Starting phenix.real_space_refine on Wed Jan 22 23:22:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9are_43779/01_2025/9are_43779.cif Found real_map, /net/cci-nas-00/data/ceres_data/9are_43779/01_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_43779/01_2025/9are_43779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9are_43779/01_2025/9are_43779.map" model { file = "/net/cci-nas-00/data/ceres_data/9are_43779/01_2025/9are_43779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9are_43779/01_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 17.94, per 1000 atoms: 0.93 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=6, 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 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: 5.05 Conformation dependent library (CDL) restraints added in 3.3 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: 2.87 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: 7.28 Time building geometry restraints manager: 5.82 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: 495 35.28 - 52.92: 122 52.92 - 70.56: 16 70.56 - 88.20: 5 Dihedral angle restraints: 11228 sinusoidal: 2102 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=" 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 dihedral pdb=" C HIS C 780 " pdb=" N HIS C 780 " pdb=" CA HIS C 780 " pdb=" CB HIS C 780 " ideal model delta harmonic sigma weight residual -122.60 -98.68 -23.92 0 2.50e+00 1.60e-01 9.15e+01 ... (remaining 11225 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: 2.02 - 2.60: 92 2.60 - 3.17: 15903 3.17 - 3.75: 27390 3.75 - 4.32: 31808 4.32 - 4.90: 54592 Nonbonded interactions: 129785 Sorted by model distance: nonbonded pdb=" SG CYS C 744 " pdb=" SG CYS C 798 " model vdw 2.020 3.760 nonbonded pdb=" SG CYS D 429 " pdb=" SG CYS D 456 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS D 436 " pdb=" SG CYS D 457 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS C 420 " pdb=" SG CYS C 454 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS D 746 " pdb=" SG CYS D 801 " model vdw 2.031 3.760 ... (remaining 129780 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: 0.11 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 52.270 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.960 ------------------------------------------------------------------------------- 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 19522 Z= 0.496 Angle : 0.982 32.582 26914 Z= 0.640 Chirality : 0.068 1.031 3416 Planarity : 0.006 0.068 3546 Dihedral : 11.574 74.183 5290 Min Nonbonded Distance : 2.020 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 *********************** 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 : 2.042 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: 0.2440 time to fit residues: 148.5168 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 : 2.287 ------------------------------------------------------------------------------- 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 = 0.4494 r_free = 0.4494 target = 0.200840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.177705 restraints weight = 30593.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.174490 restraints weight = 47221.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.172905 restraints weight = 47548.960| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 19522 Z= 0.443 Angle : 0.661 8.277 26914 Z= 0.366 Chirality : 0.048 0.257 3416 Planarity : 0.004 0.078 3546 Dihedral : 6.737 59.355 3327 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.95 % Favored : 93.92 % Rotamer: Outliers : 7.30 % Allowed : 17.04 % Favored : 75.66 % 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: -1.32 (0.15), residues: 3144 helix: 0.77 (0.14), residues: 1352 sheet: -1.47 (0.26), residues: 326 loop : -2.41 (0.14), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 636 HIS 0.006 0.002 HIS C 780 PHE 0.039 0.003 PHE C 533 TYR 0.035 0.002 TYR B 479 ARG 0.006 0.001 ARG A 763 *********************** 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 314 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 236 time to evaluate : 2.215 Fit side-chains REVERT: A 501 MET cc_start: 0.7709 (mtp) cc_final: 0.7473 (mtm) REVERT: A 565 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7736 (tp) REVERT: B 391 TRP cc_start: 0.7012 (OUTLIER) cc_final: 0.6168 (t60) REVERT: B 554 PHE cc_start: 0.6857 (OUTLIER) cc_final: 0.6092 (m-10) REVERT: B 671 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.6699 (m-10) REVERT: C 501 MET cc_start: 0.7652 (mtp) cc_final: 0.7406 (mtm) REVERT: D 391 TRP cc_start: 0.7116 (OUTLIER) cc_final: 0.5822 (t60) REVERT: D 554 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6622 (m-10) REVERT: D 671 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.6609 (m-10) outliers start: 78 outliers final: 50 residues processed: 298 average time/residue: 0.2204 time to fit residues: 113.9654 Evaluate side-chains 272 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 2.143 ------------------------------------------------------------------------------- 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 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 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 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 747 VAL 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 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 655 ILE 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: 6.9990 chunk 123 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 chunk 266 optimal weight: 30.0000 chunk 23 optimal weight: 40.0000 chunk 221 optimal weight: 0.9980 chunk 265 optimal weight: 0.9990 chunk 106 optimal weight: 50.0000 chunk 64 optimal weight: 9.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.4461 r_free = 0.4461 target = 0.198436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.172251 restraints weight = 30665.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.168528 restraints weight = 42844.