Starting phenix.real_space_refine on Mon Aug 25 13:08:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9di8_46901/08_2025/9di8_46901.cif Found real_map, /net/cci-nas-00/data/ceres_data/9di8_46901/08_2025/9di8_46901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9di8_46901/08_2025/9di8_46901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9di8_46901/08_2025/9di8_46901.map" model { file = "/net/cci-nas-00/data/ceres_data/9di8_46901/08_2025/9di8_46901.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9di8_46901/08_2025/9di8_46901.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 7 9.91 5 K 5 8.98 5 Mg 4 5.21 5 S 172 5.16 5 C 18328 2.51 5 N 4588 2.21 5 O 5116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28220 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7051 Classifications: {'peptide': 899} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 7051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7051 Classifications: {'peptide': 899} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 7051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7051 Classifications: {'peptide': 899} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 7051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7051 Classifications: {'peptide': 899} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 72 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' K': 5, ' CA': 2, ' MG': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.15, per 1000 atoms: 0.22 Number of scatterers: 28220 At special positions: 0 Unit cell: (143.505, 143.505, 123.308, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 7 19.99 K 5 19.00 S 172 16.00 Mg 4 11.99 O 5116 8.00 N 4588 7.00 C 18328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6784 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 24 sheets defined 57.6% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 15 through 44 removed outlier: 3.582A pdb=" N SER A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 30 " --> pdb=" O THR A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 132 through 135 Processing helix chain 'A' and resid 136 through 160 removed outlier: 3.667A pdb=" N ALA A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 169 through 188 Proline residue: A 180 - end of helix removed outlier: 4.134A pdb=" N ILE A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 204 removed outlier: 4.022A pdb=" N PHE A 197 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 218 through 249 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 286 through 316 removed outlier: 3.586A pdb=" N ILE A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLY A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 341 through 353 removed outlier: 3.574A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 451 through 460 removed outlier: 3.780A pdb=" N LYS A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A 456 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR A 457 " --> pdb=" O HIS A 453 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.749A pdb=" N LEU A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 498 Processing helix chain 'A' and resid 499 through 501 No H-bonds generated for 'chain 'A' and resid 499 through 501' Processing helix chain 'A' and resid 512 through 523 Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 592 through 602 removed outlier: 3.663A pdb=" N VAL A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 762 through 765 Processing helix chain 'A' and resid 769 through 773 removed outlier: 3.502A pdb=" N LEU A 773 " --> pdb=" O TYR A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 793 removed outlier: 3.727A pdb=" N ARG A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 814 Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.569A pdb=" N CYS A 819 " --> pdb=" O ILE A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 852 Processing helix chain 'A' and resid 894 through 902 removed outlier: 4.123A pdb=" N ASP A 902 " --> pdb=" O GLN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 928 through 931 Processing helix chain 'A' and resid 932 through 940 Processing helix chain 'A' and resid 940 through 953 removed outlier: 3.667A pdb=" N LEU A 944 " --> pdb=" O ASN A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 981 through 983 No H-bonds generated for 'chain 'A' and resid 981 through 983' Processing helix chain 'A' and resid 997 through 1002 removed outlier: 3.903A pdb=" N GLY A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 997 through 1002' Processing helix chain 'A' and resid 1005 through 1018 Processing helix chain 'B' and resid 15 through 44 removed outlier: 3.582A pdb=" N SER B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 132 through 135 Processing helix chain 'B' and resid 136 through 160 removed outlier: 3.667A pdb=" N ALA B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 169 through 188 Proline residue: B 180 - end of helix removed outlier: 4.134A pdb=" N ILE B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 204 removed outlier: 4.023A pdb=" N PHE B 197 " --> pdb=" O GLY B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 218 through 249 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 286 through 316 removed outlier: 3.586A pdb=" N ILE B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLY B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 341 through 353 removed outlier: 3.574A pdb=" N ASP B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 383 Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 451 through 460 removed outlier: 3.780A pdb=" N LYS B 455 " --> pdb=" O GLN B 451 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA B 456 " --> pdb=" O TYR B 452 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR B 457 " --> pdb=" O HIS B 453 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 458 " --> pdb=" O ASN B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.749A pdb=" N LEU B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 498 Processing helix chain 'B' and resid 499 through 501 No H-bonds generated for 'chain 'B' and resid 499 through 501' Processing helix chain 'B' and resid 512 through 523 Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 539 through 550 Processing helix chain 'B' and resid 592 through 602 removed outlier: 3.663A pdb=" N VAL B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ALA B 599 " --> pdb=" O GLU B 595 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 756 through 761 Processing helix chain 'B' and resid 762 through 765 Processing helix chain 'B' and resid 769 through 773 removed outlier: 3.502A pdb=" N LEU B 773 " --> pdb=" O TYR B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 793 removed outlier: 3.727A pdb=" N ARG B 787 " --> pdb=" O ASP B 783 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS B 790 " --> pdb=" O HIS B 786 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N THR B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 814 Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.569A pdb=" N CYS B 819 " --> pdb=" O ILE B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 852 Processing helix chain 'B' and resid 894 through 902 removed outlier: 4.123A pdb=" N ASP B 902 " --> pdb=" O GLN B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 915 Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 928 through 931 Processing helix chain 'B' and resid 932 through 940 Processing helix chain 'B' and resid 940 through 953 removed outlier: 3.667A pdb=" N LEU B 944 " --> pdb=" O ASN B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 965 Processing helix chain 'B' and resid 975 through 980 Processing helix chain 'B' and resid 981 through 983 No H-bonds generated for 'chain 'B' and resid 981 through 983' Processing helix chain 'B' and resid 997 through 1002 removed outlier: 3.903A pdb=" N GLY B1001 " --> pdb=" O LEU B 997 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B1002 " --> pdb=" O ALA B 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 997 through 1002' Processing helix chain 'B' and resid 1005 through 1018 Processing helix chain 'C' and resid 15 through 44 removed outlier: 3.583A pdb=" N SER C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 93 Processing helix chain 'C' and resid 96 through 123 Processing helix chain 'C' and resid 132 through 135 Processing helix chain 'C' and resid 136 through 160 removed outlier: 3.668A pdb=" N ALA C 144 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 169 through 188 Proline residue: C 180 - end of helix removed outlier: 4.134A pdb=" N ILE C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 204 removed outlier: 4.023A pdb=" N PHE C 197 " --> pdb=" O GLY C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 218 through 249 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 286 through 316 removed outlier: 3.586A pdb=" N ILE C 301 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLY C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 341 through 353 removed outlier: 3.574A pdb=" N ASP C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 421 through 440 Processing helix chain 'C' and resid 451 through 460 removed outlier: 3.780A pdb=" N LYS C 455 " --> pdb=" O GLN C 451 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA C 456 " --> pdb=" O TYR C 452 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR C 457 " --> pdb=" O HIS C 453 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 458 " --> pdb=" O ASN C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.749A pdb=" N LEU C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 498 Processing helix chain 'C' and resid 499 through 501 No H-bonds generated for 'chain 'C' and resid 499 through 501' Processing helix chain 'C' and resid 512 through 523 Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 539 through 550 Processing helix chain 'C' and resid 592 through 602 removed outlier: 3.664A pdb=" N VAL C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG C 598 " --> pdb=" O GLU C 594 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA C 599 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 721 through 725 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 756 through 761 Processing helix chain 'C' and resid 762 through 765 Processing helix chain 'C' and resid 769 through 773 removed outlier: 3.503A pdb=" N LEU C 773 " --> pdb=" O TYR C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 793 removed outlier: 3.727A pdb=" N ARG C 787 " --> pdb=" O ASP C 783 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS C 790 " --> pdb=" O HIS C 786 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 792 " --> pdb=" O GLU C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 814 Processing helix chain 'C' and resid 815 through 819 removed outlier: 3.569A pdb=" N CYS C 819 " --> pdb=" O ILE C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 852 Processing helix chain 'C' and resid 894 through 902 removed outlier: 4.123A pdb=" N ASP C 902 " --> pdb=" O GLN C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 915 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 928 through 931 Processing helix chain 'C' and resid 932 through 940 Processing helix chain 'C' and resid 940 through 953 removed outlier: 3.666A pdb=" N LEU C 944 " --> pdb=" O ASN C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 965 Processing helix chain 'C' and resid 975 through 980 Processing helix chain 'C' and resid 981 through 983 No H-bonds generated for 'chain 'C' and resid 981 through 983' Processing helix chain 'C' and resid 997 through 1002 removed outlier: 3.904A pdb=" N GLY C1001 " --> pdb=" O LEU C 997 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN C1002 " --> pdb=" O ALA C 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 997 through 1002' Processing helix chain 'C' and resid 1005 through 1018 Processing helix chain 'D' and resid 15 through 44 removed outlier: 3.581A pdb=" N SER D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 30 " --> pdb=" O THR D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 93 Processing helix chain 'D' and resid 96 through 123 Processing helix chain 'D' and resid 132 through 135 Processing helix chain 'D' and resid 136 through 160 removed outlier: 3.668A pdb=" N ALA D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 169 through 188 Proline residue: D 180 - end of helix removed outlier: 4.134A pdb=" N ILE D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 204 removed outlier: 4.022A pdb=" N PHE D 197 " --> pdb=" O GLY D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 218 through 249 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 286 through 316 removed outlier: 3.586A pdb=" N ILE D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLY D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) Proline residue: D 309 - end of helix Processing helix chain 'D' and resid 341 through 353 removed outlier: 3.574A pdb=" N ASP D 351 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'D' and resid 404 through 408 Processing helix chain 'D' and resid 421 through 440 Processing helix chain 'D' and resid 451 through 460 removed outlier: 3.780A pdb=" N LYS D 455 " --> pdb=" O GLN D 451 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA D 456 " --> pdb=" O TYR D 452 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR D 457 " --> pdb=" O HIS D 453 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 458 " --> pdb=" O ASN D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.749A pdb=" N LEU D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 498 Processing helix chain 'D' and resid 499 through 501 No H-bonds generated for 'chain 'D' and resid 499 through 501' Processing helix chain 'D' and resid 512 through 523 Processing helix chain 'D' and resid 532 through 536 Processing helix chain 'D' and resid 539 through 550 Processing helix chain 'D' and resid 592 through 602 removed outlier: 3.664A pdb=" N VAL D 596 " --> pdb=" O SER D 592 