Starting phenix.real_space_refine on Sun Jul 5 16:25:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jm7_22389/07_2026/7jm7_22389_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jm7_22389/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jm7_22389/07_2026/7jm7_22389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jm7_22389/07_2026/7jm7_22389.map" model { file = "/net/cci-nas-00/data/ceres_data/7jm7_22389/07_2026/7jm7_22389_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jm7_22389/07_2026/7jm7_22389_trim.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 77 Ad-hoc single atom residues: {' CL': 3} Unusual residues: {' MG': 1, '0J1': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 3 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, 77 Ad-hoc single atom residues: {' CL': 3} Unusual residues: {' MG': 1, '0J1': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 3 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: 5.79, per 1000 atoms: 0.20 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: 2.87 Conformation dependent library (CDL) restraints added in 857.2 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: 0.84 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: 7.26 Time building geometry restraints manager: 4.00 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: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.570 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.720 ------------------------------------------------------------------------------- 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 : 0.769 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: 0.9618 time to fit residues: 281.7576 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 : 0.760 ------------------------------------------------------------------------------- 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... 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 = 0.4105 r_free = 0.4105 target = 0.185326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.157221 restraints weight = 41106.216| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.97 r_work: 0.3735 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14838 Z= 0.179 Angle : 0.715 14.127 20196 Z= 0.346 Chirality : 0.121 1.740 2412 Planarity : 0.005 0.047 2474 Dihedral : 13.069 84.597 2666 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.91 % Allowed : 7.50 % Favored : 91.59 % 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: 2.00 (0.20), residues: 1774 helix: 2.45 (0.14), residues: 1160 sheet: None (None), residues: 0 loop : -0.95 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 271 TYR 0.014 0.001 TYR A 505 PHE 0.021 0.002 PHE A 392 TRP 0.011 0.001 TRP C 524 HIS 0.004 0.001 HIS C 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (14810) covalent geometry : angle 0.68861 / 0.34 (20124) SS BOND : bond 0.00292 / 0.15 ( 12) SS BOND : angle 1.21722 / 1.61 ( 24) hydrogen bonds : bond 0.05410 / 3.68 ( 938) hydrogen bonds : angle 4.52517 / 3.31 ( 2772) link_ALPHA1-3 : bond 0.00844 / 0.43 ( 2) link_ALPHA1-3 : angle 5.20745 / 2.41 ( 6) link_ALPHA1-6 : bond 0.01123 / 0.56 ( 2) link_ALPHA1-6 : angle 1.48092 / 0.62 ( 6) link_BETA1-4 : bond 0.00518 / 0.25 ( 8) link_BETA1-4 : angle 2.36943 / 1.76 ( 24) link_NAG-ASN : bond 0.00388 / 0.19 ( 4) link_NAG-ASN : angle 6.00655 / 2.94 ( 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 225 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 HIS cc_start: 0.7229 (m-70) cc_final: 0.6878 (m-70) REVERT: A 607 GLN cc_start: 0.7710 (mt0) cc_final: 0.7360 (mt0) REVERT: A 628 ARG cc_start: 0.7244 (ttp-110) cc_final: 0.6984 (ttp-170) REVERT: A 678 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8622 (tt) REVERT: A 739 GLU cc_start: 0.7635 (pm20) cc_final: 0.7113 (pm20) REVERT: A 751 GLU cc_start: 0.7683 (mm-30) cc_final: 0.6810 (mp0) REVERT: C 373 HIS cc_start: 0.7345 (m-70) cc_final: 0.7031 (m-70) REVERT: C 607 GLN cc_start: 0.7831 (mt0) cc_final: 0.7493 (mt0) REVERT: C 739 GLU cc_start: 0.7574 (pm20) cc_final: 0.7234 (pm20) outliers start: 14 outliers final: 9 residues processed: 219 average time/residue: 1.0789 time to fit residues: 266.5823 Evaluate side-chains 216 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 