Starting phenix.real_space_refine on Tue May 20 01:29:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9are_43779/05_2025/9are_43779.cif Found real_map, /net/cci-nas-00/data/ceres_data/9are_43779/05_2025/9are_43779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9are_43779/05_2025/9are_43779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9are_43779/05_2025/9are_43779.map" model { file = "/net/cci-nas-00/data/ceres_data/9are_43779/05_2025/9are_43779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9are_43779/05_2025/9are_43779.cif" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 174 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 12190 2.51 5 N 3414 2.21 5 O 3538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19222 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 4880 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1458 Unresolved non-hydrogen angles: 1832 Unresolved non-hydrogen dihedrals: 1184 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'GLN:plan1': 25, 'ASP:plan': 29, 'TYR:plan': 11, 'ASN:plan1': 29, 'TRP:plan': 1, 'HIS:plan': 13, 'PHE:plan': 9, 'GLU:plan': 46, 'ARG:plan': 36} Unresolved non-hydrogen planarities: 843 Chain: "B" Number of atoms: 4716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 4716 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 434} Link IDs: {'PTRANS': 29, 'TRANS': 759} Chain breaks: 2 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1590 Unresolved non-hydrogen angles: 2028 Unresolved non-hydrogen dihedrals: 1331 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 22, 'ASP:plan': 45, 'TYR:plan': 20, 'ASN:plan1': 24, 'TRP:plan': 7, 'HIS:plan': 9, 'PHE:plan': 19, 'GLU:plan': 45, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 932 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: C, D Time building chain proxies: 17.68, per 1000 atoms: 0.92 Number of scatterers: 19222 At special positions: 0 Unit cell: (150.675, 133.455, 181.671, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 3538 8.00 N 3414 7.00 C 12190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.02 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.02 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.88 Conformation dependent library (CDL) restraints added in 3.1 seconds 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5920 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 28 sheets defined 44.2% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.616A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 103 through 112 removed outlier: 4.069A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 158 removed outlier: 3.876A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 removed outlier: 4.011A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.653A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 261 removed outlier: 4.064A pdb=" N LEU A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 296 removed outlier: 3.804A pdb=" N ILE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 527 removed outlier: 4.125A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.622A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.845A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 655 removed outlier: 3.617A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 694 Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'A' and resid 733 through 743 Processing helix chain 'A' and resid 766 through 780 removed outlier: 4.097A pdb=" N SER A 773 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 822 through 840 removed outlier: 3.929A pdb=" N ALA A 826 " --> pdb=" O GLY A 822 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 56 removed outlier: 3.531A pdb=" N ASP B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 53 " --> pdb=" O ALA B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 4.015A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 removed outlier: 4.320A pdb=" N ALA B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 176 through 192 removed outlier: 3.888A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.642A pdb=" N LYS B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 Processing helix chain 'B' and resid 288 through 311 Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.989A pdb=" N ARG B 328 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR B 330 " --> pdb=" O LYS B 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 330' Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.621A pdb=" N ASN B 336 " --> pdb=" O SER B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.826A pdb=" N SER B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 516 through 523 Processing helix chain 'B' and resid 548 through 552 Processing helix chain 'B' and resid 555 through 581 Processing helix chain 'B' and resid 601 through 615 removed outlier: 3.570A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 646 Processing helix chain 'B' and resid 649 through 654 Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.557A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 713 through 724 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 771 through 787 removed outlier: 4.437A pdb=" N GLN B 775 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.813A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 844 removed outlier: 4.053A pdb=" N MET B 818 " --> pdb=" O ASP B 814 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 821 " --> pdb=" O ASN B 817 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N MET B 824 " --> pdb=" O GLY B 820 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP B 844 " --> pdb=" O HIS B 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 50 removed outlier: 3.616A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 Processing helix chain 'C' and resid 103 through 112 removed outlier: 4.068A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 158 removed outlier: 3.876A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 187 removed outlier: 