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG D 598 " --> pdb=" O GLU D 594 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 616 Processing helix chain 'D' and resid 721 through 725 Processing helix chain 'D' and resid 728 through 735 Processing helix chain 'D' and resid 756 through 761 Processing helix chain 'D' and resid 762 through 765 Processing helix chain 'D' and resid 769 through 773 removed outlier: 3.502A pdb=" N LEU D 773 " --> pdb=" O TYR D 770 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 793 removed outlier: 3.727A pdb=" N ARG D 787 " --> pdb=" O ASP D 783 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS D 790 " --> pdb=" O HIS D 786 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N THR D 791 " --> pdb=" O ARG D 787 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 814 Processing helix chain 'D' and resid 815 through 819 removed outlier: 3.569A pdb=" N CYS D 819 " --> pdb=" O ILE D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 852 Processing helix chain 'D' and resid 894 through 902 removed outlier: 4.122A pdb=" N ASP D 902 " --> pdb=" O GLN D 899 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 915 Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 928 through 931 Processing helix chain 'D' and resid 932 through 940 Processing helix chain 'D' and resid 940 through 953 removed outlier: 3.666A pdb=" N LEU D 944 " --> pdb=" O ASN D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 965 Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 981 through 983 No H-bonds generated for 'chain 'D' and resid 981 through 983' Processing helix chain 'D' and resid 997 through 1002 removed outlier: 3.904A pdb=" N GLY D1001 " --> pdb=" O LEU D 997 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN D1002 " --> pdb=" O ALA D 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 997 through 1002' Processing helix chain 'D' and resid 1005 through 1018 Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 391 removed outlier: 6.944A pdb=" N ARG A 332 " --> pdb=" O GLU A 363 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL A 365 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 334 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU A 367 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL A 336 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N HIS A 333 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N LEU A 412 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL A 335 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU A 414 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N CYS A 337 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N CYS A 411 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLN A 448 " --> pdb=" O CYS A 411 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 413 " --> pdb=" O GLN A 448 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 525 through 530 removed outlier: 6.960A pdb=" N GLN A 585 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 558 " --> pdb=" O GLN A 585 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 587 " --> pdb=" O LEU A 556 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 708 through 709 Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 802 removed outlier: 6.533A pdb=" N THR A 776 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU A 801 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE A 778 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 741 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL A 779 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 743 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS A 822 " --> pdb=" O ILE A 889 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU A 891 " --> pdb=" O CYS A 822 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE A 824 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 986 through 991 removed outlier: 3.834A pdb=" N GLY A1023 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A1062 " --> pdb=" O CYS A1021 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N CYS A1021 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA8, first strand: chain 'B' and resid 387 through 391 removed outlier: 6.944A pdb=" N ARG B 332 " --> pdb=" O GLU B 363 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL B 365 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL B 334 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 367 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 336 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N HIS B 333 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LEU B 412 " --> pdb=" O HIS B 333 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B 335 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU B 414 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N CYS B 337 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N CYS B 411 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLN B 448 " --> pdb=" O CYS B 411 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL B 413 " --> pdb=" O GLN B 448 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 525 through 530 removed outlier: 6.960A pdb=" N GLN B 585 " --> pdb=" O ILE B 558 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE B 558 " --> pdb=" O GLN B 585 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE B 587 " --> pdb=" O LEU B 556 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 708 through 709 Processing sheet with id=AB2, first strand: chain 'B' and resid 798 through 802 removed outlier: 6.533A pdb=" N THR B 776 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU B 801 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE B 778 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 741 " --> pdb=" O ILE B 777 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL B 779 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL B 743 " --> pdb=" O VAL B 779 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS B 822 " --> pdb=" O ILE B 889 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU B 891 " --> pdb=" O CYS B 822 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE B 824 " --> pdb=" O GLU B 891 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 986 through 991 removed outlier: 3.834A pdb=" N GLY B1023 " --> pdb=" O TYR B1060 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B1062 " --> pdb=" O CYS B1021 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N CYS B1021 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 130 Processing sheet with id=AB5, first strand: chain 'C' and resid 387 through 391 removed outlier: 6.944A pdb=" N ARG C 332 " --> pdb=" O GLU C 363 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL C 365 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL C 334 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU C 367 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL C 336 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N HIS C 333 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LEU