 1.38 ( 24) hydrogen bonds : bond 0.05108 / 3.50 ( 938) hydrogen bonds : angle 4.19996 / 3.07 ( 2772) link_ALPHA1-3 : bond 0.00608 / 0.30 ( 2) link_ALPHA1-3 : angle 2.99196 / 1.31 ( 6) link_ALPHA1-6 : bond 0.00312 / 0.15 ( 2) link_ALPHA1-6 : angle 1.60781 / 0.67 ( 6) link_BETA1-4 : bond 0.00318 / 0.19 ( 8) link_BETA1-4 : angle 2.00798 / 1.69 ( 24) link_NAG-ASN : bond 0.00345 / 0.17 ( 4) link_NAG-ASN : angle 5.89676 / 2.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 251 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8068 (t) REVERT: A 373 HIS cc_start: 0.7339 (m-70) cc_final: 0.7038 (m-70) REVERT: A 405 ARG cc_start: 0.8062 (ptp-170) cc_final: 0.7620 (ptp-170) REVERT: A 607 GLN cc_start: 0.7799 (mt0) cc_final: 0.7449 (mt0) REVERT: A 678 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8645 (tt) REVERT: A 739 GLU cc_start: 0.7919 (pm20) cc_final: 0.7490 (pm20) REVERT: A 751 GLU cc_start: 0.7708 (mm-30) cc_final: 0.6837 (mp0) REVERT: D 192 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8476 (mp) REVERT: C 98 ASP cc_start: 0.8235 (m-30) cc_final: 0.7772 (m-30) REVERT: C 222 VAL cc_start: 0.8422 (m) cc_final: 0.8101 (t) REVERT: C 373 HIS cc_start: 0.7336 (m-70) cc_final: 0.6999 (m-70) REVERT: C 607 GLN cc_start: 0.7740 (mt0) cc_final: 0.7403 (mt0) REVERT: C 707 ARG cc_start: 0.6643 (mtt180) cc_final: 0.6320 (mtm-85) REVERT: C 739 GLU cc_start: 0.7847 (pm20) cc_final: 0.7541 (pm20) outliers start: 26 outliers final: 18 residues processed: 240 average time/residue: 1.1201 time to fit residues: 302.0426 Evaluate side-chains 238 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 777 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 0.4980 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 ASN B 163 ASN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN C 396 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.176064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148218 restraints weight = 41746.066| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.92 r_work: 0.3651 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14838 Z= 0.145 Angle : 0.652 14.831 20196 Z= 0.317 Chirality : 0.120 1.734 2412 Planarity : 0.004 0.041 2474 Dihedral : 10.196 87.690 2662 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.50 % Allowed : 11.41 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.95 (0.20), residues: 1774 helix: 2.50 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.23 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 405 TYR 0.011 0.001 TYR A 505 PHE 0.014 0.001 PHE A 392 TRP 0.012 0.001 TRP C 524 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (14810) covalent geometry : angle 0.62971 / 0.31 (20124) SS BOND : bond 0.00198 / 0.14 ( 12) SS BOND : angle 1.25554 / 1.24 ( 24) hydrogen bonds : bond 0.04872 / 3.34 ( 938) hydrogen bonds : angle 4.11962 / 3.01 ( 2772) link_ALPHA1-3 : bond 0.00447 / 0.22 ( 2) link_ALPHA1-3 : angle 2.78306 / 1.20 ( 6) link_ALPHA1-6 : bond 0.00298 / 0.15 ( 2) link_ALPHA1-6 : angle 1.63043 / 0.71 ( 6) link_BETA1-4 : bond 0.00221 / 0.11 ( 8) link_BETA1-4 : angle 1.97539 / 1.62 ( 24) link_NAG-ASN : bond 0.00330 / 0.16 ( 4) link_NAG-ASN : angle 5.91500 / 2.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 HIS cc_start: 0.7334 (m-70) cc_final: 0.7033 (m-70) REVERT: A 405 ARG cc_start: 0.8070 (ptp-170) cc_final: 0.7653 (ptp-170) REVERT: A 607 GLN cc_start: 0.7758 (mt0) cc_final: 0.7444 (mt0) REVERT: A 678 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8626 (tt) REVERT: A 739 GLU cc_start: 0.7881 (pm20) cc_final: 0.7402 (pm20) REVERT: A 751 GLU cc_start: 0.7711 (mm-30) cc_final: 0.6830 (mp0) REVERT: C 222 VAL cc_start: 0.8417 (m) cc_final: 0.8122 (t) REVERT: C 373 HIS cc_start: 0.7316 (m-70) cc_final: 0.6971 (m-70) REVERT: C 607 GLN cc_start: 0.7716 (mt0) cc_final: 0.7353 (mt0) REVERT: C 707 ARG cc_start: 0.6617 (mtt180) cc_final: 0.6334 (mtm-85) REVERT: C 739 GLU cc_start: 0.7860 (pm20) cc_final: 0.7521 (pm20) outliers start: 23 outliers final: 16 residues processed: 233 average time/residue: 1.1619 time to fit residues: 302.1364 Evaluate side-chains 231 