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.166193 restraints weight = 44081.378| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19522 Z= 0.257 Angle : 0.539 7.284 26914 Z= 0.296 Chirality : 0.044 0.177 3416 Planarity : 0.004 0.077 3546 Dihedral : 5.675 58.523 3274 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 6.84 % Allowed : 22.75 % Favored : 70.41 % 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: -0.73 (0.15), residues: 3144 helix: 1.35 (0.15), residues: 1342 sheet: -1.45 (0.24), residues: 394 loop : -2.08 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 636 HIS 0.006 0.001 HIS A 477 PHE 0.043 0.002 PHE C 654 TYR 0.026 0.002 TYR D 479 ARG 0.003 0.000 ARG C 763 *********************** 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 301 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 228 time to evaluate : 2.074 Fit side-chains REVERT: A 565 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7756 (tp) REVERT: A 615 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8622 (mt) REVERT: B 434 VAL cc_start: 0.8896 (m) cc_final: 0.8676 (m) REVERT: B 554 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.6241 (m-10) REVERT: B 834 ILE cc_start: 0.8852 (pt) cc_final: 0.8540 (mt) REVERT: C 615 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8618 (mt) REVERT: C 669 ASP cc_start: 0.6239 (OUTLIER) cc_final: 0.6038 (t0) REVERT: D 554 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6617 (m-10) outliers start: 73 outliers final: 44 residues processed: 290 average time/residue: 0.2199 time to fit residues: 111.8473 Evaluate side-chains 270 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 2.466 ------------------------------------------------------------------------------- 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 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 521 GLU 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 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 654 PHE 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 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 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 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: 10.0000 chunk 170 optimal weight: 0.9980 chunk 159 optimal weight: 0.0370 chunk 162 optimal weight: 50.0000 chunk 275 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 193 optimal weight: 9.9990 chunk 2 optimal weight: 50.0000 chunk 216 optimal weight: 0.9980 overall best weight: 1.2062 ------------------------------------------------------------------------------- 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 = 0.4466 r_free = 0.4466 target = 0.198775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.172229 restraints weight = 30853.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.169969 restraints weight = 45899.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.168036 restraints weight = 43666.690| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19522 Z= 0.210 Angle : 0.517 8.023 26914 Z= 0.279 Chirality : 0.043 0.169 3416 Planarity : 0.003 0.070 3546 Dihedral : 5.250 55.788 3270 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.44 % Favored : 94.50 % Rotamer: Outliers : 7.87 % Allowed : 22.75 % Favored : 69.38 % 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: -0.44 (0.15), residues: 3144 helix: 1.60 (0.15), residues: 1334 sheet: -1.54 (0.25), residues: 360 loop : -1.85 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 636 HIS 0.004 0.001 HIS A 477 PHE 0.038 0.002 PHE A 654 TYR 0.024 0.001 TYR B 479 ARG 0.002 0.000 ARG A 763 *********************** 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 310 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 226 time to evaluate : 2.092 Fit side-chains REVERT: B 554 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6351 (m-10) REVERT: B 643 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8485 (mt) REVERT: B 671 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.6624 (m-10) REVERT: C 669 ASP cc_start: 0.6195 (OUTLIER) cc_final: 0.5987 (t0) REVERT: D 464 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8411 (tp) REVERT: D 554 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6608 (m-10) REVERT: D 671 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.6674 (m-10) REVERT: D 834 ILE cc_start: 0.8739 (pt) cc_final: 0.8526 (mt) outliers start: 84 outliers final: 57 residues processed: 294 average time/residue: 0.2232 time to fit residues: 113.4051 Evaluate side-chains 282 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 218 time to evaluate : 1.990 ------------------------------------------------------------------------------- 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 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 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 780 HIS 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 521 GLU 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 B residue 671 PHE Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 748 LEU 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 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 699 LEU 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 134 optimal weight: 2.9990 chunk 30 optimal weight: 30.0000 chunk 253 optimal weight: 50.0000 chunk 218 optimal weight: 0.4980 chunk 206 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 286 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 298 optimal weight: 0.0470 chunk 283 optimal weight: 0.9980 chunk 242 optimal weight: 10.0000 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 = 0.4484 r_free = 0.4484 target = 0.200689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.174041 restraints weight = 31113.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.170678 restraints weight = 46009.