Starting phenix.real_space_refine on Fri May 23 20:26:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfs_44505/05_2025/9bfs_44505.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfs_44505/05_2025/9bfs_44505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bfs_44505/05_2025/9bfs_44505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfs_44505/05_2025/9bfs_44505.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfs_44505/05_2025/9bfs_44505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfs_44505/05_2025/9bfs_44505.cif" } resolution = 3.06 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= 0.000 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 15398 2.51 5 N 4266 2.21 5 O 4520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24272 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1516, 11958 Classifications: {'peptide': 1516} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 101, 'TRANS': 1413} Chain breaks: 8 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 11958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1516, 11958 Classifications: {'peptide': 1516} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 101, 'TRANS': 1413} Chain breaks: 8 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 15.09, per 1000 atoms: 0.62 Number of scatterers: 24272 At special positions: 0 Unit cell: (123.67, 221.61, 117.03, 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 88 16.00 O 4520 8.00 N 4266 7.00 C 15398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 257 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 981 " - pdb=" SG CYS A 991 " distance=2.03 Simple disulfide: pdb=" SG CYS A1597 " - pdb=" SG CYS A1606 " distance=2.03 Simple disulfide: pdb=" SG CYS A1679 " - pdb=" SG CYS A1713 " distance=2.03 Simple disulfide: pdb=" SG CYS A1695 " - pdb=" SG CYS A1700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 257 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 253 " distance=2.02 Simple disulfide: pdb=" SG CYS B 239 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 286 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 981 " - pdb=" SG CYS B 991 " distance=2.03 Simple disulfide: pdb=" SG CYS B1597 " - pdb=" SG CYS B1606 " distance=2.02 Simple disulfide: pdb=" SG CYS B1679 " - pdb=" SG CYS B1713 " distance=2.03 Simple disulfide: pdb=" SG CYS B1695 " - pdb=" SG CYS B1700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG E 1 " - " FUC E 3 " NAG-ASN " NAG A2601 " - " ASN A1557 " " NAG A2602 " - " ASN A1550 " " NAG A2603 " - " ASN A1228 " " NAG A2604 " - " ASN A1639 " " NAG A2605 " - " ASN A1313 " " NAG A2606 " - " ASN A1725 " " NAG A2607 " - " ASN A1756 " " NAG A2608 " - " ASN A 505 " " NAG B2601 " - " ASN B1557 " " NAG B2602 " - " ASN B1550 " " NAG B2603 " - " ASN B1228 " " NAG B2604 " - " ASN B1639 " " NAG B2605 " - " ASN B1313 " " NAG B2606 " - " ASN B1725 " " NAG B2607 " - " ASN B1756 " " NAG B2608 " - " ASN B 505 " " NAG C 1 " - " ASN A1353 " " NAG D 1 " - " ASN A 966 " " NAG E 1 " - " ASN B1353 " " NAG F 1 " - " ASN B 966 " Time building additional restraints: 5.37 Conformation dependent library (CDL) restraints added in 3.0 seconds 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5680 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 70 sheets defined 7.1% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.76 Creating SS restraints... Processing helix chain 'A' and resid 207 through 227 Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.808A pdb=" N ARG A 252 " --> pdb=" O CYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 266 removed outlier: 3.618A pdb=" N ALA A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 283 through 312 removed outlier: 5.463A pdb=" N HIS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1070 removed outlier: 3.766A pdb=" N ALA A1070 " --> pdb=" O PRO A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1507 No H-bonds generated for 'chain 'A' and resid 1505 through 1507' Processing helix chain 'A' and resid 1611 through 1616 Processing helix chain 'A' and resid 1619 through 1624 Processing helix chain 'A' and resid 1676 through 1681 Processing helix chain 'A' and resid 1774 through 1780 removed outlier: 3.654A pdb=" N LYS A1778 " --> pdb=" O SER A1774 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 227 Processing helix chain 'B' and resid 248 through 257 removed outlier: 3.818A pdb=" N ARG B 252 " --> pdb=" O CYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.638A pdb=" N ALA B 263 " --> pdb=" O GLN