C 412 " --> pdb=" O HIS C 333 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL C 335 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU C 414 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N CYS C 337 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N CYS C 411 " --> pdb=" O ILE C 446 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLN C 448 " --> pdb=" O CYS C 411 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 413 " --> pdb=" O GLN C 448 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 525 through 530 removed outlier: 6.960A pdb=" N GLN C 585 " --> pdb=" O ILE C 558 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE C 558 " --> pdb=" O GLN C 585 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE C 587 " --> pdb=" O LEU C 556 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AB8, first strand: chain 'C' and resid 798 through 802 removed outlier: 6.533A pdb=" N THR C 776 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU C 801 " --> pdb=" O THR C 776 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE C 778 " --> pdb=" O LEU C 801 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL C 741 " --> pdb=" O ILE C 777 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL C 779 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL C 743 " --> pdb=" O VAL C 779 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS C 822 " --> pdb=" O ILE C 889 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N GLU C 891 " --> pdb=" O CYS C 822 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE C 824 " --> pdb=" O GLU C 891 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 986 through 991 removed outlier: 3.834A pdb=" N GLY C1023 " --> pdb=" O TYR C1060 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C1062 " --> pdb=" O CYS C1021 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N CYS C1021 " --> pdb=" O LEU C1062 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 128 through 130 Processing sheet with id=AC2, first strand: chain 'D' and resid 387 through 391 removed outlier: 6.944A pdb=" N ARG D 332 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N VAL D 365 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL D 334 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU D 367 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL D 336 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N HIS D 333 " --> pdb=" O ALA D 410 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N LEU D 412 " --> pdb=" O HIS D 333 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL D 335 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N LEU D 414 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N CYS D 337 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N CYS D 411 " --> pdb=" O ILE D 446 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLN D 448 " --> pdb=" O CYS D 411 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL D 413 " --> pdb=" O GLN D 448 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 525 through 530 removed outlier: 6.961A pdb=" N GLN D 585 " --> pdb=" O ILE D 558 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE D 558 " --> pdb=" O GLN D 585 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE D 587 " --> pdb=" O LEU D 556 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 708 through 709 Processing sheet with id=AC5, first strand: chain 'D' and resid 798 through 802 removed outlier: 6.533A pdb=" N THR D 776 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU D 801 " --> pdb=" O THR D 776 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE D 778 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 741 " --> pdb=" O ILE D 777 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL D 779 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL D 743 " --> pdb=" O VAL D 779 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS D 822 " --> pdb=" O ILE D 889 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU D 891 " --> pdb=" O CYS D 822 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE D 824 " --> pdb=" O GLU D 891 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 986 through 991 removed outlier: 3.833A pdb=" N GLY D1023 " --> pdb=" O TYR D1060 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU D1062 " --> pdb=" O CYS D1021 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N CYS D1021 " --> pdb=" O LEU D1062 " (cutoff:3.500A) 1424 hydrogen bonds defined for protein. 3852 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: 5.76 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4791 1.31 - 1.44: 7838 1.44 - 1.57: 15999 1.57 - 1.69: 0 1.69 - 1.82: 260 Bond restraints: 28888 Sorted by residual: bond pdb=" C ARG B 948 " pdb=" O ARG B 948 " ideal model delta sigma weight residual 1.237 1.178 0.058 1.19e-02 7.06e+03 2.42e+01 bond pdb=" C ARG C 948 " pdb=" O ARG C 948 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.19e-02 7.06e+03 2.36e+01 bond pdb=" C ARG A 948 " pdb=" O ARG A 948 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.19e-02 7.06e+03 2.35e+01 bond pdb=" C ARG D 948 " pdb=" O ARG D 948 " ideal model delta sigma weight residual 1.237 1.180 0.057 1.19e-02 7.06e+03 2.30e+01 bond pdb=" C PHE A 492 " pdb=" O PHE A 492 " ideal model delta sigma weight residual 1.236 1.182 0.055 1.18e-02 7.18e+03 2.16e+01 ... (remaining 28883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 28579 1.78 - 3.56: 8962 3.56 - 5.34: 1505 5.34 - 7.12: 218 7.12 - 8.90: 36 Bond angle restraints: 39300 Sorted by residual: angle pdb=" N LEU C 20 " pdb=" CA LEU C 20 " pdb=" C LEU C 20 " ideal model delta sigma weight residual 111.82 103.67 8.15 1.16e+00 7.43e-01 4.93e+01 angle pdb=" N LEU A 20 " pdb=" CA LEU A 20 " pdb=" C LEU A 20 " ideal model delta sigma weight residual 111.82 103.70 8.12 1.16e+00 7.43e-01 4.89e+01 angle pdb=" N LEU D 20 " pdb=" CA LEU D 20 " pdb=" C LEU D 20 " ideal model delta sigma weight residual 111.82 103.70 8.12 1.16e+00 7.43e-01 4.89e+01 angle pdb=" N LEU B 20 " pdb=" CA LEU B 20 " pdb=" C LEU B 20 " ideal model delta sigma weight residual 111.82 103.72 8.10 1.16e+00 7.43e-01 4.88e+01 angle pdb=" N SER D 18 " pdb=" CA SER D 18 " pdb=" C SER D 18 " ideal model delta sigma weight residual 111.71 104.60 7.11 1.15e+00 7.56e-01 3.82e+01 ... (remaining 39295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 15782 17.71 - 35.41: 916 35.41 - 53.12: 126 53.12 - 70.83: 60 70.83 - 88.53: 40 Dihedral angle restraints: 16924 sinusoidal: 6432 harmonic: 10492 Sorted by residual: dihedral pdb=" CA GLY C 370 " pdb=" C GLY C 370 " pdb=" N LEU C 371 " pdb=" CA LEU C 371 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLY D 370 " pdb=" C GLY D 370 " pdb=" N LEU D 371 " pdb=" CA LEU D 371 " ideal model delta harmonic sigma weight residual 180.00 152.24 27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA GLY A 370 " pdb=" C GLY A 370 " pdb=" N LEU A 371 " pdb=" CA LEU A 371 " ideal model delta harmonic sigma weight residual 180.00 152.24 27.76 