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.167340 restraints weight = 48134.198| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19522 Z= 0.152 Angle : 0.480 8.156 26914 Z= 0.255 Chirality : 0.042 0.159 3416 Planarity : 0.003 0.056 3546 Dihedral : 4.864 53.620 3268 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 7.58 % Allowed : 23.31 % Favored : 69.10 % 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: -0.18 (0.15), residues: 3144 helix: 1.80 (0.15), residues: 1342 sheet: -1.34 (0.26), residues: 342 loop : -1.72 (0.16), residues: 1460 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 0.014 0.001 PHE A 533 TYR 0.022 0.001 TYR A 703 ARG 0.001 0.000 ARG A 523 *********************** 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 306 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 225 time to evaluate : 2.139 Fit side-chains REVERT: A 709 HIS cc_start: 0.8090 (OUTLIER) cc_final: 0.7541 (p90) REVERT: B 554 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6337 (m-10) REVERT: B 671 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.6682 (m-10) REVERT: C 709 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.7603 (p90) REVERT: D 464 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8435 (tp) REVERT: D 554 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.6545 (m-10) REVERT: D 671 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.6636 (m-10) outliers start: 81 outliers final: 55 residues processed: 291 average time/residue: 0.2363 time to fit residues: 118.6902 Evaluate side-chains 282 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 220 time to evaluate : 2.113 ------------------------------------------------------------------------------- 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 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 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 772 VAL Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 798 CYS 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 521 GLU 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 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 446 SER 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 699 LEU 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 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 545 VAL Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 608 LEU 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 748 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 165 optimal weight: 7.9990 chunk 225 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 145 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 299 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 90 optimal weight: 40.0000 chunk 302 optimal weight: 0.9980 chunk 62 optimal weight: 0.0470 chunk 45 optimal weight: 8.9990 overall best weight: 1.3480 ------------------------------------------------------------------------------- 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 = 0.198295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.170409 restraints weight = 30905.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.167372 restraints weight = 46398.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.165787 restraints weight = 46041.906| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19522 Z= 0.224 Angle : 0.520 8.616 26914 Z= 0.277 Chirality : 0.043 0.205 3416 Planarity : 0.003 0.052 3546 Dihedral : 4.871 56.683 3266 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 8.15 % Allowed : 22.94 % Favored : 68.91 % 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: -0.08 (0.16), residues: 3144 helix: 1.87 (0.15), residues: 1344 sheet: -0.93 (0.29), residues: 296 loop : -1.76 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 636 HIS 0.005 0.001 HIS A 477 PHE 0.027 0.002 PHE A 533 TYR 0.026 0.001 TYR D 479 ARG 0.002 0.000 ARG C 763 *********************** 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 304 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 217 time to evaluate : 2.214 Fit side-chains REVERT: A 565 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7651 (tp) REVERT: A 709 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7558 (p90) REVERT: B 391 TRP cc_start: 0.7080 (OUTLIER) cc_final: 0.6168 (t60) REVERT: B 554 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.6237 (m-10) REVERT: B 671 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.6812 (m-10) REVERT: C 709 HIS cc_start: 0.8222 (OUTLIER) cc_final: 0.7563 (p90) REVERT: D 391 TRP cc_start: 0.7200 (OUTLIER) cc_final: 0.5832 (t60) REVERT: D 554 PHE cc_start: 0.6999 (OUTLIER) cc_final: 0.6533 (m-10) REVERT: D 671 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.6685 (m-10) outliers start: 87 outliers final: 57 residues processed: 289 average time/residue: 0.2277 time to fit residues: 113.9445 Evaluate side-chains 274 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 2.402 ------------------------------------------------------------------------------- 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 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 643 ILE 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 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 780 HIS Chi-restraints excluded: chain A residue 798 CYS 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 521 GLU 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 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 748 LEU 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 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 699 LEU 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 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 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 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 749 VAL 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: 0.6980 chunk 248 optimal weight: 8.9990 chunk 127 optimal weight: 0.9980 chunk 25 optimal weight: 30.0000 chunk 265 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 57 optimal weight: 0.0170 chunk 272 optimal weight: 1.9990 chunk 50 optimal weight: 0.0060 overall best weight: 0.5434 ------------------------------------------------------------------------------- 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 = 0.4489 r_free = 0.4489 target = 0.201250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.175621 restraints weight = 31010.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.174119 restraints weight = 47488.