4.012A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.653A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 256 through 261 removed outlier: 4.063A pdb=" N LEU C 259 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.804A pdb=" N ILE C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 527 removed outlier: 4.125A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.622A pdb=" N VAL C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 removed outlier: 3.845A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 655 removed outlier: 3.616A pdb=" N GLY C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 695 Processing helix chain 'C' and resid 696 through 698 No H-bonds generated for 'chain 'C' and resid 696 through 698' Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 713 through 723 Processing helix chain 'C' and resid 733 through 743 Processing helix chain 'C' and resid 766 through 780 removed outlier: 4.097A pdb=" N SER C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 Processing helix chain 'C' and resid 812 through 822 Processing helix chain 'C' and resid 822 through 840 removed outlier: 3.929A pdb=" N ALA C 826 " --> pdb=" O GLY C 822 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.531A pdb=" N ASP D 52 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 53 " --> pdb=" O ALA D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 4.015A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 removed outlier: 4.320A pdb=" N ALA D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 176 through 192 removed outlier: 3.888A pdb=" N ASN D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.642A pdb=" N LYS D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 Processing helix chain 'D' and resid 288 through 311 Processing helix chain 'D' and resid 325 through 330 removed outlier: 3.989A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D 329 " --> pdb=" O GLU D 326 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR D 330 " --> pdb=" O LYS D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 330' Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.622A pdb=" N ASN D 336 " --> pdb=" O SER D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 473 removed outlier: 3.826A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 473 " --> pdb=" O SER D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 503 Processing helix chain 'D' and resid 516 through 523 Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 555 through 581 Processing helix chain 'D' and resid 601 through 615 removed outlier: 3.569A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 646 Processing helix chain 'D' and resid 649 through 654 Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.557A pdb=" N ASN D 698 " --> pdb=" O ASN D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 713 through 724 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 752 through 754 No H-bonds generated for 'chain 'D' and resid 752 through 754' Processing helix chain 'D' and resid 771 through 787 removed outlier: 4.437A pdb=" N GLN D 775 " --> pdb=" O GLY D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.813A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 844 removed outlier: 4.053A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 821 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N MET D 824 " --> pdb=" O GLY D 820 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 825 " --> pdb=" O VAL D 821 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP D 844 " --> pdb=" O HIS D 840 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65 removed outlier: 3.767A pdb=" N VAL A 65 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 7.103A pdb=" N ILE A 163 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 219 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 268 removed outlier: 3.576A pdb=" N MET A 354 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 478 removed outlier: 7.003A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 412 removed outlier: 3.556A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 528 through 529 removed outlier: 3.642A pdb=" N GLU A 528 " --> pdb=" O MET A 762 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 7.019A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 73 removed outlier: 6.750A pdb=" N GLY B 36 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL B 97 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA B 38 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N PHE B 99 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE B 40 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASP B 101 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 42 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LEU B 124 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE B 126 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE B 99 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 128 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP B 101 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 144 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 203 removed outlier: 8.124A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 168 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU B 229 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER B 279 " --> pdb=" O ILE B 365 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 476 through 480 removed outlier: 3.552A pdb=" N ASP B 524 " --> pdb=" O ILE B 766 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 418 through 420 removed outlier: 3.512A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 490 removed outlier: 4.078A pdb=" N ILE B 490 " --> pdb=" O THR B 493 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 729 through 732 removed outlier: 3.934A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 729 through 732 removed outlier: 3.934A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR B 532 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER B 759 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 62 