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 16921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3217 0.097 - 0.194: 1091 0.194 - 0.291: 160 0.291 - 0.388: 20 0.388 - 0.485: 8 Chirality restraints: 4496 Sorted by residual: chirality pdb=" CA LEU B 458 " pdb=" N LEU B 458 " pdb=" C LEU B 458 " pdb=" CB LEU B 458 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" CA LEU D 458 " pdb=" N LEU D 458 " pdb=" C LEU D 458 " pdb=" CB LEU D 458 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" CA LEU C 458 " pdb=" N LEU C 458 " pdb=" C LEU C 458 " pdb=" CB LEU C 458 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.86e+00 ... (remaining 4493 not shown) Planarity restraints: 4968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 167 " -0.196 2.00e-02 2.50e+03 9.92e-02 2.46e+02 pdb=" CG TRP C 167 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 167 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TRP C 167 " 0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP C 167 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 TRP C 167 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP C 167 " 0.133 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 167 " -0.120 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 167 " 0.055 2.00e-02 2.50e+03 pdb=" CH2 TRP C 167 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 167 " 0.196 2.00e-02 2.50e+03 9.92e-02 2.46e+02 pdb=" CG TRP D 167 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP D 167 " -0.079 2.00e-02 2.50e+03 pdb=" CD2 TRP D 167 " -0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP D 167 " -0.064 2.00e-02 2.50e+03 pdb=" CE2 TRP D 167 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP D 167 " -0.133 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 167 " 0.120 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 167 " -0.055 2.00e-02 2.50e+03 pdb=" CH2 TRP D 167 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 167 " -0.196 2.00e-02 2.50e+03 9.92e-02 2.46e+02 pdb=" CG TRP B 167 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 167 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TRP B 167 " 0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP B 167 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 TRP B 167 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP B 167 " 0.133 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 167 " -0.120 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 167 " 0.054 2.00e-02 2.50e+03 pdb=" CH2 TRP B 167 " -0.097 2.00e-02 2.50e+03 ... (remaining 4965 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.61: 200 2.61 - 3.24: 29787 3.24 - 3.88: 55661 3.88 - 4.51: 76964 4.51 - 5.14: 123096 Nonbonded interactions: 285708 Sorted by model distance: nonbonded pdb=" OE2 GLU B 363 " pdb="MG MG B1101 " model vdw 1.982 2.170 nonbonded pdb=" OE2 GLU A 363 " pdb="MG MG A1106 " model vdw 1.983 2.170 nonbonded pdb=" OE2 GLU C 363 " pdb="MG MG C1101 " model vdw 1.983 2.170 nonbonded pdb=" OE2 GLU D 363 " pdb="MG MG D1101 " model vdw 1.983 2.170 nonbonded pdb=" OE2 GLU A 328 " pdb="MG MG A1106 " model vdw 1.985 2.170 ... (remaining 285703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 1065) selection = (chain 'B' and resid 14 through 1065) selection = (chain 'C' and resid 14 through 1065) selection = (chain 'D' and resid 14 through 1065) } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.180 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 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 : 0.013 0.058 28888 Z= 0.803 Angle : 1.718 8.898 39300 Z= 1.149 Chirality : 0.094 0.485 4496 Planarity : 0.012 0.099 4968 Dihedral : 13.372 88.532 10140 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.93 % Allowed : 4.51 % Favored : 94.56 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.13), residues: 3548 helix: -1.42 (0.10), residues: 1764 sheet: 0.09 (0.25), residues: 388 loop : -0.42 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 982 TYR 0.117 0.016 TYR A 938 PHE 0.072 0.011 PHE C 500 TRP 0.196 0.022 TRP D 167 HIS 0.010 0.003 HIS B 368 Details of bonding type rmsd covalent geometry : bond 0.01254 (28888) covalent geometry : angle 1.71811 (39300) hydrogen bonds : bond 0.18219 ( 1424) hydrogen bonds : angle 7.65109 ( 3852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.9359 (mtp) cc_final: 0.9154 (mtp) REVERT: B 204 MET cc_start: 0.9372 (mtp) cc_final: 0.9154 (mtp) REVERT: C 204 MET cc_start: 0.9370 (mtp) cc_final: 0.9146 (mtp) REVERT: D 204 MET cc_start: 0.9373 (mtp) cc_final: 0.9154 (mtp) outliers start: 28 outliers final: 14 residues processed: 185 average time/residue: 0.1641 time to fit residues: 49.6101 Evaluate side-chains 111 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 1037 PRO Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 895 ASP Chi-restraints excluded: chain B residue 1037 PRO Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 895 ASP Chi-restraints excluded: chain C residue 1037 PRO Chi-restraints excluded: chain D residue 495 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 895 ASP Chi-restraints excluded: chain D residue 1037 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN A 424 GLN A 609 ASN B 398 ASN B 424 GLN B 609 ASN C 398 ASN C 424 GLN C 609 ASN D 398 ASN D 424 GLN D 609 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.071284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.053241 restraints weight = 68127.413| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 3.04 r_work: 0.2500 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28888 Z= 0.137 Angle : 0.586 8.872 39300 Z= 0.305 Chirality : 0.043 0.165 4496 Planarity : 0.004 0.037 4968 Dihedral : 5.548 67.877 3876 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.70 % Allowed : 5.01 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.14), residues: 3548 helix: 0.35 (0.12), residues: 1824 sheet: 0.01 (0.24), residues: 416 loop : 0.22 (0.18), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1015 TYR 0.013 0.001 TYR A1025 PHE 0.017 0.001 PHE A 107 TRP 0.018 0.002 TRP A 514 HIS 0.003 0.001 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00296 (28888) covalent geometry : angle 0.58569 (39300) hydrogen bonds : bond 0.05042 ( 1424) hydrogen bonds : angle 4.96636 ( 3852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.963 Fit side-chains REVERT: A 542 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8561 (mp0) REVERT: A 832 MET cc_start: 0.8096 (ppp) cc_final: 0.7756 (ppp) REVERT: B 257 ASN cc_start: 0.8231 (t0) cc_final: 0.7813 (t0) REVERT: B 542 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8546 (mp0) REVERT: B 832 MET cc_start: 0.8111 (ppp) cc_final: 0.7787 (ppp) REVERT: C 257 ASN cc_start: 0.8247 (t0) cc_final: 0.7833 (t0) REVERT: C 542 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: C 832 MET cc_start: 0.8129 (ppp) cc_final: 0.7797 (ppp) REVERT: D 257 ASN cc_start: 0.8245 (t0) cc_final: 0.7827 (t0) REVERT: D 542 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: D 832 MET cc_start: 