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 776 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 158 optimal weight: 0.4980 chunk 137 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 173 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 19 optimal weight: 0.2980 chunk 169 optimal weight: 0.0970 chunk 83 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 396 ASN D 163 ASN C 359 ASN C 750 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.181138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.153581 restraints weight = 41747.367| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.93 r_work: 0.3669 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14838 Z= 0.116 Angle : 0.628 14.879 20196 Z= 0.303 Chirality : 0.120 1.729 2412 Planarity : 0.004 0.040 2474 Dihedral : 9.703 82.783 2662 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.63 % Allowed : 11.67 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 2.22 (0.20), residues: 1774 helix: 2.72 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.15 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.010 0.001 TYR A 505 PHE 0.011 0.001 PHE B 193 TRP 0.012 0.001 TRP C 524 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (14810) covalent geometry : angle 0.60498 / 0.30 (20124) SS BOND : bond 0.00181 / 0.12 ( 12) SS BOND : angle 1.13333 / 1.07 ( 24) hydrogen bonds : bond 0.04452 / 3.05 ( 938) hydrogen bonds : angle 4.00618 / 2.92 ( 2772) link_ALPHA1-3 : bond 0.00312 / 0.16 ( 2) link_ALPHA1-3 : angle 2.60446 / 1.11 ( 6) link_ALPHA1-6 : bond 0.00372 / 0.19 ( 2) link_ALPHA1-6 : angle 1.53701 / 0.67 ( 6) link_BETA1-4 : bond 0.00234 / 0.11 ( 8) link_BETA1-4 : angle 1.87150 / 1.50 ( 24) link_NAG-ASN : bond 0.00319 / 0.16 ( 4) link_NAG-ASN : angle 5.99791 / 2.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 HIS cc_start: 0.7230 (m-70) cc_final: 0.6940 (m-70) REVERT: A 405 ARG cc_start: 0.8047 (ptp-170) cc_final: 0.7723 (ptp-170) REVERT: A 607 GLN cc_start: 0.7739 (mt0) cc_final: 0.7363 (mt0) REVERT: A 678 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8577 (tt) REVERT: A 739 GLU cc_start: 0.7840 (pm20) cc_final: 0.7440 (pm20) REVERT: A 751 GLU cc_start: 0.7696 (mm-30) cc_final: 0.6839 (mp0) REVERT: C 222 VAL cc_start: 0.8273 (m) cc_final: 0.8002 (t) REVERT: C 373 HIS cc_start: 0.7283 (m-70) cc_final: 0.6948 (m-70) REVERT: C 405 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7496 (ptp90) REVERT: C 607 GLN cc_start: 0.7726 (mt0) cc_final: 0.7398 (mt0) REVERT: C 739 GLU cc_start: 0.7780 (pm20) cc_final: 0.7442 (pm20) outliers start: 25 outliers final: 14 residues processed: 242 average time/residue: 1.1591 time to fit residues: 314.7183 Evaluate side-chains 237 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 776 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 69 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.176876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149050 restraints weight = 41686.832| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.92 r_work: 0.3657 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14838 Z= 0.133 Angle : 0.638 14.923 20196 Z= 0.309 Chirality : 0.120 1.755 2412 Planarity : 0.004 0.040 2474 Dihedral : 9.606 82.365 2662 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.69 % Allowed : 12.19 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 2.22 (0.20), residues: 1774 helix: 2.73 (0.14), residues: 1166 sheet: None (None), residues: 0 loop : -1.18 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 107 TYR 0.011 0.001 TYR A 505 PHE 0.012 0.001 PHE A 392 TRP 0.012 0.001 TRP C 524 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (14810) covalent geometry : angle 0.61515 / 0.30 (20124) SS BOND : bond 0.00192 / 0.14 ( 12) SS BOND : angle 1.10993 / 1.07 ( 24) hydrogen bonds : bond 0.04539 / 3.12 ( 938) hydrogen bonds : angle 3.98690 / 2.91 ( 2772) link_ALPHA1-3 : bond 0.00235 / 0.12 ( 2) link_ALPHA1-3 : angle 2.37145 / 0.98 ( 6) link_ALPHA1-6 : bond 0.00301 / 0.15 ( 2) link_ALPHA1-6 : angle 1.59054 / 0.68 ( 6) link_BETA1-4 : bond 0.00226 / 0.11 ( 8) link_BETA1-4 : angle 1.90160 / 1.55 ( 24) link_NAG-ASN : bond 0.00322 / 0.16 ( 4) link_NAG-ASN : angle 5.99622 / 2.