through 65 removed outlier: 3.767A pdb=" N VAL C 65 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 197 removed outlier: 7.103A pdb=" N ILE C 163 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 219 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 267 through 268 removed outlier: 3.576A pdb=" N MET C 354 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 473 through 478 removed outlier: 7.003A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.556A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 528 through 529 removed outlier: 3.642A pdb=" N GLU C 528 " --> pdb=" O MET C 762 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 682 removed outlier: 7.019A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 67 through 73 removed outlier: 6.751A pdb=" N GLY D 36 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N VAL D 97 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA D 38 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N PHE D 99 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE D 40 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP D 101 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL D 42 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LEU D 124 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE D 126 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N PHE D 99 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY D 128 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP D 101 " --> pdb=" O GLY D 128 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 144 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 198 through 203 removed outlier: 8.124A pdb=" N PHE D 169 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N LEU D 203 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE D 168 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU D 229 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER D 170 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N TYR D 231 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 10.006A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER D 279 " --> pdb=" O ILE D 365 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 476 through 480 removed outlier: 3.551A pdb=" N ASP D 524 " --> pdb=" O ILE D 766 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 418 through 420 removed outlier: 3.511A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 489 through 490 removed outlier: 4.078A pdb=" N ILE D 490 " --> pdb=" O THR D 493 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 729 through 732 removed outlier: 3.934A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 729 through 732 removed outlier: 3.934A pdb=" N TYR D 731 " --> pdb=" O SER D 535 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER D 535 " --> pdb=" O TYR D 731 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR D 532 " --> pdb=" O SER D 759 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER D 759 " --> pdb=" O THR D 532 " (cutoff:3.500A) 1059 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.21 Time building geometry restraints manager: 5.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 56 1.21 - 1.36: 6669 1.36 - 1.52: 5633 1.52 - 1.67: 7032 1.67 - 1.82: 132 Bond restraints: 19522 Sorted by residual: bond pdb=" C LYS A 534 " pdb=" O LYS A 534 " ideal model delta sigma weight residual 1.235 1.060 0.175 1.26e-02 6.30e+03 1.93e+02 bond pdb=" C LYS C 534 " pdb=" O LYS C 534 " ideal model delta sigma weight residual 1.235 1.061 0.175 1.26e-02 6.30e+03 1.92e+02 bond pdb=" C PRO C 532 " pdb=" O PRO C 532 " ideal model delta sigma weight residual 1.233 1.076 0.157 1.24e-02 6.50e+03 1.61e+02 bond pdb=" C PRO A 532 " pdb=" O PRO A 532 " ideal model delta sigma weight residual 1.233 1.076 0.157 1.24e-02 6.50e+03 1.60e+02 bond pdb=" C PHE A 533 " pdb=" O PHE A 533 " ideal model delta sigma weight residual 1.236 1.066 0.170 1.39e-02 5.18e+03 1.50e+02 ... (remaining 19517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.52: 26836 6.52 - 13.03: 74 13.03 - 19.55: 2 19.55 - 26.07: 0 26.07 - 32.58: 2 Bond angle restraints: 26914 Sorted by residual: angle pdb=" CB MET C 762 " pdb=" CG MET C 762 " pdb=" SD MET C 762 " ideal model delta sigma weight residual 112.70 80.12 32.58 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CB MET A 762 " pdb=" CG MET A 762 " pdb=" SD MET A 762 " ideal model delta sigma weight residual 112.70 80.13 32.57 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C HIS A 780 " pdb=" CA HIS A 780 " pdb=" CB HIS A 780 " ideal model delta sigma weight residual 109.29 89.83 19.46 1.82e+00 3.02e-01 1.14e+02 angle pdb=" C HIS C 780 " pdb=" CA HIS C 780 " pdb=" CB HIS C 780 " ideal model delta sigma weight residual 109.29 89.85 19.44 1.82e+00 3.02e-01 1.14e+02 angle pdb=" CA PHE A 533 " pdb=" C PHE A 533 " pdb=" O PHE A 533 " ideal model delta sigma weight residual 119.32 108.56 10.76 1.19e+00 7.06e-01 8.17e+01 ... (remaining 26909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 10590 17.64 - 35.28: 502 35.28 - 52.92: 132 52.92 - 70.56: 16 70.56 - 88.20: 6 Dihedral angle restraints: 11246 sinusoidal: 2120 harmonic: 9126 Sorted by residual: dihedral pdb=" CB CYS A 744 " pdb=" SG CYS A 744 " pdb=" SG CYS A 798 " pdb=" CB CYS A 798 " ideal model delta sinusoidal sigma weight residual 93.00 -178.80 -88.20 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS C 744 " pdb=" SG CYS C 744 " pdb=" SG CYS C 798 " pdb=" CB CYS C 798 " ideal model delta sinusoidal sigma weight residual 93.00 -178.83 -88.17 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" C HIS A 780 " pdb=" N HIS A 780 " pdb=" CA HIS A 780 " pdb=" CB HIS A 780 " ideal model delta harmonic sigma weight residual -122.60 -98.64 -23.96 0 2.50e+00 1.60e-01 9.18e+01 ... (remaining 11243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 3362 0.206 - 0.412: 36 0.412 - 0.619: 16 0.619 - 0.825: 0 0.825 - 1.031: 2 Chirality restraints: 3416 Sorted by residual: chirality pdb=" CA SER B 617 " pdb=" N SER B 617 " pdb=" C SER B 617 " pdb=" CB