0.8130 (ppp) cc_final: 0.7815 (ppp) outliers start: 21 outliers final: 0 residues processed: 132 average time/residue: 0.1364 time to fit residues: 32.2331 Evaluate side-chains 103 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 99 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain D residue 542 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 259 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 354 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 319 optimal weight: 9.9990 chunk 271 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.070260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.052041 restraints weight = 68445.451| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 3.03 r_work: 0.2477 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 28888 Z= 0.155 Angle : 0.521 6.829 39300 Z= 0.270 Chirality : 0.042 0.170 4496 Planarity : 0.003 0.034 4968 Dihedral : 4.778 60.228 3848 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.46 % Allowed : 6.93 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.15), residues: 3548 helix: 0.92 (0.13), residues: 1808 sheet: -0.01 (0.24), residues: 428 loop : 0.49 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1041 TYR 0.011 0.001 TYR A1025 PHE 0.014 0.001 PHE B 107 TRP 0.017 0.001 TRP D 514 HIS 0.002 0.001 HIS A 453 Details of bonding type rmsd covalent geometry : bond 0.00353 (28888) covalent geometry : angle 0.52113 (39300) hydrogen bonds : bond 0.04489 ( 1424) hydrogen bonds : angle 4.52833 ( 3852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.002 Fit side-chains REVERT: A 1015 ARG cc_start: 0.9096 (mtp85) cc_final: 0.8817 (mtt-85) REVERT: B 41 LEU cc_start: 0.8181 (mm) cc_final: 0.7933 (mt) REVERT: B 1015 ARG cc_start: 0.9160 (mtp85) cc_final: 0.8895 (mtt-85) REVERT: C 41 LEU cc_start: 0.8153 (mm) cc_final: 0.7898 (mt) REVERT: C 1015 ARG cc_start: 0.9162 (mtp85) cc_final: 0.8892 (mtt-85) REVERT: D 41 LEU cc_start: 0.8202 (mm) cc_final: 0.7948 (mt) REVERT: D 1015 ARG cc_start: 0.9146 (mtp85) cc_final: 0.8885 (mtt-85) outliers start: 14 outliers final: 5 residues processed: 118 average time/residue: 0.1637 time to fit residues: 32.9382 Evaluate side-chains 107 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain D residue 1020 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 246 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 328 optimal weight: 6.9990 chunk 251 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 194 optimal weight: 0.6980 chunk 196 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 51 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.071670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.053770 restraints weight = 67875.149| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.00 r_work: 0.2523 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 28888 Z= 0.102 Angle : 0.466 6.662 39300 Z= 0.238 Chirality : 0.040 0.139 4496 Planarity : 0.003 0.035 4968 Dihedral : 4.393 52.317 3848 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.16 % Allowed : 7.16 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.15), residues: 3548 helix: 1.12 (0.13), residues: 1824 sheet: 0.19 (0.25), residues: 428 loop : 0.58 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1041 TYR 0.009 0.001 TYR A1025 PHE 0.011 0.001 PHE B 107 TRP 0.011 0.001 TRP D 514 HIS 0.002 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00217 (28888) covalent geometry : angle 0.46644 (39300) hydrogen bonds : bond 0.03818 ( 1424) hydrogen bonds : angle 4.31282 ( 3852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8646 (mp0) REVERT: A 1015 ARG cc_start: 0.9104 (mtp85) cc_final: 0.8845 (mtt-85) REVERT: B 542 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8655 (mp0) REVERT: B 1015 ARG cc_start: 0.9137 (mtp85) cc_final: 0.8912 (mtt-85) REVERT: C 313 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8592 (tm-30) REVERT: C 542 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8653 (mp0) REVERT: C 1015 ARG cc_start: 0.9133 (mtp85) cc_final: 0.8900 (mtt-85) REVERT: D 542 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8638 (mp0) REVERT: D 1015 ARG cc_start: 0.9135 (mtp85) cc_final: 0.8909 (mtt-85) outliers start: 35 outliers final: 8 residues processed: 145 average time/residue: 0.1436 time to fit residues: 35.7505 Evaluate side-chains 120 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 1020 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 41 optimal weight: 10.0000 chunk 319 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 271 optimal weight: 8.9990 chunk 116 optimal weight: 0.6980 chunk 260 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.072206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.054281 restraints weight = 67442.558| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.00 r_work: 0.2539 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 28888 Z= 0.093 Angle : 0.468 8.011 39300 Z= 0.233 Chirality : 0.040 0.159 4496 Planarity : 0.003 0.035 4968 Dihedral : 4.116 44.647 3848 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.76 % Allowed : 8.02 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.15), residues: 3548 helix: 1.35 (0.13), residues: 1808 sheet: 0.25 (0.25), residues: 464 loop : 0.68 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 808 TYR 0.009 0.001 TYR A 17 PHE 0.011 0.001 PHE A 107 TRP 0.011 0.001 TRP B 514 HIS 0.001 0.000 HIS B 333 Details of bonding type rmsd covalent geometry : bond 0.00196 (28888) covalent geometry : angle 0.46765 (39300) hydrogen bonds : bond 0.03541 ( 1424) hydrogen bonds : angle 4.16301 ( 3852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8670 (mp0) REVERT: A 1015 ARG cc_start: 0.9122 (mtp85) cc_final: 0.8874 (mtt-85) REVERT: B 257 ASN cc_start: 0.8374 (t0) cc_final: 0.8038 (p0) REVERT: B 313 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8600 (tm-30) REVERT: B 542 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8691 (mp0) REVERT: B 1015 ARG cc_start: 0.9148 (mtp85) cc_final: 0.8917 (mtt-85) REVERT: C 257 ASN cc_start: 0.8364 (t0) cc_final: 0.8051 (p0) REVERT: C 313 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8669 (tm-30) REVERT: C 542 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8700 (mp0) REVERT: C 1015 ARG cc_start: 0.9127 (mtp85) cc_final: 0.8887 (mtt-85) REVERT: D 257 ASN cc_start: 0.8395 (t0) cc_final: 0.8055 (p0) REVERT: D 313 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8602 (tm-30) REVERT: D 542 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8673 (mp0) REVERT: D 1015 ARG cc_start: 0.9139 (mtp85) cc_final: 0.8912 (mtt-85) outliers start: 23 outliers final: 4 residues processed: 139 average time/residue: 0.1598 time to fit residues: 36.5781 Evaluate side-chains 126 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 1020 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 230 optimal weight: 0.0020 chunk 8 optimal weight: 9.9990 chunk 282 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 336 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 