206 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 D residue 171 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: 0.0170 chunk 42 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 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: 2.9990 chunk 71 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.177541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149361 restraints weight = 41659.491| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.93 r_work: 0.3630 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14838 Z= 0.207 Angle : 0.708 14.429 20196 Z= 0.347 Chirality : 0.122 1.729 2412 Planarity : 0.005 0.042 2474 Dihedral : 11.794 87.511 2662 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.04 % Allowed : 8.67 % Favored : 90.29 % 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: 1.70 (0.20), residues: 1774 helix: 2.25 (0.14), residues: 1160 sheet: None (None), residues: 0 loop : -1.16 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 271 TYR 0.014 0.002 TYR C 505 PHE 0.017 0.002 PHE A 392 TRP 0.011 0.001 TRP C 524 HIS 0.005 0.001 HIS C 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (14810) covalent geometry : angle 0.68412 / 0.34 (20124) SS BOND : bond 0.00246 / 0.16 ( 12) SS BOND : angle 1.45211 / 2.01 ( 24) hydrogen bonds : bond 0.05667 / 3.87 ( 938) hydrogen bonds : angle 4.41462 / 3.23 ( 2772) link_ALPHA1-3 : bond 0.01340 / 0.67 ( 2) link_ALPHA1-3 : angle 4.07386 / 1.87 ( 6) link_ALPHA1-6 : bond 0.00094 / 0.05 ( 2) link_ALPHA1-6 : angle 2.01489 / 0.91 ( 6) link_BETA1-4 : bond 0.00373 / 0.18 ( 8) link_BETA1-4 : angle 2.36372 / 1.91 ( 24) link_NAG-ASN : bond 0.00415 / 0.21 ( 4) link_NAG-ASN : angle 5.81147 / 2.93 ( 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 246 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 230 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 76 ASP cc_start: 0.6996 (p0) cc_final: 0.6767 (p0) REVERT: B 231 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8574 (mt) REVERT: A 95 GLU cc_start: 0.8141 (tp30) cc_final: 0.7913 (tp30) REVERT: A 373 HIS cc_start: 0.7352 (m-70) cc_final: 0.7023 (m-70) REVERT: A 607 GLN cc_start: 0.7772 (mt0) cc_final: 0.7489 (mt0) REVERT: A 678 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8671 (tt) REVERT: A 739 GLU cc_start: 0.7945 (pm20) cc_final: 0.7450 (pm20) REVERT: A 751 GLU cc_start: 0.7709 (mm-30) cc_final: 0.6889 (mp0) REVERT: D 148 MET cc_start: 0.7339 (ptt) cc_final: 0.7137 (ptt) REVERT: D 262 MET cc_start: 0.8186 (tpt) cc_final: 0.7567 (tpt) REVERT: C 177 LEU cc_start: 0.7854 (mp) cc_final: 0.7644 (mm) REVERT: C 373 HIS cc_start: 0.7338 (m-70) cc_final: 0.7020 (m-70) REVERT: C 595 ASP cc_start: 0.8244 (m-30) cc_final: 0.7832 (m-30) REVERT: C 607 GLN cc_start: 0.7832 (mt0) cc_final: 0.7556 (mt0) REVERT: C 739 GLU cc_start: 0.7861 (pm20) cc_final: 0.7469 (pm20) outliers start: 16 outliers final: 9 residues processed: 239 average time/residue: 1.0911 time to fit residues: 293.4707 Evaluate side-chains 219 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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: 0.9980 chunk 26 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 137 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 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: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN C 396 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.178426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150530 restraints weight = 41425.989| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.92 r_work: 0.3675 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2169 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= 0.142 Angle : 0.660 14.566 20196 Z= 0.319 Chirality : 0.120 1.725 2412 Planarity : 0.004 0.042 2474 Dihedral : 10.523 86.658 2662 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.04 % Allowed : 10.10 % 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: 1.94 (0.20), residues: 1774 helix: 2.47 (0.14), residues: 1160 sheet: None (None), residues: 0 loop : -1.15 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 107 TYR 0.011 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 0.00318 / 0.14 (14810) covalent geometry : angle 0.63664 / 0.31 (20124) SS BOND : bond 0.00185 / 0.12 ( 12) SS BOND : angle 1.23113 / 1.33 ( 24) hydrogen bonds : bond 0.04948 / 3.39 ( 938) hydrogen bonds : angle 4.21248 / 3.08 ( 2772) link_ALPHA1-3 : bond 0.00670 / 0.33 ( 2) link_ALPHA1-3 : angle 3.19757 / 1.41 ( 6) link_ALPHA1-6 : bond 0.00543 / 0.27 ( 2) link_ALPHA1-6 : angle 2.60254 / 1.19 ( 6) link_BETA1-4 : bond 0.00234 / 0.15 ( 8) link_BETA1-4 : angle 2.00489 / 1.59 ( 24) link_NAG-ASN : bond 0.00372 / 0.18 ( 4) link_NAG-ASN : angle 5.87630 / 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 243 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 227 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 373 HIS cc_start: 0.7267 (m-70) cc_final: 0.6943 (m-70) REVERT: A 607 GLN cc_start: 0.7745 (mt0) cc_final: 0.7401 (mt0) REVERT: A 678 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8620 (tt) REVERT: A 739 GLU cc_start: 0.7865 (pm20) cc_final: 0.7408 (pm20) REVERT: A 751 GLU cc_start: 0.7708 (mm-30) cc_final: 0.6845 (mp0) REVERT: D 148 MET cc_start: 0.7390 (ptt) cc_final: 0.7186 (ptt) REVERT: C 177 LEU cc_start: 0.7741 (mp) cc_final: 0.7522 (mm) REVERT: C 373 HIS cc_start: 0.7259 (m-70) cc_final: 0.6911 (m-70) REVERT: C 607 GLN cc_start: 0.7781 (mt0) cc_final: 0.7429 (mt0) REVERT: C 739 GLU cc_start: 0.7809 (pm20) cc_final: 0.7481 (pm20) outliers start: 16 outliers final: 10 residues processed: 235 average time/residue: 1.1053 time to fit residues: 290.4224 Evaluate side-chains 226 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 215 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 461 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 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: 0.0050 chunk 86 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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** A 750 GLN C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.177735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.149846 restraints weight = 41515.392| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.92 r_work: 0.3671 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14838 Z= 0.144 Angle : 0.650 14.879 20196 Z= 0.315 Chirality : 0.120 1.738 2412 Planarity : 0.004 0.040 2474 Dihedral : 10.292 89.096 2662 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.30 % Allowed : 11.08 % Favored : 87.61 % 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: 2.06 (0.20), residues: 1774 helix: 2.58 (0.14), residues: 1168 sheet: None (None), residues: 0 loop : -1.18 (0.24), residues: 606 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 0.013 0.001 PHE A 392 TRP 0.012 0.001 TRP C 524 HIS 0.004 0.001 HIS C 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (14810) covalent geometry : angle 0.62610 / 0.31 (20124) SS BOND : bond 0.00182 / 0.12 ( 12) SS BOND : angle 1.44723 / 1.29 ( 24) hydrogen bonds : bond 0.04843 / 3.31 ( 938) hydrogen bonds : angle 4.12479 / 3.02 ( 2772) link_ALPHA1-3 : bond 0.00654 / 0.33 ( 2) link_ALPHA1-3 : angle 2.87474 / 1.23 ( 6) link_ALPHA1-6 : bond 0.00194 / 0.09 ( 2) link_ALPHA1-6 : angle 1.63660 / 0.67 ( 6) link_BETA1-4 : bond 0.00379 / 0.19 ( 8) link_BETA1-4 : angle 1.93234 / 1.60 ( 24) link_NAG-ASN : bond 0.00353 / 0.18 ( 4) link_NAG-ASN : angle 5.95903 / 2.96 ( 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 246 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 HIS cc_start: 0.7273 (m-70) cc_final: 0.6971 (m-70) REVERT: A 607 GLN cc_start: 0.7756 (mt0) cc_final: 0.7304 (mt0) REVERT: A 678 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8633 (tt) REVERT: A 739 GLU cc_start: 0.7865 (pm20) cc_final: 0.7466 (pm20) REVERT: A 751 GLU cc_start: 0.7732 (mm-30) cc_final: 0.6864 (mp0) REVERT: D 148 MET cc_start: 0.7317 (ptt) cc_final: 0.7102 (ptt) REVERT: D 262 MET cc_start: 0.8238 (tpt) cc_final: 0.8030 (tpt) REVERT: C 222 VAL cc_start: 0.8389 (m) cc_final: 0.8079 (t) REVERT: C 373 HIS cc_start: 0.7257 (m-70) cc_final: 0.6904 (m-70) REVERT: C 607 GLN cc_start: 0.7786 (mt0) cc_final: 0.7276 (mt0) REVERT: C 739 GLU cc_start: 0.7819 (pm20) cc_final: 0.7506 (pm20) outliers start: 20 outliers final: 15 residues processed: 238 average time/residue: 1.0964 time to fit residues: 292.2588 Evaluate side-chains 233 