SER B 617 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" CA SER D 617 " pdb=" N SER D 617 " pdb=" C SER D 617 " pdb=" CB SER D 617 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" CA LEU A 651 " pdb=" N LEU A 651 " pdb=" C LEU A 651 " pdb=" CB LEU A 651 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.80e+00 ... (remaining 3413 not shown) Planarity restraints: 3546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 609 " 0.034 2.00e-02 2.50e+03 6.83e-02 4.66e+01 pdb=" C LEU B 609 " -0.118 2.00e-02 2.50e+03 pdb=" O LEU B 609 " 0.044 2.00e-02 2.50e+03 pdb=" N TRP B 610 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 609 " -0.034 2.00e-02 2.50e+03 6.80e-02 4.63e+01 pdb=" C LEU D 609 " 0.118 2.00e-02 2.50e+03 pdb=" O LEU D 609 " -0.044 2.00e-02 2.50e+03 pdb=" N TRP D 610 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 533 " 0.025 2.00e-02 2.50e+03 5.47e-02 2.99e+01 pdb=" C PHE A 533 " -0.095 2.00e-02 2.50e+03 pdb=" O PHE A 533 " 0.036 2.00e-02 2.50e+03 pdb=" N LYS A 534 " 0.034 2.00e-02 2.50e+03 ... (remaining 3543 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 367 2.68 - 3.23: 18024 3.23 - 3.79: 27037 3.79 - 4.34: 31120 4.34 - 4.90: 53219 Nonbonded interactions: 129767 Sorted by model distance: nonbonded pdb=" O MET B 818 " pdb=" CD1 PHE B 822 " model vdw 2.124 3.340 nonbonded pdb=" O MET D 818 " pdb=" CD1 PHE D 822 " model vdw 2.125 3.340 nonbonded pdb=" O SER B 617 " pdb=" OG SER B 617 " model vdw 2.232 3.040 nonbonded pdb=" O SER D 617 " pdb=" OG SER D 617 " model vdw 2.232 3.040 nonbonded pdb=" O THR C 35 " pdb=" N HIS C 38 " model vdw 2.283 3.120 ... (remaining 129762 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 52.130 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.175 19534 Z= 0.492 Angle : 0.983 32.582 26938 Z= 0.640 Chirality : 0.068 1.031 3416 Planarity : 0.006 0.068 3546 Dihedral : 11.574 74.183 5290 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.80 % Favored : 95.07 % Rotamer: Outliers : 5.24 % Allowed : 6.27 % Favored : 88.48 % Cbeta Deviations : 1.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.13), residues: 3144 helix: -0.41 (0.13), residues: 1312 sheet: -2.02 (0.22), residues: 432 loop : -2.74 (0.14), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 610 HIS 0.012 0.002 HIS C 780 PHE 0.058 0.003 PHE D 460 TYR 0.026 0.001 TYR C 692 ARG 0.006 0.000 ARG A 722 Details of bonding type rmsd hydrogen bonds : bond 0.17908 ( 1055) hydrogen bonds : angle 6.18503 ( 3075) SS BOND : bond 0.00454 ( 12) SS BOND : angle 2.02788 ( 24) covalent geometry : bond 0.00722 (19522) covalent geometry : angle 0.98171 (26914) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 315 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7155 (mtp) cc_final: 0.6735 (ttm) REVERT: A 641 MET cc_start: 0.8762 (tmt) cc_final: 0.8422 (tmt) REVERT: A 651 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8869 (tp) REVERT: A 693 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7522 (t80) REVERT: B 391 TRP cc_start: 0.6977 (OUTLIER) cc_final: 0.6223 (t60) REVERT: B 554 PHE cc_start: 0.6370 (OUTLIER) cc_final: 0.5556 (m-10) REVERT: B 630 ILE cc_start: 0.8291 (mm) cc_final: 0.8026 (mt) REVERT: B 643 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9092 (tt) REVERT: C 501 MET cc_start: 0.7269 (mtp) cc_final: 0.6747 (ttm) REVERT: C 536 GLN cc_start: 0.7924 (pp30) cc_final: 0.7711 (pp30) REVERT: C 641 MET cc_start: 0.8838 (tmt) cc_final: 0.8477 (tmt) REVERT: C 651 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8927 (tp) REVERT: C 693 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7444 (t80) REVERT: D 391 TRP cc_start: 0.7153 (OUTLIER) cc_final: 0.5901 (t60) REVERT: D 630 ILE cc_start: 0.8324 (mm) cc_final: 0.8051 (mt) REVERT: D 643 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9040 (tt) outliers start: 56 outliers final: 37 residues processed: 365 average time/residue: 0.2303 time to fit residues: 141.4757 Evaluate side-chains 285 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 532 PRO Chi-restraints excluded: chain A residue 533 PHE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 608 TRP Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 456 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 550 PHE Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 532 PRO Chi-restraints excluded: chain C residue 533 PHE Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 608 TRP Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 692 TYR Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 507 TYR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 620 VAL Chi-restraints excluded: chain D residue 643 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 50.0000 chunk 237 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 81 optimal weight: 50.0000 chunk 160 optimal weight: 50.0000 chunk 127 optimal weight: 0.7980 chunk 246 optimal weight: 50.0000 chunk 95 optimal weight: 30.0000 chunk 149 optimal weight: 0.9980 chunk 183 optimal weight: 30.0000 chunk 285 optimal weight: 1.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 HIS A 477 HIS A 771 GLN C 477 HIS C 771 GLN D 694 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.200509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.177432 restraints weight = 30630.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.174440 restraints weight = 47319.