B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 283 through 312 removed outlier: 5.542A pdb=" N HIS B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1070 removed outlier: 3.726A pdb=" N ALA B1070 " --> pdb=" O PRO B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1505 through 1507 No H-bonds generated for 'chain 'B' and resid 1505 through 1507' Processing helix chain 'B' and resid 1610 through 1616 removed outlier: 4.178A pdb=" N GLN B1614 " --> pdb=" O ALA B1610 " (cutoff:3.500A) Processing helix chain 'B' and resid 1619 through 1624 removed outlier: 3.626A pdb=" N ILE B1623 " --> pdb=" O GLY B1619 " (cutoff:3.500A) Processing helix chain 'B' and resid 1676 through 1681 Processing helix chain 'B' and resid 1774 through 1780 removed outlier: 3.635A pdb=" N LYS B1778 " --> pdb=" O SER B1774 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 315 through 317 Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 381 Processing sheet with id=AA3, first strand: chain 'A' and resid 380 through 381 Processing sheet with id=AA4, first strand: chain 'A' and resid 385 through 388 removed outlier: 6.260A pdb=" N ALA B1384 " --> pdb=" O VAL B1378 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL B1378 " --> pdb=" O ALA B1384 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU B1334 " --> pdb=" O ASN B1353 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN B1353 " --> pdb=" O LEU B1334 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR B1336 " --> pdb=" O ARG B1351 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG B1351 " --> pdb=" O TYR B1336 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B1338 " --> pdb=" O GLU B1349 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU B1349 " --> pdb=" O ILE B1338 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS B1340 " --> pdb=" O HIS B1347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 443 through 448 removed outlier: 6.677A pdb=" N HIS A 457 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU A 446 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA A 455 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLY A 448 " --> pdb=" O HIS A 453 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N HIS A 453 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 454 " --> pdb=" O PHE A 497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 489 Processing sheet with id=AA7, first strand: chain 'A' and resid 563 through 568 removed outlier: 6.377A pdb=" N ASN A 563 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER A 556 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N MET A 565 " --> pdb=" O TRP A 554 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TRP A 554 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER A 543 " --> pdb=" O LEU A 814 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 573 through 578 removed outlier: 7.143A pdb=" N LEU A 588 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE A 576 " --> pdb=" O TRP A 586 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP A 586 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TRP A 578 " --> pdb=" O GLN A 584 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN A 584 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 597 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU A 594 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS A 598 " --> pdb=" O PRO A 607 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLU A 600 " --> pdb=" O VAL A 605 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL A 605 " --> pdb=" O GLU A 600 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 624 through 625 Processing sheet with id=AB1, first strand: chain 'A' and resid 676 through 680 removed outlier: 4.065A pdb=" N GLN A 676 " --> pdb=" O ARG A 689 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 689 " --> pdb=" O GLN A 676 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU A 694 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 716 through 719 removed outlier: 3.780A pdb=" N GLN A 719 " --> pdb=" O ILE A 724 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE A 724 " --> pdb=" O GLN A 719 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 736 " --> pdb=" O LEU A 727 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 770 through 772 removed outlier: 3.538A pdb=" N ALA A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 829 through 835 removed outlier: 5.960A pdb=" N SER A 830 " --> pdb=" O LYS A 845 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A 845 " --> pdb=" O SER A 830 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 874 through 881 removed outlier: 3.581A pdb=" N SER A 874 " --> pdb=" O ASP A 869 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 878 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 865 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 880 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR A 863 " --> pdb=" O ASN A 880 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 874 through 881 removed outlier: 3.581A pdb=" N SER A 874 " --> pdb=" O ASP A 869 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 878 " --> pdb=" O LEU A 865 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 865 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 880 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR A 863 " --> pdb=" O ASN A 880 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 899 " --> pdb=" O LEU A 917 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 949 through 954 removed outlier: 5.333A pdb=" N VAL A 938 " --> pdb=" O GLN A 951 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N SER A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A1180 " --> pdb=" O ALA A 932 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 963 through 964 Processing sheet with id=AB9, first strand: chain 'A' and resid 1000 through 1006 removed outlier: 6.746A pdb=" N THR A1015 " --> pdb=" O GLY A1001 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL A1003 " --> pdb=" O TYR A1013 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR A1013 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR A1005 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG A1011 " --> pdb=" O TYR A1005 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A1022 " --> pdb=" O LEU A1035 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1042 through 1045 Processing sheet with id=AC2, first strand: chain 'A' and resid 1082 through 1089 removed outlier: 6.617A pdb=" N LEU A1098 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE A1086 " --> pdb=" O PHE A1096 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N PHE A1096 " --> pdb=" O PHE A1086 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU A1088 " --> pdb=" O GLN A1094 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLN A1094 " --> pdb=" O LEU A1088 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP A1097 " --> pdb=" O TYR A1108 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN A1123 " --> pdb=" O LEU A1107 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG A1109 " --> pdb=" O MET A1121 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N MET A1121 " --> pdb=" O ARG A1109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1137 through 1139 Processing sheet with id=AC4, first strand: chain 'A' and resid 1217 through 1219 Processing sheet with id=AC5, first strand: chain 'A' and resid 1242 through 1248 removed outlier: 3.503A pdb=" N ARG A1242 " --> pdb=" O PHE A1239 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A1244 " --> pdb=" O LEU A1237 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A1266 " --> pdb=" O GLU A1238 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1299 through 1305 removed outlier: 4.189A pdb=" N VAL A1314 " --> pdb=" O LEU A1364 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA A1316 " --> pdb=" O GLU A1362 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLU A1362 " --> pdb=" O ALA A1316 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU A1318 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ARG A1360 " --> pdb=" O LEU A1318 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TRP A1320 " --> pdb=" O GLU A1358 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLU A1358 " --> pdb=" O TRP A1320 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1345 through 1354 removed outlier: 6.697A pdb=" N CYS A1340 " --> pdb=" O HIS A1347 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU A1349 " --> pdb=" O ILE A1338 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A1338 " --> pdb=" O GLU A1349 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG A1351 " --> pdb=" O TYR A1336 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR A1336 " --> pdb=" O ARG A1351 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A1353 " --> pdb=" O LEU A1334 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A1334 " --> pdb=" O ASN A1353 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL A1378 " --> pdb=" O ALA A1384 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA A1384 " --> pdb=" O VAL A1378 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AC9, first strand: chain 'A' and resid 1421 through 1422 removed outlier: 3.551A pdb=" N ALA A1407 " --> pdb=" O LEU A1665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1432 through 1438 removed outlier: 4.777A pdb=" N GLU A1452 " --> pdb=" O ASN A1448 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A1453 " --> pdb=" O LEU A1465 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1472 through 1478 removed outlier: 6.969A pdb=" N VAL A1472 " --> pdb=" O LEU A1489 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A1489 " --> pdb=" O VAL A1472 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA A1474 " --> pdb=" O ALA A1487 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE A1499 " --> pdb=" O VAL A1517 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 1524 through 1532 removed outlier: 5.099A pdb=" N LEU A1526 " --> pdb=" O TYR A1543 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR A1543 " --> pdb=" O LEU A1526 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ASP A1528 " --> pdb=" O LEU A1541 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A1541 " --> pdb=" O ASP A1528 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A1554 " --> pdb=" O TRP A1540 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU A1544 " --> pdb=" O ASN A1550 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASN A1550 " --> pdb=" O GLU A1544 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU A1553 " --> pdb=" O TRP A1566 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1572 through 1577 removed outlier: 3.865A pdb=" N ARG A1574 " --> pdb=" O VAL A1590 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A1598 " --> pdb=" O THR A1607 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A1605 " --> pdb=" O ASP A1600 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1627 through 1629 removed outlier: 6.425A pdb=" N ILE A1642 " --> pdb=" O THR A1655 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR A1655 " --> pdb=" O ILE A1642 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA A1644 " --> pdb=" O GLU A1653 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 1702 through 1703 Processing sheet with id=AD7, first strand: chain 'A' and resid 1745 through 1750 removed outlier: 4.113A pdb=" N GLY A1745 " --> pdb=" O LEU A1726 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A1726 " --> pdb=" O GLY A1745 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A1722 " --> pdb=" O LEU A1749 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A1785 " --> pdb=" O LEU A1772 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 1745 through 1750 removed outlier: 4.113A pdb=" N GLY A1745 " --> pdb=" O LEU A1726 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A1726 " --> pdb=" O GLY A1745 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR A1722 " --> pdb=" O LEU A1749 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 315 through 317 Processing sheet with id=AE1, first strand: chain 'B' and resid 380 through 381 Processing sheet with id=AE2, first strand: chain 'B' and resid 380 through 381 Processing sheet with id=AE3, first strand: chain 'B' and resid 443 through 448 removed outlier: 6.682A pdb=" N HIS B 457 " --> pdb=" O GLU B 444 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU B 446 " --> pdb=" O ALA B 455 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA B 455 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLY B 448 " --> pdb=" O HIS B 453 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N HIS B 453 " --> pdb=" O GLY B 448 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 454 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 484 through 489 Processing sheet with id=AE5, first strand: chain 'B' and resid 484 through 489 Processing sheet with id=AE6, first strand: chain 'B' and resid 563 through 568 removed outlier: 3.682A pdb=" N ILE B 566 " --> pdb=" O VAL B 552 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL B 552 " --> pdb=" O ILE B 566 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 573 through 578 removed outlier: 7.025A pdb=" N LEU B 588 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE B 576 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TRP B 586 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TRP B 578 " --> pdb=" O GLN B 584 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN B 584 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS B 598 " --> pdb=" O PRO B 607 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLU B 600 " --> pdb=" O VAL B 605 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL B 605 " --> pdb=" O GLU B 600 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 624 through 625 removed outlier: 3.511A pdb=" N ARG B 636 " --> pdb=" O ASP B 631 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 624 through 625 Processing sheet with id=AF1, first strand: chain 'B' and resid 674 through 680 removed outlier: 3.962A pdb=" N GLN B 676 " --> pdb=" O ARG B 689 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B 693 " --> pdb=" O ASN B 690 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU B 694 " --> pdb=" O LEU B 707 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 716 through 719 removed outlier: 3.691A pdb=" N GLN B 719 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE B 724 " --> pdb=" O GLN B 719 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS B 746 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 770 through 772 removed outlier: 3.507A pdb=" N ALA B 770 " --> pdb=" O LEU B 777 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 829 through 835 removed outlier: 6.052A pdb=" N SER B 830 " --> pdb=" O LYS B 845 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS B 845 " --> pdb=" O SER B 830 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 874 through 881 removed outlier: 3.600A pdb=" N SER B 874 " --> pdb=" O ASP B 869 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 878 " --> pdb=" O LEU B 865 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 865 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN B 880 " --> pdb=" O TYR B 863 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR B 863 " --> pdb=" O ASN B 880 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 874 through 881 removed outlier: 3.600A pdb=" N SER B 874 " --> pdb=" O ASP B 869 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 878 " --> pdb=" O LEU B 865 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 865 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN B 880 " --> pdb=" O TYR B 863 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR B 863 " --> pdb=" O ASN B 880 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 899 " --> pdb=" O LEU B 917 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 949 through 954 removed outlier: 5.356A pdb=" N VAL B 938 " --> pdb=" O GLN B 951 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER B 937 " --> pdb=" O SER B 933 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B1180 " --> pdb=" O ALA B 932 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 963 through 964 Processing sheet with id=AF9, first strand: chain 'B' and resid 1000 through 1006 removed outlier: 6.736A pdb=" N THR B1015 " --> pdb=" O GLY B1001 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL B1003 " --> pdb=" O TYR B1013 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TYR B1013 " --> pdb=" O VAL B1003 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR B1005 " --> pdb=" O ARG B1011 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ARG B1011 " --> pdb=" O TYR B1005 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B1022 " --> pdb=" O LEU B1035 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 1042 through 1045 Processing sheet with id=AG2, first strand: chain 'B' and resid 1082 through 1089 removed outlier: 6.618A pdb=" N LEU B1098 " --> pdb=" O ALA B1084 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE B1086 " --> pdb=" O PHE B1096 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N PHE B1096 " --> pdb=" O PHE B1086 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU B1088 " --> pdb=" O GLN B1094 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N GLN B1094 " --> pdb=" O LEU B1088 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TRP B1097 " --> pdb=" O TYR B1108 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN B1123 " --> pdb=" O LEU B1107 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ARG B1109 " --> pdb=" O MET B1121 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N MET B1121 " --> pdb=" O ARG B1109 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 1137 through 1139 Processing sheet with id=AG4, first strand: chain 'B' and resid 1217 through 1219 Processing sheet with id=AG5, first strand: chain 'B' and resid 1242 through 1248 removed outlier: 3.504A pdb=" N LEU B1236 " --> pdb=" O SER B1268 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B1266 " --> pdb=" O GLU B1238 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 1299 through 1305 Processing sheet with id=AG7, first strand: chain 'B' and resid 1421 through 1422 Processing sheet with id=AG8, first strand: chain 'B' and resid 1421 through 1422 Processing sheet with id=AG9, first strand: chain 'B' and resid 1434 through 1438 removed outlier: 3.525A pdb=" N HIS B1434 " --> pdb=" O VAL B1447 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B1453 " --> pdb=" O LEU B1465 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 1472 through 1478 removed outlier: 7.041A pdb=" N VAL B1472 " --> pdb=" O LEU B1489 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B1489 " --> pdb=" O VAL B1472 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA B1474 " --> pdb=" O ALA B1487 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA B1497 " --> pdb=" O SER B1519 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N SER B1519 " --> pdb=" O ALA B1497 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE B1499 " --> pdb=" O VAL B1517 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 1524 through 1532 removed outlier: 5.132A pdb=" N LEU B1526 " --> pdb=" O TYR B1543 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TYR B1543 " --> pdb=" O LEU B1526 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASP B1528 " --> pdb=" O LEU B1541 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU B1541 " --> pdb=" O ASP B1528 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG B1556 " --> pdb=" O LEU B1538 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B1554 " --> pdb=" O TRP B1540 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU B1544 " --> pdb=" O ASN B1550 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASN B1550 " --> pdb=" O GLU B1544 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 1572 through 1577 removed outlier: 3.981A pdb=" N ARG B1574 " --> pdb=" O VAL B1590 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL B1598 " --> pdb=" O THR B1607 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B1605 " --> pdb=" O ASP B1600 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 1627 through 1629 removed outlier: 6.420A pdb=" N ILE B1642 " --> pdb=" O THR B1655 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR B1655 " --> pdb=" O ILE B1642 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B1644 " --> pdb=" O GLU B1653 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 1702 through 1703 Processing sheet with id=AH6, first strand: chain 'B' and resid 1745 through 1750 removed outlier: 4.164A pdb=" N GLY B1745 " --> pdb=" O LEU B1726 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B1726 " --> pdb=" O GLY B1745 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU B1785 " --> pdb=" O LEU B1772 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 1745 through 1750 removed outlier: 4.164A pdb=" N GLY B1745 " --> pdb=" O LEU B1726 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B1726 " --> pdb=" O GLY B1745 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2073 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: 13.94 Time building geometry restraints manager: 6.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4014 1.31 - 1.44: 6731 1.44 - 1.57: 13981 1.57 - 1.70: 16 1.70 - 1.82: 128 Bond restraints: 24870 Sorted by residual: bond pdb=" C ALA A1291 " pdb=" N PRO A1292 " ideal model delta sigma weight residual 1.331 1.416 -0.085 1.28e-02 6.10e+03 4.37e+01 bond pdb=" C ALA B1291 " pdb=" N PRO B1292 " ideal model delta sigma weight residual 1.331 1.415 -0.084 1.28e-02 6.10e+03 4.26e+01 bond pdb=" C VAL B1302 " pdb=" O VAL B1302 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.09e-02 8.42e+03 2.19e+01 bond pdb=" C VAL A1302 " pdb=" O VAL A1302 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.09e-02 8.42e+03 2.15e+01 bond pdb=" C HIS A1371 " pdb=" O HIS A1371 " ideal model delta sigma weight residual 1.236 1.183 0.053 1.20e-02 6.94e+03 1.93e+01 ... (remaining 24865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 32913 3.37 - 6.75: 812 6.75 - 10.12: 125 10.12 - 13.49: 29 13.49 - 16.86: 3 Bond angle restraints: 33882 Sorted by residual: angle pdb=" C ASP A 386 " pdb=" CA ASP A 386 " pdb=" CB ASP A 386 " ideal model delta sigma weight residual 110.62 99.84 10.78 1.46e+00 4.69e-01 5.46e+01 angle pdb=" C ASP B 386 " pdb=" CA ASP B 386 " pdb=" CB ASP B 386 " ideal model delta sigma weight residual 110.62 100.45 10.17 1.46e+00 4.69e-01 4.85e+01 angle pdb=" C ARG A 957 " pdb=" N LEU A 958 " pdb=" CA LEU A 958 " ideal model delta sigma weight residual 122.83 130.29 -7.46 1.08e+00 8.57e-01 4.77e+01 angle pdb=" N ARG B1296 " pdb=" CA ARG B1296 " pdb=" CB ARG B1296 " ideal model delta sigma weight residual 110.29 100.60 9.69 1.52e+00 4.33e-01 4.07e+01 angle pdb=" C ARG B 957 " pdb=" N LEU B 958 " pdb=" CA LEU B 958 " ideal model delta sigma weight residual 122.83 129.56 -6.73 1.08e+00 8.57e-01 3.88e+01 ... (remaining 33877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13760 17.95 - 35.91: 1282 35.91 - 53.86: 203 53.86 - 71.82: 45 71.82 - 89.77: 20 Dihedral angle restraints: 15310 sinusoidal: 6518 harmonic: 8792 Sorted by residual: dihedral pdb=" CB CYS B1597 " pdb=" SG CYS B1597 " pdb=" SG CYS B1606 " pdb=" CB CYS B1606 " ideal model delta sinusoidal sigma weight residual -86.00 -161.04 75.04 1 1.00e+01 1.00e-02 7.12e+01 dihedral pdb=" CB CYS A1597 " pdb=" SG CYS A1597 " pdb=" SG CYS A1606 " pdb=" CB CYS A1606 " ideal model delta sinusoidal sigma weight residual -86.00 -149.34 63.34 1 1.00e+01 1.00e-02 5.29e+01 dihedral pdb=" CA ALA B 640 " pdb=" C ALA B 640 " pdb=" N MET B 641 " pdb=" CA MET B 641 " ideal model delta harmonic sigma weight residual -180.00 -144.44 -35.56 0 5.00e+00 4.00e-02 5.06e+01 ... (remaining 15307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 3723 0.179 - 0.358: 58 0.358 - 0.537: 6 0.537 - 0.716: 1 0.716 - 0.895: 2 Chirality restraints: 3790 Sorted by residual: chirality pdb=" C1 NAG A2607 " pdb=" ND2 ASN A1756 " pdb=" C2 NAG A2607 " pdb=" O5 NAG A2607 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" C1 NAG B2607 " pdb=" ND2 ASN B1756 " pdb=" C2 NAG B2607 " pdb=" O5 NAG B2607 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.87e+01 chirality pdb=" CB ILE A 566 " pdb=" CA ILE A 566 " pdb=" CG1 ILE A 566 " pdb=" CG2 ILE A 566 " both_signs ideal model delta sigma weight residual False 2.64 2.10 0.55 2.00e-01 2.50e+01 7.47e+00 ... (remaining 3787 not shown) Planarity restraints: 4416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1756 " -0.003 2.00e-02 2.50e+03 4.52e-02 2.55e+01 pdb=" CG ASN A1756 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A1756 " -0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN A1756 " 0.051 2.00e-02 2.50e+03 pdb=" C1 NAG A2607 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1756 " -0.003 2.00e-02 2.50e+03 3.98e-02 1.98e+01 pdb=" CG ASN B1756 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN B1756 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN B1756 " 0.046 2.00e-02 2.50e+03 pdb=" C1 NAG B2607 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 746 " -0.068 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO B 747 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO B 747 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 747 " -0.056 5.00e-02 4.00e+02 ... (remaining 4413 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 7660 2.86 - 3.37: 17676 3.37 - 3.88: 41516 3.88 - 4.39: 44719 4.39 - 4.90: 79314 Nonbonded interactions: 190885 Sorted by model distance: nonbonded pdb=" OD2 ASP B 680 " pdb=" OH TYR B 740 " model vdw 2.355 3.040 nonbonded pdb=" O ASP B1173 " pdb=" OG SER B1176 " model vdw 2.360 3.040 nonbonded pdb=" O ASP A1173 " pdb=" OG SER A1176 " model vdw 2.364 3.040 nonbonded pdb=" OG SER A 933 " pdb=" OG SER A 937 " model vdw 2.365 3.040 nonbonded pdb=" OG SER B 933 " pdb=" OG SER B 937 " model vdw 2.366 3.040 ... (remaining 190880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.920 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 59.540 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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 0.088 24916 Z= 0.340 Angle : 1.271 17.382 34000 Z= 0.654 Chirality : 0.069 0.895 3790 Planarity : 0.011 0.107 4396 Dihedral : 14.101 89.774 9570 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.04 % 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: -2.34 (0.13), residues: 2996 helix: -3.78 (0.20), residues: 198 sheet: -0.70 (0.14), residues: 1238 loop : -1.97 (0.12), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP B 861 HIS 0.030 0.002 HIS A 591 PHE 0.067 0.004 PHE B 599 TYR 0.032 0.003 TYR A 740 ARG 0.025 0.001 ARG B1549 Details of bonding type rmsd link_NAG-ASN : bond 0.01522 ( 20) link_NAG-ASN : angle 4.66724 ( 60) link_BETA1-4 : bond 0.00450 ( 4) link_BETA1-4 : angle 1.86897 ( 12) hydrogen bonds : bond 0.23318 ( 726) hydrogen bonds : angle 9.50379 ( 2073) link_BETA1-6 : bond 0.00199 ( 2) link_BETA1-6 : angle 1.25182 ( 6) SS