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 231 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 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 735 MET 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: 1.9990 chunk 17 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 0.0770 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- 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 C 750 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.177544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.149568 restraints weight = 42040.850| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.93 r_work: 0.3627 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14838 Z= 0.199 Angle : 0.692 14.737 20196 Z= 0.340 Chirality : 0.122 1.751 2412 Planarity : 0.005 0.091 2474 Dihedral : 10.577 89.332 2662 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.96 % Allowed : 11.02 % Favored : 87.03 % 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: 1.77 (0.20), residues: 1774 helix: 2.37 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.32 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 265 TYR 0.014 0.002 TYR A 505 PHE 0.018 0.002 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 0.00462 / 0.20 (14810) covalent geometry : angle 0.67082 / 0.34 (20124) SS BOND : bond 0.00273 / 0.20 ( 12) SS BOND : angle 1.34570 / 1.34 ( 24) hydrogen bonds : bond 0.05328 / 3.66 ( 938) hydrogen bonds : angle 4.18611 / 3.06 ( 2772) link_ALPHA1-3 : bond 0.00471 / 0.24 ( 2) link_ALPHA1-3 : angle 2.64868 / 1.14 ( 6) link_ALPHA1-6 : bond 0.00252 / 0.13 ( 2) link_ALPHA1-6 : angle 1.70255 / 0.74 ( 6) link_BETA1-4 : bond 0.00288 / 0.20 ( 8) link_BETA1-4 : angle 2.12679 / 1.75 ( 24) link_NAG-ASN : bond 0.00306 / 0.16 ( 4) link_NAG-ASN : angle 5.84343 / 2.92 ( 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 263 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8092 (t) REVERT: A 373 HIS cc_start: 0.7377 (m-70) cc_final: 0.7077 (m-70) REVERT: A 405 ARG cc_start: 0.8076 (ptp-170) cc_final: 0.7704 (ptp-170) REVERT: A 607 GLN cc_start: 0.7753 (mt0) cc_final: 0.7422 (mt0) REVERT: A 678 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8645 (tt) REVERT: A 739 GLU cc_start: 0.7933 (pm20) cc_final: 0.7510 (pm20) REVERT: A 751 GLU cc_start: 0.7746 (mm-30) cc_final: 0.6857 (mp0) REVERT: D 148 MET cc_start: 0.7668 (ptt) cc_final: 0.7461 (ptt) REVERT: C 98 ASP cc_start: 0.8259 (m-30) cc_final: 0.7778 (m-30) REVERT: C 222 VAL cc_start: 0.8553 (m) cc_final: 0.8262 (t) REVERT: C 238 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8120 (t) REVERT: C 373 HIS cc_start: 0.7328 (m-70) cc_final: 0.6979 (m-70) REVERT: C 595 ASP cc_start: 0.8172 (m-30) cc_final: 0.7952 (m-30) REVERT: C 607 GLN cc_start: 0.7739 (mt0) cc_final: 0.7373 (mt0) REVERT: C 707 ARG cc_start: 0.6679 (mtt180) cc_final: 0.6358 (mtm-85) REVERT: C 739 GLU cc_start: 0.7895 (pm20) cc_final: 0.7552 (pm20) outliers start: 30 outliers final: 20 residues processed: 250 average time/residue: 1.1715 time to fit residues: 327.4685 Evaluate side-chains 247 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 231 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 167 THR 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 656 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 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 735 MET Chi-restraints excluded: chain C residue 776 ASN Chi-restraints excluded: chain C residue 777 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 158 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.178464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.150674 restraints weight = 41871.032| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.93 r_work: 0.3639 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14838 Z= 0.158 Angle : 0.659 14.688 20196 Z= 0.322 Chirality : 0.121 1.739 2412 Planarity : 0.005 0.049 2474 Dihedral : 10.273 88.079 2662 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.02 % Allowed : 11.47 % Favored : 86.51 % 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: 1.90 (0.20), residues: 1774 helix: 2.47 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.27 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 107 TYR 0.011 