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.171184 restraints weight = 48800.916| |-----------------------------------------------------------------------------| r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 19534 Z= 0.268 Angle : 0.674 8.287 26938 Z= 0.373 Chirality : 0.048 0.253 3416 Planarity : 0.005 0.077 3546 Dihedral : 6.786 59.408 3327 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.08 % Favored : 93.73 % Rotamer: Outliers : 7.87 % Allowed : 16.57 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.15), residues: 3144 helix: 0.76 (0.14), residues: 1352 sheet: -1.49 (0.26), residues: 322 loop : -2.38 (0.14), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 607 HIS 0.006 0.002 HIS C 780 PHE 0.039 0.003 PHE C 533 TYR 0.033 0.002 TYR D 479 ARG 0.004 0.001 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.05694 ( 1055) hydrogen bonds : angle 4.97614 ( 3075) SS BOND : bond 0.00743 ( 12) SS BOND : angle 1.57048 ( 24) covalent geometry : bond 0.00648 (19522) covalent geometry : angle 0.67250 (26914) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 234 time to evaluate : 2.178 Fit side-chains REVERT: A 565 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7767 (tp) REVERT: B 391 TRP cc_start: 0.7064 (OUTLIER) cc_final: 0.6199 (t60) REVERT: B 554 PHE cc_start: 0.6889 (OUTLIER) cc_final: 0.6173 (m-10) REVERT: B 630 ILE cc_start: 0.8576 (mm) cc_final: 0.8368 (mt) REVERT: B 671 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.6732 (m-10) REVERT: D 391 TRP cc_start: 0.7186 (OUTLIER) cc_final: 0.5850 (t60) REVERT: D 554 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.6651 (m-10) REVERT: D 671 PHE cc_start: 0.7933 (OUTLIER) cc_final: 0.6775 (m-10) outliers start: 84 outliers final: 55 residues processed: 300 average time/residue: 0.2129 time to fit residues: 111.4999 Evaluate side-chains 277 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 215 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 835 ILE Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 33 optimal weight: 50.0000 chunk 286 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 207 optimal weight: 0.0980 chunk 275 optimal weight: 7.9990 chunk 266 optimal weight: 0.8980 chunk 23 optimal weight: 40.0000 chunk 221 optimal weight: 1.9990 chunk 265 optimal weight: 0.0060 chunk 106 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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 = 0.4464 r_free = 0.4464 target = 0.198647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.171839 restraints weight = 30695.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.169025 restraints weight = 45748.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.166902 restraints weight = 43084.836| |-----------------------------------------------------------------------------| r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19534 Z= 0.147 Angle : 0.534 7.260 26938 Z= 0.292 Chirality : 0.044 0.180 3416 Planarity : 0.004 0.077 3546 Dihedral : 5.663 59.223 3274 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.44 % Favored : 94.50 % Rotamer: Outliers : 6.46 % Allowed : 22.47 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 3144 helix: 1.30 (0.15), residues: 1356 sheet: -1.47 (0.23), residues: 426 loop : -2.11 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 636 HIS 0.005 0.001 HIS C 477 PHE 0.043 0.002 PHE C 654 TYR 0.025 0.001 TYR B 479 ARG 0.004 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 1055) hydrogen bonds : angle 4.38764 ( 3075) SS BOND : bond 0.00245 ( 12) SS BOND : angle 1.05743 ( 24) covalent geometry : bond 0.00335 (19522) covalent geometry : angle 0.53301 (26914) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 229 time to evaluate : 2.014 Fit side-chains REVERT: A 565 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7755 (tp) REVERT: A 615 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8660 (mt) REVERT: B 554 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6193 (m-10) REVERT: B 834 ILE cc_start: 0.8870 (pt) cc_final: 0.8532 (mt) REVERT: C 615 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8628 (mt) REVERT: D 554 PHE cc_start: 0.7019 (OUTLIER) cc_final: 0.6640 (m-10) outliers start: 69 outliers final: 46 residues processed: 289 average time/residue: 0.2080 time to fit residues: 104.7562 Evaluate side-chains 275 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 280 optimal weight: 0.9990 chunk 0 optimal weight: 100.0000 chunk 242 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 162 optimal weight: 50.0000 chunk 275 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 193 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 216 optimal weight: 0.9980 overall best weight: 4.5992 ------------------------------------------------------------------------------- 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 = 0.4398 r_free = 0.4398 target = 0.191966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.165358 restraints weight = 31036.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.161835 restraints weight = 50176.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.159388 restraints weight = 47319.848| |-----------------------------------------------------------------------------| r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 19534 Z= 0.385 Angle : 0.784 10.317 26938 Z= 0.432 Chirality : 0.052 0.243 3416 Planarity : 0.005 0.081 3546 Dihedral : 6.321 53.451 3270 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.73 % Favored : 92.14 % Rotamer: Outliers : 10.11 % Allowed : 23.22 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3144 helix: 1.15 (0.15), residues: 1318 sheet: -1.43 (0.27), residues: 334 loop : -2.26 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 636 HIS 0.013 0.002 HIS C 477 PHE 0.044 0.004 PHE C 533 TYR 0.040 0.003 TYR D 479 ARG 0.006 0.001 ARG C 763 Details of bonding type rmsd hydrogen bonds : bond 0.06902 ( 1055) hydrogen bonds : angle 5.25254 ( 3075) SS BOND : bond 0.00856 ( 12) SS BOND : angle 1.55602 ( 24) covalent geometry : bond 0.00940 (19522) covalent geometry : angle 0.78264 (26914) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 219 time to evaluate : 1.992 Fit side-chains REVERT: A 478 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8721 (mp) REVERT: A 615 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8658 (mm) REVERT: A 746 LEU cc_start: 0.8817 (mt) cc_final: 0.8554 (mt) REVERT: B 391 TRP cc_start: 0.7182 (OUTLIER) cc_final: 0.6246 (t60) REVERT: B 554 PHE cc_start: 0.7199 (OUTLIER) cc_final: 0.6631 (m-10) REVERT: B 630 ILE cc_start: 0.8701 (mm) cc_final: 0.8393 (mp) REVERT: B 671 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7044 (m-10) REVERT: C 478 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8732 (mp) REVERT: C 536 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8336 (pp30) REVERT: C 746 LEU cc_start: 0.8800 (mt) cc_final: 0.8556 (mt) REVERT: D 391 TRP cc_start: 0.7357 (OUTLIER) cc_final: 0.5984 (t60) REVERT: D 468 ILE cc_start: 0.8624 (mt) cc_final: 0.8392 (mt) REVERT: D 554 PHE cc_start: 0.7165 (OUTLIER) cc_final: 0.6638 (m-10) REVERT: D 671 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7140 (m-10) outliers start: 108 outliers final: 76 residues processed: 310 average time/residue: 0.2157 time to fit residues: 115.6093 Evaluate side-chains 290 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 204 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain C residue 128 TYR Chi-restraints excluded: chain C residue 432 LYS Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 536 GLN Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 434 VAL Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 522 VAL Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 751 ILE Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 134 optimal weight: 0.4980 chunk 30 optimal weight: 50.0000 chunk 253 optimal weight: 50.0000 chunk 218 optimal weight: 10.0000 chunk 206 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 286 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 298 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 242 optimal weight: 40.0000 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.4468 r_free = 0.4468 target = 0.199157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.171872 restraints weight = 31124.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.167891 restraints weight = 44794.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.166094 restraints weight = 46584.873| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19534 Z= 0.109 Angle : 0.515 8.039 26938 Z= 0.276 Chirality : 0.043 0.169 3416 Planarity : 0.003 0.063 3546 Dihedral : 5.271 52.897 3270 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.06 % Favored : 94.88 % Rotamer: Outliers : 6.65 % Allowed : 27.25 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.15), residues: 3144 helix: 1.60 (0.15), residues: 1332 sheet: -1.45 (0.26), residues: 364 loop : -1.99 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 636 HIS 0.004 0.001 HIS C 404 PHE 0.020 0.001 PHE A 654 TYR 0.019 0.001 TYR D 479 ARG 0.002 0.000 ARG C 763 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 1055) hydrogen bonds : angle 4.19670 ( 3075) SS BOND : bond 0.00273 ( 12) SS BOND : angle 2.13328 ( 24) covalent geometry : bond 0.00237 (19522) covalent geometry : angle 0.51112 (26914) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 215 time to evaluate : 2.112 Fit side-chains REVERT: B 507 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6529 (t80) REVERT: B 554 PHE cc_start: 0.7087 (OUTLIER) cc_final: 0.6414 (m-10) REVERT: B 671 PHE cc_start: 0.7882 (OUTLIER) cc_final: 0.6665 (m-10) REVERT: D 434 VAL cc_start: 0.8849 (m) cc_final: 0.8623 (m) REVERT: D 468 ILE cc_start: 0.8509 (mt) cc_final: 0.8306 (mt) REVERT: D 554 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6647 (m-10) REVERT: D 643 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8438 (tt) REVERT: D 671 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.6614 (m-10) outliers start: 71 outliers final: 43 residues processed: 270 average time/residue: 0.2182 time to fit residues: 103.8125 Evaluate side-chains 257 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 2.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 507 TYR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 165 optimal weight: 50.0000 chunk 225 optimal weight: 1.9990 chunk 27 optimal weight: 50.0000 chunk 145 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 299 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 90 optimal weight: 40.0000 chunk 302 optimal weight: 2.9990 chunk 62 optimal weight: 0.0010 chunk 45 optimal weight: 7.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- 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 = 0.4460 r_free = 0.4460 target = 0.198340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.171168 restraints weight = 30941.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.166337 restraints weight = 43274.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.162729 restraints weight = 44239.385| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19534 Z= 0.118 Angle : 0.511 8.500 26938 Z= 0.272 Chirality : 0.043 0.162 3416 Planarity : 0.003 0.058 3546 Dihedral : 5.002 57.700 3268 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.85 % Favored : 94.08 % Rotamer: Outliers : 7.68 % Allowed : 25.94 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 3144 helix: 1.83 (0.15), residues: 1336 sheet: -1.31 (0.26), residues: 364 loop : -1.87 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 636 HIS 0.004 0.001 HIS C 404 PHE 0.021 0.001 PHE C 533 TYR 0.026 0.001 TYR A 703 ARG 0.001 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 1055) hydrogen bonds : angle 4.10059 ( 3075) SS BOND : bond 0.00245 ( 12) SS BOND : angle 1.28323 ( 24) covalent geometry : bond 0.00267 (19522) covalent geometry : angle 0.50956 (26914) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 208 time to evaluate : 1.990 Fit side-chains REVERT: A 709 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7554 (p90) REVERT: B 391 TRP cc_start: 0.7085 (OUTLIER) cc_final: 0.6167 (t60) REVERT: B 554 PHE cc_start: 0.7188 (OUTLIER) cc_final: 0.6368 (m-10) REVERT: B 671 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.6640 (m-10) REVERT: C 709 HIS cc_start: 0.8138 (OUTLIER) cc_final: 0.7468 (p90) REVERT: D 468 ILE cc_start: 0.8500 (mt) cc_final: 0.8287 (mt) REVERT: D 554 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6679 (m-10) REVERT: D 643 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8391 (tt) REVERT: D 671 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.6654 (m-10) outliers start: 82 outliers final: 57 residues processed: 274 average time/residue: 0.2080 time to fit residues: 99.7957 Evaluate side-chains 270 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 205 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 709 HIS Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 709 HIS Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 779 SER Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 750 THR Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 259 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 265 optimal weight: 50.0000 chunk 150 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 0.0670 chunk 272 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.199372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.171902 restraints weight = 30975.