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6851 (tm-30) REVERT: A 222 VAL cc_start: 0.8323 (m) cc_final: 0.8013 (t) REVERT: A 373 HIS cc_start: 0.7255 (m-70) cc_final: 0.6960 (m-70) REVERT: A 607 GLN cc_start: 0.7767 (mt0) cc_final: 0.7443 (mt0) REVERT: A 678 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8626 (tt) REVERT: A 691 LYS cc_start: 0.7958 (tmtt) cc_final: 0.7572 (tmtt) REVERT: A 739 GLU cc_start: 0.7855 (pm20) cc_final: 0.7435 (pm20) REVERT: A 751 GLU cc_start: 0.7696 (mm-30) cc_final: 0.6846 (mp0) REVERT: C 222 VAL cc_start: 0.8404 (m) cc_final: 0.8143 (t) REVERT: C 373 HIS cc_start: 0.7285 (m-70) cc_final: 0.6944 (m-70) REVERT: C 405 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7427 (ptp90) REVERT: C 607 GLN cc_start: 0.7726 (mt0) cc_final: 0.7393 (mt0) REVERT: C 707 ARG cc_start: 0.6588 (mtt180) cc_final: 0.6299 (mtm-85) REVERT: C 739 GLU cc_start: 0.7811 (pm20) cc_final: 0.7519 (pm20) outliers start: 26 outliers final: 19 residues processed: 240 average time/residue: 1.1862 time to fit residues: 318.7990 Evaluate side-chains 240 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 776 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 77 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 359 ASN C 750 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.180285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.152681 restraints weight = 41919.924| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.93 r_work: 0.3660 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14838 Z= 0.127 Angle : 0.634 14.813 20196 Z= 0.307 Chirality : 0.120 1.751 2412 Planarity : 0.004 0.040 2474 Dihedral : 9.465 81.047 2662 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.69 % Allowed : 12.06 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 2.28 (0.20), residues: 1774 helix: 2.78 (0.14), residues: 1166 sheet: None (None), residues: 0 loop : -1.15 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.010 0.001 TYR A 505 PHE 0.013 0.001 PHE B 193 TRP 0.012 0.001 TRP C 524 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14810) covalent geometry : angle 0.61188 / 0.30 (20124) SS BOND : bond 0.00205 / 0.14 ( 12) SS BOND : angle 1.09867 / 1.07 ( 24) hydrogen bonds : bond 0.04443 / 3.05 ( 938) hydrogen bonds : angle 3.96236 / 2.89 ( 2772) link_ALPHA1-3 : bond 0.00214 / 0.11 ( 2) link_ALPHA1-3 : angle 2.33748 / 0.98 ( 6) link_ALPHA1-6 : bond 0.00355 / 0.18 ( 2) link_ALPHA1-6 : angle 1.54476 / 0.67 ( 6) link_BETA1-4 : bond 0.00215 / 0.10 ( 8) link_BETA1-4 : angle 1.83691 / 1.48 ( 24) link_NAG-ASN : bond 0.00304 / 0.15 ( 4) link_NAG-ASN : angle 5.96340 / 2.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 254 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLN cc_start: 0.6464 (OUTLIER) cc_final: 0.6024 (mm110) REVERT: A 222 VAL cc_start: 0.8258 (m) cc_final: 0.7960 (t) REVERT: A 373 HIS cc_start: 0.7258 (m-70) cc_final: 0.6964 (m-70) REVERT: A 446 MET cc_start: 0.6595 (ptp) cc_final: 0.6309 (ptt) REVERT: A 607 GLN cc_start: 0.7762 (mt0) cc_final: 0.7432 (mt0) REVERT: A 678 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8603 (tt) REVERT: A 691 LYS cc_start: 0.7964 (tmtt) cc_final: 0.7582 (tmtt) REVERT: A 739 GLU cc_start: 0.7895 (pm20) cc_final: 0.7436 (pm20) REVERT: A 751 GLU cc_start: 0.7680 (mm-30) cc_final: 0.6823 (mp0) REVERT: C 222 VAL cc_start: 0.8293 (m) cc_final: 0.8062 (t) REVERT: C 373 HIS cc_start: 0.7287 (m-70) cc_final: 0.6945 (m-70) REVERT: C 405 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7220 (ptp90) REVERT: C 607 GLN cc_start: 0.7718 (mt0) cc_final: 0.7392 (mt0) REVERT: C 707 ARG cc_start: 0.6629 (mtt180) cc_final: 0.6342 (mtm-85) REVERT: C 739 GLU cc_start: 0.7823 (pm20) cc_final: 0.7531 (pm20) outliers start: 26 outliers final: 20 residues processed: 244 average time/residue: 1.1738 time to fit residues: 320.6683 Evaluate side-chains 245 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 105 GLN Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 776 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 90 