277 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.072366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.054394 restraints weight = 67452.987| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.03 r_work: 0.2540 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 28888 Z= 0.091 Angle : 0.452 6.708 39300 Z= 0.226 Chirality : 0.039 0.148 4496 Planarity : 0.003 0.036 4968 Dihedral : 3.905 35.567 3848 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.90 % Allowed : 8.36 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.15), residues: 3548 helix: 1.38 (0.13), residues: 1840 sheet: 0.39 (0.26), residues: 464 loop : 0.77 (0.19), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 808 TYR 0.008 0.001 TYR D 117 PHE 0.011 0.001 PHE D 107 TRP 0.012 0.001 TRP D 42 HIS 0.002 0.000 HIS D 333 Details of bonding type rmsd covalent geometry : bond 0.00196 (28888) covalent geometry : angle 0.45165 (39300) hydrogen bonds : bond 0.03411 ( 1424) hydrogen bonds : angle 4.07539 ( 3852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8730 (mp0) REVERT: A 1015 ARG cc_start: 0.9097 (mtp85) cc_final: 0.8880 (mtt-85) REVERT: B 257 ASN cc_start: 0.8359 (t0) cc_final: 0.8058 (p0) REVERT: B 313 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8626 (tm-30) REVERT: B 542 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8748 (mp0) REVERT: B 1015 ARG cc_start: 0.9121 (mtp85) cc_final: 0.8868 (mtt-85) REVERT: C 154 PHE cc_start: 0.8958 (m-80) cc_final: 0.8693 (m-80) REVERT: C 257 ASN cc_start: 0.8373 (t0) cc_final: 0.8100 (p0) REVERT: C 313 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8694 (tm-30) REVERT: C 542 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8726 (mp0) REVERT: C 1015 ARG cc_start: 0.9129 (mtp85) cc_final: 0.8904 (mtt-85) REVERT: D 154 PHE cc_start: 0.8970 (m-80) cc_final: 0.8708 (m-80) REVERT: D 257 ASN cc_start: 0.8375 (t0) cc_final: 0.8078 (p0) REVERT: D 313 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8627 (tm-30) REVERT: D 542 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8706 (mp0) REVERT: D 1015 ARG cc_start: 0.9120 (mtp85) cc_final: 0.8868 (mtt-85) outliers start: 27 outliers final: 8 residues processed: 135 average time/residue: 0.1544 time to fit residues: 34.5276 Evaluate side-chains 133 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 1020 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 322 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 178 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 235 optimal weight: 7.9990 chunk 326 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.072318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.053961 restraints weight = 67326.964| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 3.06 r_work: 0.2529 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 28888 Z= 0.099 Angle : 0.450 6.989 39300 Z= 0.226 Chirality : 0.039 0.140 4496 Planarity : 0.003 0.036 4968 Dihedral : 3.792 27.347 3848 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.46 % Allowed : 8.82 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.15), residues: 3548 helix: 1.50 (0.13), residues: 1816 sheet: 0.39 (0.26), residues: 464 loop : 0.79 (0.19), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 808 TYR 0.009 0.001 TYR D 117 PHE 0.012 0.001 PHE A 107 TRP 0.010 0.001 TRP B 514 HIS 0.002 0.001 HIS D 333 Details of bonding type rmsd covalent geometry : bond 0.00221 (28888) covalent geometry : angle 0.45027 (39300) hydrogen bonds : bond 0.03435 ( 1424) hydrogen bonds : angle 4.04739 ( 3852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8790 (mt-10) REVERT: A 1015 ARG cc_start: 0.9098 (mtp85) cc_final: 0.8877 (mtt-85) REVERT: B 313 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8644 (tm-30) REVERT: B 542 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8816 (mt-10) REVERT: B 1015 ARG cc_start: 0.9141 (mtp85) cc_final: 0.8907 (mtt-85) REVERT: C 154 PHE cc_start: 0.8970 (m-80) cc_final: 0.8697 (m-80) REVERT: C 257 ASN cc_start: 0.8360 (t0) cc_final: 0.8101 (p0) REVERT: C 313 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8713 (tm-30) REVERT: C 542 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8756 (mp0) REVERT: C 1015 ARG cc_start: 0.9145 (mtp85) cc_final: 0.8905 (mtt-85) REVERT: D 154 PHE cc_start: 0.8980 (m-80) cc_final: 0.8708 (m-80) REVERT: D 313 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8645 (tm-30) REVERT: D 542 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8798 (mt-10) REVERT: D 1015 ARG cc_start: 0.9137 (mtp85) cc_final: 0.8904 (mtt-85) outliers start: 14 outliers final: 5 residues processed: 128 average time/residue: 0.1496 time to fit residues: 32.4774 Evaluate side-chains 127 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 1020 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 15 optimal weight: 0.9980 chunk 267 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 299 optimal weight: 0.9990 chunk 259 optimal weight: 30.0000 chunk 137 optimal weight: 10.0000 chunk 296 optimal weight: 5.9990 chunk 234 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 352 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.072772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.054739 restraints weight = 67594.780| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.04 r_work: 0.2553 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 28888 Z= 0.088 Angle : 0.439 7.056 39300 Z= 0.219 Chirality : 0.039 0.138 4496 Planarity : 0.003 0.036 4968 Dihedral : 3.661 19.949 3848 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.73 % Allowed : 8.75 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.15), residues: 3548 helix: 1.58 (0.13), residues: 1816 sheet: 0.43 (0.26), residues: 464 loop : 0.79 (0.19), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 520 TYR 0.008 0.001 TYR D 117 PHE 0.010 0.001 PHE D 107 TRP 0.010 0.001 TRP C 514 HIS 0.002 0.000 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00188 (28888) covalent geometry : angle 0.43893 (39300) hydrogen bonds : bond 0.03247 ( 1424) hydrogen bonds : angle 3.97701 ( 3852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 542 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8819 (mt-10) REVERT: A 1015 ARG cc_start: 0.9098 (mtp85) cc_final: 0.8880 (mtt-85) REVERT: B 257 ASN cc_start: 0.8330 (t0) cc_final: 0.8091 (p0) REVERT: B 313 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8661 (tm-30) REVERT: B 542 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8817 (mt-10) REVERT: B 1015 ARG cc_start: 0.9134 (mtp85) cc_final: 0.8912 (mtt-85) REVERT: C 154 PHE cc_start: 0.8955 (m-80) cc_final: 0.8676 (m-80) REVERT: C 257 ASN cc_start: 0.8310 (t0) cc_final: 0.8105 (p0) REVERT: C 313 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8692 (tm-30) REVERT: C 542 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8815 (mt-10) REVERT: C 1015 ARG cc_start: 0.9141 (mtp85) cc_final: 0.8909 (mtt-85) REVERT: D 154 PHE cc_start: 0.8964 (m-80) cc_final: 0.8685 (m-80) REVERT: D 257 ASN cc_start: 0.8342 (t0) cc_final: 0.8104 (p0) REVERT: D 313 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8666 (tm-30) REVERT: D 542 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8794 (mt-10) REVERT: D 1015 ARG cc_start: 0.9132 (mtp85) cc_final: 0.8910 (mtt-85) outliers start: 22 outliers final: 13 residues processed: 137 average time/residue: 0.1384 time to fit residues: 32.2658 Evaluate side-chains 140 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 1020 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 297 optimal weight: 4.9990 chunk 287 optimal weight: 0.0870 chunk 119 optimal weight: 4.9990 chunk 339 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 329 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 chunk 288 optimal weight: 0.8980 chunk 315 optimal weight: 6.9990 chunk 284 optimal weight: 0.