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.170147 restraints weight = 44812.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.168000 restraints weight = 41527.775| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19534 Z= 0.106 Angle : 0.492 8.803 26938 Z= 0.259 Chirality : 0.042 0.217 3416 Planarity : 0.003 0.053 3546 Dihedral : 4.590 58.506 3264 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 7.21 % Allowed : 26.22 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.16), residues: 3144 helix: 1.92 (0.15), residues: 1340 sheet: -1.61 (0.26), residues: 358 loop : -1.67 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 636 HIS 0.004 0.001 HIS C 404 PHE 0.023 0.001 PHE C 654 TYR 0.027 0.001 TYR C 703 ARG 0.001 0.000 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 1055) hydrogen bonds : angle 3.93846 ( 3075) SS BOND : bond 0.00087 ( 12) SS BOND : angle 0.98534 ( 24) covalent geometry : bond 0.00237 (19522) covalent geometry : angle 0.49118 (26914) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 210 time to evaluate : 1.992 Fit side-chains REVERT: B 391 TRP cc_start: 0.7059 (OUTLIER) cc_final: 0.6165 (t60) REVERT: B 554 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6391 (m-10) REVERT: B 671 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.6597 (m-10) REVERT: C 772 VAL cc_start: 0.7731 (OUTLIER) cc_final: 0.7491 (t) REVERT: D 554 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.6719 (m-10) REVERT: D 671 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.6561 (m-10) outliers start: 77 outliers final: 52 residues processed: 273 average time/residue: 0.2129 time to fit residues: 101.8128 Evaluate side-chains 261 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 299 optimal weight: 3.9990 chunk 31 optimal weight: 40.0000 chunk 61 optimal weight: 0.0970 chunk 57 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 300 optimal weight: 0.3980 chunk 86 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.197894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.170568 restraints weight = 30984.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.167325 restraints weight = 46076.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.164402 restraints weight = 49983.958| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19534 Z= 0.133 Angle : 0.528 9.360 26938 Z= 0.277 Chirality : 0.043 0.207 3416 Planarity : 0.003 0.080 3546 Dihedral : 4.544 59.716 3258 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.08 % Favored : 93.86 % Rotamer: Outliers : 7.21 % Allowed : 25.94 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.16), residues: 3144 helix: 1.97 (0.15), residues: 1338 sheet: -1.37 (0.28), residues: 344 loop : -1.61 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 636 HIS 0.004 0.001 HIS A 404 PHE 0.026 0.002 PHE C 533 TYR 0.025 0.001 TYR B 479 ARG 0.002 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 1055) hydrogen bonds : angle 4.01419 ( 3075) SS BOND : bond 0.00144 ( 12) SS BOND : angle 1.35614 ( 24) covalent geometry : bond 0.00313 (19522) covalent geometry : angle 0.52634 (26914) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 210 time to evaluate : 2.015 Fit side-chains REVERT: B 391 TRP cc_start: 0.7080 (OUTLIER) cc_final: 0.6192 (t60) REVERT: B 554 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.6449 (m-10) REVERT: B 671 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.6747 (m-10) REVERT: D 391 TRP cc_start: 0.7305 (OUTLIER) cc_final: 0.6006 (t60) REVERT: D 468 ILE cc_start: 0.8568 (mt) cc_final: 0.8357 (mt) REVERT: D 554 PHE cc_start: 0.7155 (OUTLIER) cc_final: 0.6678 (m-10) REVERT: D 671 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.6726 (m-10) outliers start: 77 outliers final: 57 residues processed: 278 average time/residue: 0.2045 time to fit residues: 99.2262 Evaluate side-chains 268 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 205 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 779 SER Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 521 GLU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 678 SER Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 80 optimal weight: 0.8980 chunk 228 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 148 optimal weight: 0.0030 chunk 270 optimal weight: 50.0000 chunk 281 optimal weight: 0.5980 chunk 205 optimal weight: 0.6980 chunk 79 optimal weight: 50.0000 chunk 88 optimal weight: 50.0000 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.200267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.173009 restraints weight = 31016.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.169191 restraints weight = 45203.