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.170820 restraints weight = 35379.361| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19522 Z= 0.135 Angle : 0.476 8.433 26914 Z= 0.248 Chirality : 0.042 0.161 3416 Planarity : 0.003 0.043 3546 Dihedral : 4.454 58.854 3264 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.96 % Favored : 94.97 % Rotamer: Outliers : 5.71 % Allowed : 25.94 % Favored : 68.35 % 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: 0.07 (0.16), residues: 3144 helix: 1.99 (0.15), residues: 1348 sheet: -1.22 (0.26), residues: 374 loop : -1.58 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 636 HIS 0.003 0.001 HIS A 404 PHE 0.018 0.001 PHE C 654 TYR 0.014 0.001 TYR D 479 ARG 0.001 0.000 ARG A 523 *********************** 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 275 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 214 time to evaluate : 2.317 Fit side-chains REVERT: B 391 TRP cc_start: 0.7110 (OUTLIER) cc_final: 0.6184 (t60) REVERT: B 554 PHE cc_start: 0.7007 (OUTLIER) cc_final: 0.6318 (m-10) REVERT: B 671 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.6650 (m-10) REVERT: D 554 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6668 (m-10) REVERT: D 671 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.6621 (m-10) REVERT: B 1001 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6782 (tt0) outliers start: 61 outliers final: 44 residues processed: 268 average time/residue: 0.2243 time to fit residues: 104.5007 Evaluate side-chains 257 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 2.099 ------------------------------------------------------------------------------- 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 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 693 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 798 CYS 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 521 GLU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 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 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 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 D residue 422 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 299 optimal weight: 0.7980 chunk 31 optimal weight: 30.0000 chunk 61 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 176 optimal weight: 9.9990 chunk 133 optimal weight: 0.0050 chunk 148 optimal weight: 0.9990 chunk 244 optimal weight: 50.0000 chunk 300 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 = 0.4474 r_free = 0.4474 target = 0.199759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.173470 restraints weight = 31000.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.172314 restraints weight = 45747.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.170961 restraints weight = 33817.753| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19522 Z= 0.176 Angle : 0.498 11.094 26914 Z= 0.259 Chirality : 0.043 0.262 3416 Planarity : 0.003 0.039 3546 Dihedral : 4.259 57.050 3257 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 6.18 % Allowed : 26.31 % Favored : 67.51 % 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: 2.07 (0.15), residues: 1344 sheet: -1.07 (0.27), residues: 346 loop : -1.53 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 636 HIS 0.003 0.001 HIS A 404 PHE 0.022 0.001 PHE C 533 TYR 0.022 0.001 TYR D 479 ARG 0.001 0.000 ARG C 763 *********************** 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 273 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 207 time to evaluate : 1.985 Fit side-chains REVERT: B 391 TRP cc_start: 0.7126 (OUTLIER) cc_final: 0.6210 (t60) REVERT: B 554 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6385 (m-10) REVERT: B 671 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.6722 (m-10) REVERT: D 554 PHE cc_start: 0.7111 (OUTLIER) cc_final: 0.6681 (m-10) REVERT: D 671 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.6659 (m-10) REVERT: B 1001 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6727 (tt0) outliers start: 66 outliers final: 50 residues processed: 267 average time/residue: 0.2275 time to fit residues: 106.7481 Evaluate side-chains 259 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 203 time to evaluate : 2.146 ------------------------------------------------------------------------------- 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 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 693 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 798 CYS 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 521 GLU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 671 PHE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 451 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 746 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 422 VAL 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 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: 3.9990 chunk 228 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 148 optimal weight: 0.0970 chunk 270 optimal weight: 40.0000 chunk 281 optimal weight: 0.7980 chunk 205 optimal weight: 0.8980 chunk 79 optimal weight: 50.0000 chunk 88 optimal weight: 50.0000 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.4485 r_free = 0.4485 target = 0.200859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.174508 restraints weight = 31069.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.172829 restraints weight = 44319.