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 0.00362 / 0.16 (14810) covalent geometry : angle 0.63693 / 0.32 (20124) SS BOND : bond 0.00219 / 0.17 ( 12) SS BOND : angle 1.28004 / 1.24 ( 24) hydrogen bonds : bond 0.04991 / 3.42 ( 938) hydrogen bonds : angle 4.10530 / 3.00 ( 2772) link_ALPHA1-3 : bond 0.00390 / 0.20 ( 2) link_ALPHA1-3 : angle 2.60436 / 1.10 ( 6) link_ALPHA1-6 : bond 0.00354 / 0.17 ( 2) link_ALPHA1-6 : angle 1.58048 / 0.68 ( 6) link_BETA1-4 : bond 0.00282 / 0.15 ( 8) link_BETA1-4 : angle 2.00570 / 1.70 ( 24) link_NAG-ASN : bond 0.00291 / 0.15 ( 4) link_NAG-ASN : angle 5.85031 / 2.90 ( 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 254 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 HIS cc_start: 0.7360 (m-70) cc_final: 0.7071 (m-70) REVERT: A 607 GLN cc_start: 0.7748 (mt0) cc_final: 0.7351 (mt0) REVERT: A 678 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8624 (tt) REVERT: A 739 GLU cc_start: 0.7912 (pm20) cc_final: 0.7505 (pm20) REVERT: A 751 GLU cc_start: 0.7694 (mm-30) cc_final: 0.6842 (mp0) REVERT: C 222 VAL cc_start: 0.8339 (m) cc_final: 0.8052 (t) REVERT: C 373 HIS cc_start: 0.7331 (m-70) cc_final: 0.6968 (m-70) REVERT: C 405 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7486 (ptp90) REVERT: C 607 GLN cc_start: 0.7708 (mt0) cc_final: 0.7334 (mt0) REVERT: C 707 ARG cc_start: 0.6654 (mtt180) cc_final: 0.6360 (mtm-85) REVERT: C 739 GLU cc_start: 0.7817 (pm20) cc_final: 0.7453 (pm20) outliers start: 31 outliers final: 21 residues processed: 244 average time/residue: 1.1828 time to fit residues: 322.6748 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 : 0.760 ------------------------------------------------------------------------------- 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 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 531 SER Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 656 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 192 LEU Chi-restraints excluded: chain D residue 223 ASN 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 776 ASN Chi-restraints excluded: chain C residue 777 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 69 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 396 ASN D 163 ASN C 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.179487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.151892 restraints weight = 41901.814| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.92 r_work: 0.3651 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14838 Z= 0.132 Angle : 0.642 14.879 20196 Z= 0.312 Chirality : 0.120 1.743 2412 Planarity : 0.004 0.041 2474 Dihedral : 9.897 84.383 2662 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.69 % Allowed : 12.13 % Favored : 86.18 % 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: 2.07 (0.20), residues: 1774 helix: 2.62 (0.15), residues: 1166 sheet: None (None), residues: 0 loop : -1.24 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 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 C 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (14810) covalent geometry : angle 0.61927 / 0.31 (20124) SS BOND : bond 0.00204 / 0.15 ( 12) SS BOND : angle 1.12780 / 1.09 ( 24) hydrogen bonds : bond 0.04648 / 3.19 ( 938) hydrogen bonds : angle 4.01584 / 2.93 ( 2772) link_ALPHA1-3 : bond 0.00345 / 0.17 ( 2) link_ALPHA1-3 : angle 2.44751 / 1.03 ( 6) link_ALPHA1-6 : bond 0.00390 / 0.19 ( 2) link_ALPHA1-6 : angle 1.58538 / 0.70 ( 6) link_BETA1-4 : bond 0.00254 / 0.15 ( 8) link_BETA1-4 : angle 2.05780 / 1.70 ( 24) link_NAG-ASN : bond 0.00310 / 0.15 ( 4) link_NAG-ASN : angle 5.95306 / 2.94 ( 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 252 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6939 (tm-30) REVERT: A 222 VAL cc_start: 0.8326 (m) cc_final: 0.8031 (t) REVERT: A 373 HIS cc_start: 0.7310 (m-70) cc_final: 0.7026 (m-70) REVERT: A 607 GLN cc_start: 0.7750 (mt0) cc_final: 0.7357 (mt0) REVERT: A 678 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8613 (tt) REVERT: A 691 LYS cc_start: 0.7952 (tmtt) cc_final: 0.7577 (tmtt) REVERT: A 739 GLU cc_start: 0.7860 (pm20) cc_final: 0.7435 (pm20) REVERT: A 751 GLU cc_start: 0.7684 (mm-30) cc_final: 0.6821 (mp0) REVERT: C 222 VAL