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.166957 restraints weight = 50539.591| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19534 Z= 0.107 Angle : 0.517 11.066 26938 Z= 0.266 Chirality : 0.043 0.296 3416 Planarity : 0.003 0.069 3546 Dihedral : 4.419 57.773 3258 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 6.84 % Allowed : 26.59 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 3144 helix: 2.04 (0.15), residues: 1338 sheet: -1.47 (0.26), residues: 374 loop : -1.54 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 636 HIS 0.004 0.001 HIS C 404 PHE 0.020 0.001 PHE C 654 TYR 0.020 0.001 TYR B 479 ARG 0.001 0.000 ARG D 693 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 1055) hydrogen bonds : angle 3.91320 ( 3075) SS BOND : bond 0.00172 ( 12) SS BOND : angle 1.74387 ( 24) covalent geometry : bond 0.00241 (19522) covalent geometry : angle 0.51459 (26914) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 204 time to evaluate : 2.218 Fit side-chains REVERT: B 391 TRP cc_start: 0.7118 (OUTLIER) cc_final: 0.6216 (t60) REVERT: B 554 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6487 (m-10) REVERT: B 671 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.6659 (m-10) REVERT: D 554 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6665 (m-10) REVERT: D 671 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6622 (m-10) outliers start: 73 outliers final: 56 residues processed: 270 average time/residue: 0.2227 time to fit residues: 104.6743 Evaluate side-chains 263 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 202 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 746 LEU Chi-restraints excluded: chain C residue 779 SER Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 418 ILE Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 231 optimal weight: 0.8980 chunk 302 optimal weight: 0.8980 chunk 272 optimal weight: 0.7980 chunk 116 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 187 optimal weight: 30.0000 chunk 308 optimal weight: 0.5980 chunk 292 optimal weight: 0.2980 chunk 161 optimal weight: 50.0000 chunk 307 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.201490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.174430 restraints weight = 30943.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.172715 restraints weight = 44048.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.170372 restraints weight = 40916.804| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19534 Z= 0.096 Angle : 0.508 15.981 26938 Z= 0.257 Chirality : 0.042 0.295 3416 Planarity : 0.003 0.063 3546 Dihedral : 4.262 57.730 3258 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 6.09 % Allowed : 27.43 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 3144 helix: 2.05 (0.15), residues: 1354 sheet: -1.27 (0.27), residues: 354 loop : -1.39 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 636 HIS 0.004 0.001 HIS C 404 PHE 0.019 0.001 PHE C 654 TYR 0.016 0.001 TYR D 479 ARG 0.001 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.02882 ( 1055) hydrogen bonds : angle 3.81673 ( 3075) SS BOND : bond 0.00117 ( 12) SS BOND : angle 1.16942 ( 24) covalent geometry : bond 0.00212 (19522) covalent geometry : angle 0.50690 (26914) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6288 Ramachandran restraints generated. 3144 Oldfield, 0 Emsley, 3144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 209 time to evaluate : 2.213 Fit side-chains REVERT: B 391 TRP cc_start: 0.7128 (OUTLIER) cc_final: 0.6241 (t60) REVERT: B 554 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.6430 (m-10) REVERT: B 671 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.6696 (m-10) REVERT: D 391 TRP cc_start: 0.7224 (OUTLIER) cc_final: 0.5959 (t60) REVERT: D 554 PHE cc_start: 0.7075 (OUTLIER) cc_final: 0.6607 (m-10) REVERT: D 671 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.6662 (m-10) REVERT: B 1001 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6643 (tt0) outliers start: 65 outliers final: 53 residues processed: 270 average time/residue: 0.2235 time to fit residues: 104.7494 Evaluate side-chains 261 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 201 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 528 GLU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 679 PHE Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 693 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 528 GLU Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 558 PHE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 669 ASP Chi-restraints excluded: chain C residue 679 PHE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 693 PHE Chi-restraints excluded: chain C residue 718 ILE Chi-restraints excluded: chain C residue 730 ILE Chi-restraints excluded: chain C residue 779 SER Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 671 PHE Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain B residue 1001 GLU Chi-restraints excluded: chain D residue 1001 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 299 optimal weight: 2.9990 chunk 135 optimal weight: 0.1980 chunk 220 optimal weight: 6.9990 chunk 113 optimal weight: 40.0000 chunk 205 optimal weight: 1.9990 chunk 97 optimal weight: 50.0000 chunk 235 optimal weight: 6.9990 chunk 175 optimal weight: 30.0000 chunk 122 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.199064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.172043 restraints weight = 31013.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.167487 restraints weight = 46242.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.165552 restraints weight = 48469.026| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19534 Z= 0.136 Angle : 0.541 13.980 26938 Z= 0.278 Chirality : 0.043 0.288 3416 Planarity : 0.003 0.063 3546 Dihedral : 4.412 59.830 3258 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 5.99 % Allowed : 27.53 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 3144 helix: 1.99 (0.15), residues: 1358 sheet: -1.06 (0.29), residues: 324 loop : -1.47 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 636 HIS 0.004 0.001 HIS A 477 PHE 0.027 0.002 PHE A 533 TYR 0.026 0.001 TYR B 479 ARG 0.002 0.000 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.03637 ( 1055) hydrogen bonds : angle 3.95676 ( 3075) SS BOND : bond 0.00320 ( 12) SS BOND : angle 0.84548 ( 24) covalent geometry : bond 0.00322 (19522) covalent geometry : angle 0.54045 (26914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5716.24 seconds wall clock time: 100 minutes 12.75 seconds (6012.75 seconds total)