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.175038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146883 restraints weight = 41694.196| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.93 r_work: 0.3600 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14838 Z= 0.169 Angle : 0.665 14.809 20196 Z= 0.326 Chirality : 0.121 1.763 2412 Planarity : 0.004 0.041 2474 Dihedral : 9.693 84.877 2662 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.56 % Allowed : 12.58 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 2.10 (0.20), residues: 1774 helix: 2.65 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.23 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 107 TYR 0.011 0.001 TYR A 505 PHE 0.015 0.001 PHE C 392 TRP 0.011 0.001 TRP A 524 HIS 0.004 0.001 HIS C 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (14810) covalent geometry : angle 0.64423 / 0.32 (20124) SS BOND : bond 0.00251 / 0.18 ( 12) SS BOND : angle 1.18614 / 1.18 ( 24) hydrogen bonds : bond 0.04852 / 3.33 ( 938) hydrogen bonds : angle 4.01786 / 2.94 ( 2772) link_ALPHA1-3 : bond 0.00260 / 0.13 ( 2) link_ALPHA1-3 : angle 2.25865 / 0.92 ( 6) link_ALPHA1-6 : bond 0.00258 / 0.13 ( 2) link_ALPHA1-6 : angle 1.62714 / 0.70 ( 6) link_BETA1-4 : bond 0.00241 / 0.16 ( 8) link_BETA1-4 : angle 1.92751 / 1.58 ( 24) link_NAG-ASN : bond 0.00283 / 0.14 ( 4) link_NAG-ASN : angle 5.91299 / 2.95 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 249 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6961 (tm-30) REVERT: A 222 VAL cc_start: 0.8363 (m) cc_final: 0.8093 (t) REVERT: A 373 HIS cc_start: 0.7332 (m-70) cc_final: 0.7052 (m-70) REVERT: A 607 GLN cc_start: 0.7754 (mt0) cc_final: 0.7349 (mt0) REVERT: A 691 LYS cc_start: 0.7919 (tmtt) cc_final: 0.7530 (tmtt) REVERT: A 739 GLU cc_start: 0.7916 (pm20) cc_final: 0.7510 (pm20) REVERT: A 751 GLU cc_start: 0.7697 (mm-30) cc_final: 0.6804 (mp0) REVERT: C 222 VAL cc_start: 0.8452 (m) cc_final: 0.8216 (t) REVERT: C 373 HIS cc_start: 0.7323 (m-70) cc_final: 0.6961 (m-70) REVERT: C 607 GLN cc_start: 0.7721 (mt0) cc_final: 0.7418 (mt0) REVERT: C 707 ARG cc_start: 0.6740 (mtt180) cc_final: 0.6462 (mtm-85) REVERT: C 739 GLU cc_start: 0.7868 (pm20) cc_final: 0.7570 (pm20) outliers start: 24 outliers final: 21 residues processed: 240 average time/residue: 1.2011 time to fit residues: 322.6539 Evaluate side-chains 242 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 776 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 76 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 4 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 chunk 12 optimal weight: 4.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.176921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149035 restraints weight = 41759.731| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.92 r_work: 0.3660 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14838 Z= 0.123 Angle : 0.638 14.753 20196 Z= 0.309 Chirality : 0.120 1.753 2412 Planarity : 0.004 0.040 2474 Dihedral : 9.390 81.993 2662 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.43 % Allowed : 12.97 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 2.29 (0.20), residues: 1774 helix: 2.79 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.16 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.011 0.001 TYR C 448 PHE 0.012 0.001 PHE B 193 TRP 0.012 0.001 TRP A 524 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (14810) covalent geometry : angle 0.61685 / 0.30 (20124) SS BOND : bond 0.00206 / 0.15 ( 12) SS BOND : angle 1.12354 / 1.11 ( 24) hydrogen bonds : bond 0.04472 / 3.07 ( 938) hydrogen bonds : angle 3.94860 / 2.88 ( 2772) link_ALPHA1-3 : bond 0.00145 / 0.07 ( 2) link_ALPHA1-3 : angle 2.31535 / 0.96 ( 6) link_ALPHA1-6 : bond 0.00403 / 0.20 ( 2) link_ALPHA1-6 : angle 1.52068 / 0.66 ( 6) link_BETA1-4 : bond 0.00213 / 0.14 ( 8) link_BETA1-4 : angle 1.79794 / 1.43 ( 24) link_NAG-ASN : bond 0.00287 / 0.14 ( 4) link_NAG-ASN : angle 5.93169 / 2.93 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9452.77 seconds wall clock time: 160 minutes 34.14 seconds (9634.14 seconds total)