cc_start: 0.8419 (m) cc_final: 0.8167 (t) REVERT: C 373 HIS cc_start: 0.7310 (m-70) cc_final: 0.6952 (m-70) REVERT: C 405 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7416 (ptp90) REVERT: C 607 GLN cc_start: 0.7699 (mt0) cc_final: 0.7402 (mt0) REVERT: C 707 ARG cc_start: 0.6642 (mtt180) cc_final: 0.6390 (mtm-85) REVERT: C 739 GLU cc_start: 0.7831 (pm20) cc_final: 0.7493 (pm20) outliers start: 26 outliers final: 21 residues processed: 243 average time/residue: 1.1746 time to fit residues: 318.7691 Evaluate side-chains 243 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 678 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 223 ASN 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 Chi-restraints excluded: chain C residue 777 GLN 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: 0.9980 chunk 63 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 148 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 38 optimal weight: 0.0020 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.180343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152833 restraints weight = 41818.009| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.93 r_work: 0.3661 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14838 Z= 0.121 Angle : 0.637 14.898 20196 Z= 0.308 Chirality : 0.120 1.740 2412 Planarity : 0.004 0.040 2474 Dihedral : 9.661 81.813 2662 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.50 % Allowed : 12.71 % Favored : 85.79 % 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: 2.71 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -1.14 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 107 TYR 0.010 0.001 TYR A 505 PHE 0.014 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 0.00270 / 0.12 (14810) covalent geometry : angle 0.61407 / 0.30 (20124) SS BOND : bond 0.00196 / 0.13 ( 12) SS BOND : angle 1.11895 / 1.10 ( 24) hydrogen bonds : bond 0.04466 / 3.06 ( 938) hydrogen bonds : angle 3.97326 / 2.91 ( 2772) link_ALPHA1-3 : bond 0.00210 / 0.11 ( 2) link_ALPHA1-3 : angle 2.34011 / 0.97 ( 6) link_ALPHA1-6 : bond 0.00336 / 0.17 ( 2) link_ALPHA1-6 : angle 1.54900 / 0.67 ( 6) link_BETA1-4 : bond 0.00237 / 0.14 ( 8) link_BETA1-4 : angle 1.91758 / 1.57 ( 24) link_NAG-ASN : bond 0.00316 / 0.16 ( 4) link_NAG-ASN : angle 5.98742 / 2.96 ( 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 249 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 VAL cc_start: 0.8217 (m) cc_final: 0.7921 (t) REVERT: A 373 HIS cc_start: 0.7285 (m-70) cc_final: 0.6999 (m-70) REVERT: A 607 GLN cc_start: 0.7754 (mt0) cc_final: 0.7423 (mt0) REVERT: A 678 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8586 (tt) REVERT: A 691 LYS cc_start: 0.7936 (tmtt) cc_final: 0.7553 (tmtt) REVERT: A 739 GLU cc_start: 0.7884 (pm20) cc_final: 0.7461 (pm20) REVERT: A 751 GLU cc_start: 0.7664 (mm-30) cc_final: 0.6806 (mp0) REVERT: C 222 VAL cc_start: 0.8264 (m) cc_final: 0.8032 (t) REVERT: C 373 HIS cc_start: 0.7273 (m-70) cc_final: 0.6946 (m-70) REVERT: C 405 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7424 (ptp90) REVERT: C 607 GLN cc_start: 0.7697 (mt0) cc_final: 0.7411 (mt0) REVERT: C 707 ARG cc_start: 0.6609 (mtt180) cc_final: 0.6349 (mtm-85) REVERT: C 739 GLU cc_start: 0.7804 (pm20) cc_final: 0.7464 (pm20) outliers start: 23 outliers final: 21 residues processed: 240 average time/residue: 1.1778 time to fit residues: 316.0968 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 : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 678 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 223 ASN 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 Chi-restraints excluded: chain C residue 777 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 90 optimal weight: 0.9980 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: 0.3980 chunk 18 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 359 ASN C 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.179287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.151580 restraints weight = 41756.638| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.92 r_work: 0.3652 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14838 Z= 0.146 Angle : 0.650 14.895 20196 Z= 0.317 Chirality : 0.121 1.760 2412 