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.170226 restraints weight = 39499.795| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19522 Z= 0.148 Angle : 0.484 11.143 26914 Z= 0.250 Chirality : 0.042 0.301 3416 Planarity : 0.003 0.036 3546 Dihedral : 4.147 58.182 3256 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.90 % Allowed : 26.69 % Favored : 67.42 % 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: 0.29 (0.16), residues: 3144 helix: 2.12 (0.15), residues: 1344 sheet: -0.87 (0.26), residues: 380 loop : -1.47 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 636 HIS 0.003 0.001 HIS A 404 PHE 0.017 0.001 PHE C 654 TYR 0.017 0.001 TYR D 479 ARG 0.001 0.000 ARG C 763 *********************** 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 267 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 204 time to evaluate : 2.030 Fit side-chains REVERT: B 391 TRP cc_start: 0.7093 (OUTLIER) cc_final: 0.6196 (t60) REVERT: B 554 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6417 (m-10) REVERT: B 666 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8715 (pp) REVERT: B 671 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.6711 (m-10) REVERT: D 554 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6612 (m-10) REVERT: D 671 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.6668 (m-10) REVERT: B 1001 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6766 (tt0) outliers start: 63 outliers final: 50 residues processed: 260 average time/residue: 0.2533 time to fit residues: 118.4333 Evaluate side-chains 258 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 201 time to evaluate : 2.292 ------------------------------------------------------------------------------- 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 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 693 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 798 CYS 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 521 GLU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 666 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 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 746 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 422 VAL 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 608 LEU 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 231 optimal weight: 0.8980 chunk 302 optimal weight: 0.8980 chunk 272 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 177 optimal weight: 20.0000 chunk 187 optimal weight: 30.0000 chunk 308 optimal weight: 0.6980 chunk 292 optimal weight: 0.3980 chunk 161 optimal weight: 50.0000 chunk 307 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4483 r_free = 0.4483 target = 0.200685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.174853 restraints weight = 30874.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.171230 restraints weight = 44045.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.168823 restraints weight = 49165.314| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19522 Z= 0.150 Angle : 0.485 11.625 26914 Z= 0.249 Chirality : 0.042 0.304 3416 Planarity : 0.003 0.037 3546 Dihedral : 4.048 59.880 3254 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.71 % Allowed : 27.25 % Favored : 67.04 % 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: 0.38 (0.16), residues: 3144 helix: 2.17 (0.15), residues: 1346 sheet: -0.79 (0.28), residues: 350 loop : -1.39 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 636 HIS 0.003 0.001 HIS A 404 PHE 0.017 0.001 PHE C 533 TYR 0.018 0.001 TYR D 479 ARG 0.001 0.000 ARG C 763 ********************** 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 260 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 199 time to evaluate : 2.151 Fit side-chains REVERT: B 391 TRP cc_start: 0.7124 (OUTLIER) cc_final: 0.6221 (t60) REVERT: B 554 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6225 (m-10) REVERT: B 666 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8744 (pp) REVERT: B 671 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.6695 (m-10) REVERT: D 391 TRP cc_start: 0.7189 (OUTLIER) cc_final: 0.5925 (t60) REVERT: D 554 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6580 (m-10) REVERT: D 671 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.6664 (m-10) REVERT: B 1001 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6698 (tt0) outliers start: 61 outliers final: 52 residues processed: 254 average time/residue: 0.2224 time to fit residues: 98.9648 Evaluate side-chains 259 residues out of total 2754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 2.265 ------------------------------------------------------------------------------- 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 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 693 PHE Chi-restraints excluded: chain A residue 718 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 798 CYS 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 521 GLU Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 666 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 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 780 HIS Chi-restraints excluded: chain D residue 391 TRP Chi-restraints excluded: chain D residue 422 VAL 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 608 LEU 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 749 VAL 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: 0.9990 chunk 135 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 113 optimal weight: 40.0000 chunk 205 optimal weight: 0.6980 chunk 97 optimal weight: 50.0000 chunk 235 optimal weight: 4.9990 chunk 175 optimal weight: 30.0000 chunk 122 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.4468 r_free = 0.4468 target = 0.198573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.171902 restraints weight = 31000.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.169838 restraints weight = 43756.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.165698 restraints weight = 43774.974| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19522 Z= 0.275 Angle : 0.554 11.088 26914 Z= 0.291 Chirality : 0.044 0.305 3416 Planarity : 0.003 0.043 3546 Dihedral : 4.369 59.005 3254 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.71 % Allowed : 27.34 % Favored : 66.95 % 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: 0.26 (0.16), residues: 3144 helix: 2.03 (0.15), residues: 1348 sheet: -0.56 (0.29), residues: 340 loop : -1.51 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 635 HIS 0.006 0.001 HIS A 477 PHE 0.032 0.002 PHE A 533 TYR 0.031 0.001 TYR D 479 ARG 0.003 0.000 ARG C 763 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5429.72 seconds wall clock time: 98 minutes 15.24 seconds (5895.24 seconds total)