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 HIS B 607 HIS C 607 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.071692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.053582 restraints weight = 67742.211| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 3.02 r_work: 0.2526 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28888 Z= 0.117 Angle : 0.466 10.205 39300 Z= 0.231 Chirality : 0.040 0.151 4496 Planarity : 0.003 0.035 4968 Dihedral : 3.700 17.973 3848 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.93 % Allowed : 8.85 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.15), residues: 3548 helix: 1.57 (0.13), residues: 1812 sheet: 0.42 (0.26), residues: 464 loop : 0.74 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 948 TYR 0.009 0.001 TYR D 117 PHE 0.012 0.001 PHE A 107 TRP 0.010 0.001 TRP B 514 HIS 0.003 0.001 HIS A 333 Details of bonding type rmsd covalent geometry : bond 0.00272 (28888) covalent geometry : angle 0.46601 (39300) hydrogen bonds : bond 0.03485 ( 1424) hydrogen bonds : angle 4.03398 ( 3852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 542 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8820 (mt-10) REVERT: A 1015 ARG cc_start: 0.9109 (mtp85) cc_final: 0.8876 (mtt-85) REVERT: B 257 ASN cc_start: 0.8360 (t0) cc_final: 0.8090 (p0) REVERT: B 313 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8673 (tm-30) REVERT: B 542 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8811 (mt-10) REVERT: B 1015 ARG cc_start: 0.9132 (mtp85) cc_final: 0.8898 (mtt-85) REVERT: C 313 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8700 (tm-30) REVERT: C 542 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8804 (mt-10) REVERT: C 1015 ARG cc_start: 0.9141 (mtp85) cc_final: 0.8909 (mtt-85) REVERT: D 257 ASN cc_start: 0.8369 (t0) cc_final: 0.8104 (p0) REVERT: D 313 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8679 (tm-30) REVERT: D 542 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8790 (mt-10) REVERT: D 1015 ARG cc_start: 0.9134 (mtp85) cc_final: 0.8900 (mtt-85) outliers start: 28 outliers final: 14 residues processed: 141 average time/residue: 0.1323 time to fit residues: 32.0387 Evaluate side-chains 136 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 1020 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 281 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 263 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 311 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 257 ASN D 607 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.071879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.053797 restraints weight = 67561.521| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 3.02 r_work: 0.2528 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28888 Z= 0.104 Angle : 0.463 8.234 39300 Z= 0.231 Chirality : 0.039 0.143 4496 Planarity : 0.003 0.035 4968 Dihedral : 3.736 19.224 3848 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.80 % Allowed : 9.12 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.15), residues: 3548 helix: 1.58 (0.13), residues: 1812 sheet: 0.41 (0.26), residues: 464 loop : 0.71 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 808 TYR 0.014 0.001 TYR C 17 PHE 0.011 0.001 PHE A 107 TRP 0.011 0.001 TRP B 514 HIS 0.002 0.001 HIS D 333 Details of bonding type rmsd covalent geometry : bond 0.00236 (28888) covalent geometry : angle 0.46287 (39300) hydrogen bonds : bond 0.03413 ( 1424) hydrogen bonds : angle 4.00787 ( 3852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 542 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8827 (mt-10) REVERT: A 1015 ARG cc_start: 0.9107 (mtp85) cc_final: 0.8871 (mtt-85) REVERT: B 313 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8642 (tm-30) REVERT: B 542 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8816 (mt-10) REVERT: B 1015 ARG cc_start: 0.9127 (mtp85) cc_final: 0.8891 (mtt-85) REVERT: C 313 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8665 (tm-30) REVERT: C 542 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8808 (mt-10) REVERT: D 313 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8638 (tm-30) REVERT: D 542 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8786 (mt-10) REVERT: D 1015 ARG cc_start: 0.9116 (mtp85) cc_final: 0.8880 (mtt-85) outliers start: 24 outliers final: 17 residues processed: 133 average time/residue: 0.1396 time to fit residues: 31.6605 Evaluate side-chains 137 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 542 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 542 GLU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 542 GLU Chi-restraints excluded: chain C residue 1020 LEU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 542 GLU Chi-restraints excluded: chain D residue 1020 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 104 optimal weight: 1.9990 chunk 300 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 309 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 243 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.071719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.053500 restraints weight = 67731.939| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 3.03 r_work: 0.2514 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28888 Z= 0.112 Angle : 0.463 8.185 39300 Z= 0.231 Chirality : 0.040 0.147 4496 Planarity : 0.003 0.035 4968 Dihedral : 3.749 21.086 3848 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.83 % Allowed : 9.25 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.15), residues: 3548 helix: 1.57 (0.13), residues: 1812 sheet: 0.36 (0.26), residues: 464 loop : 0.67 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1015 TYR 0.013 0.001 TYR C 17 PHE 0.012 0.001 PHE B 107 TRP 0.011 0.001 TRP B 514 HIS 0.002 0.001 HIS D 333 Details of bonding type rmsd covalent geometry : bond 0.00257 (28888) covalent geometry : angle 0.46270 (39300) hydrogen bonds : bond 0.03487 ( 1424) hydrogen bonds : angle 4.00735 ( 3852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3801.89 seconds wall clock time: 66 minutes 40.80 seconds (4000.80 seconds total)