Planarity : 0.004 0.041 2474 Dihedral : 9.676 82.336 2662 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.63 % Allowed : 12.58 % Favored : 85.79 % 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: 2.17 (0.20), residues: 1774 helix: 2.67 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -1.15 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 107 TYR 0.011 0.001 TYR A 505 PHE 0.013 0.001 PHE A 392 TRP 0.011 0.001 TRP C 524 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (14810) covalent geometry : angle 0.62850 / 0.31 (20124) SS BOND : bond 0.00211 / 0.15 ( 12) SS BOND : angle 1.13487 / 1.12 ( 24) hydrogen bonds : bond 0.04651 / 3.19 ( 938) hydrogen bonds : angle 3.98376 / 2.91 ( 2772) link_ALPHA1-3 : bond 0.00219 / 0.11 ( 2) link_ALPHA1-3 : angle 2.24787 / 0.92 ( 6) link_ALPHA1-6 : bond 0.00303 / 0.15 ( 2) link_ALPHA1-6 : angle 1.60050 / 0.69 ( 6) link_BETA1-4 : bond 0.00240 / 0.15 ( 8) link_BETA1-4 : angle 1.92888 / 1.61 ( 24) link_NAG-ASN : bond 0.00303 / 0.15 ( 4) link_NAG-ASN : angle 5.96785 / 2.96 ( 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: 25 poor density : 224 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6917 (tm-30) REVERT: A 222 VAL cc_start: 0.8310 (m) cc_final: 0.8033 (t) REVERT: A 373 HIS cc_start: 0.7322 (m-70) cc_final: 0.7030 (m-70) REVERT: A 607 GLN cc_start: 0.7756 (mt0) cc_final: 0.7357 (mt0) REVERT: A 629 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7145 (mt-10) REVERT: A 691 LYS cc_start: 0.7931 (tmtt) cc_final: 0.7543 (tmtt) REVERT: A 739 GLU cc_start: 0.7900 (pm20) cc_final: 0.7501 (pm20) REVERT: A 751 GLU cc_start: 0.7671 (mm-30) cc_final: 0.6784 (mp0) REVERT: C 222 VAL cc_start: 0.8426 (m) cc_final: 0.8196 (t) REVERT: C 373 HIS cc_start: 0.7313 (m-70) cc_final: 0.6982 (m-70) REVERT: C 405 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7463 (ptp90) REVERT: C 607 GLN cc_start: 0.7714 (mt0) cc_final: 0.7416 (mt0) REVERT: C 707 ARG cc_start: 0.6709 (mtt180) cc_final: 0.6460 (mtm-85) REVERT: C 739 GLU cc_start: 0.7813 (pm20) cc_final: 0.7510 (pm20) outliers start: 25 outliers final: 22 residues processed: 240 average time/residue: 1.1803 time to fit residues: 316.0436 Evaluate side-chains 243 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 629 GLU 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 192 LEU Chi-restraints excluded: chain D residue 223 ASN 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 Chi-restraints excluded: chain C residue 777 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 76 optimal weight: 0.0970 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 0.1980 chunk 4 optimal weight: 0.0870 chunk 53 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 ASN C 359 ASN C 750 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.178025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150260 restraints weight = 41682.199| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.93 r_work: 0.3672 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14838 Z= 0.115 Angle : 0.632 14.799 20196 Z= 0.306 Chirality : 0.120 1.754 2412 Planarity : 0.004 0.040 2474 Dihedral : 9.334 79.024 2662 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.43 % Allowed : 13.04 % Favored : 85.53 % 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: 2.36 (0.20), residues: 1774 helix: 2.77 (0.15), residues: 1174 sheet: None (None), residues: 0 loop : -1.01 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 107 TYR 0.014 0.001 TYR C 448 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 0.00257 / 0.12 (14810) covalent geometry : angle 0.61025 / 0.30 (20124) SS BOND : bond 0.00201 / 0.13 ( 12) SS BOND : angle 1.07460 / 1.06 ( 24) hydrogen bonds : bond 0.04306 / 2.95 ( 938) hydrogen bonds : angle 3.91714 / 2.86 ( 2772) link_ALPHA1-3 : bond 0.00082 / 0.04 ( 2) link_ALPHA1-3 : angle 2.21850 / 0.91 ( 6) link_ALPHA1-6 : bond 0.00405 / 0.20 ( 2) link_ALPHA1-6 : angle 1.51469 / 0.66 ( 6) link_BETA1-4 : bond 0.00231 / 0.14 ( 8) link_BETA1-4 : angle 1.87776 / 1.52 ( 24) link_NAG-ASN : bond 0.00306 / 0.15 ( 4) link_NAG-ASN : angle 5.97406 / 2.94 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9679.82 seconds wall clock time: 164 minutes 39.88 seconds (9879.88 seconds total)