BOND : bond 0.00521 ( 20) SS BOND : angle 2.37837 ( 40) covalent geometry : bond 0.00714 (24870) covalent geometry : angle 1.25468 (33882) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 2.384 Fit side-chains revert: symmetry clash REVERT: A 234 GLU cc_start: 0.7794 (pt0) cc_final: 0.7575 (pt0) REVERT: A 295 ARG cc_start: 0.7864 (mtt90) cc_final: 0.7095 (mtp-110) REVERT: A 462 ARG cc_start: 0.7358 (ttt180) cc_final: 0.7139 (ttt-90) REVERT: A 832 LYS cc_start: 0.7383 (mmtt) cc_final: 0.7173 (tptm) REVERT: A 842 ILE cc_start: 0.8843 (mt) cc_final: 0.8443 (tt) REVERT: A 864 GLU cc_start: 0.6902 (mm-30) cc_final: 0.5757 (tm-30) REVERT: A 1199 MET cc_start: 0.8465 (mtp) cc_final: 0.8217 (mmm) REVERT: A 1433 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7753 (mt-10) REVERT: A 1469 ARG cc_start: 0.7969 (mtm-85) cc_final: 0.7265 (mpt180) REVERT: B 241 LYS cc_start: 0.7460 (mptt) cc_final: 0.7241 (tttp) REVERT: B 832 LYS cc_start: 0.7450 (mmtt) cc_final: 0.7243 (tptp) REVERT: B 864 GLU cc_start: 0.5972 (tm-30) cc_final: 0.5345 (tp30) REVERT: B 1199 MET cc_start: 0.8480 (mtp) cc_final: 0.8219 (mmm) REVERT: B 1433 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7808 (mt-10) REVERT: B 1492 THR cc_start: 0.6239 (m) cc_final: 0.5589 (p) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.4207 time to fit residues: 173.0787 Evaluate side-chains 205 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 255 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 154 optimal weight: 0.0010 chunk 122 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 274 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN A 465 ASN ** A 584 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 746 HIS A1020 ASN A1124 GLN A1182 GLN A1241 GLN A1244 GLN A1399 GLN ** A1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1746 GLN B 222 GLN B 404 GLN B 501 GLN B 690 ASN ** B 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 ASN B1124 GLN B1182 GLN B1241 GLN B1399 GLN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.196678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127752 restraints weight = 28639.553| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.65 r_work: 0.3320 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24916 Z= 0.131 Angle : 0.618 9.324 34000 Z= 0.309 Chirality : 0.043 0.215 3790 Planarity : 0.006 0.078 4396 Dihedral : 5.648 55.347 3858 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.71 % Allowed : 5.56 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: -1.53 (0.14), residues: 2996 helix: -1.39 (0.33), residues: 204 sheet: -0.39 (0.14), residues: 1268 loop : -1.47 (0.13), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 688 HIS 0.004 0.001 HIS A1450 PHE 0.026 0.001 PHE B 744 TYR 0.015 0.001 TYR A1722 ARG 0.007 0.000 ARG B1075 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 20) link_NAG-ASN : angle 2.50547 ( 60) link_BETA1-4 : bond 0.00475 ( 4) link_BETA1-4 : angle 1.74578 ( 12) hydrogen bonds : bond 0.04035 ( 726) hydrogen bonds : angle 6.46827 ( 2073) link_BETA1-6 : bond 0.00077 ( 2) link_BETA1-6 : angle 1.32018 ( 6) SS BOND : bond 0.00398 ( 20) SS BOND : angle 0.91557 ( 40) covalent geometry : bond 0.00294 (24870) covalent geometry : angle 0.60850 (33882) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6721 (mtm-85) cc_final: 0.6302 (mtm-85) REVERT: A 234 GLU cc_start: 0.8003 (pt0) cc_final: 0.7768 (pt0) REVERT: A 295 ARG cc_start: 0.8023 (mtt90) cc_final: 0.7796 (mtt90) REVERT: A 462 ARG cc_start: 0.7344 (ttt180) cc_final: 0.7074 (ttt-90) REVERT: A 513 ILE cc_start: 0.8258 (mt) cc_final: 0.8056 (mm) REVERT: A 728 MET cc_start: 0.6151 (mmt) cc_final: 0.5886 (mmm) REVERT: A 832 LYS cc_start: 0.7326 (mmtt) cc_final: 0.7090 (tptp) REVERT: A 1025 MET cc_start: 0.9197 (ttp) cc_final: 0.8947 (ttp) REVERT: A 1199 MET cc_start: 0.8539 (mtp) cc_final: 0.8273 (mmm) REVERT: A 1433 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7991 (mt-10) REVERT: A 1469 ARG cc_start: 0.8026 (mtm-85) cc_final: 0.7404 (mpt180) REVERT: A 1526 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8337 (tt) REVERT: A 1603 ARG cc_start: 0.7510 (mtm110) cc_final: 0.7233 (ttm170) REVERT: A 1630 ASP cc_start: 0.8449 (p0) cc_final: 0.8013 (p0) REVERT: A 1782 LEU cc_start: 0.7328 (tp) cc_final: 0.7013 (tt) REVERT: B 210 ARG cc_start: 0.6837 (mtm-85) cc_final: 0.6477 (mtm-85) REVERT: B 241 LYS cc_start: 0.7568 (mptt) cc_final: 0.7018 (tttp) REVERT: B 246 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7556 (pt0) REVERT: B 832 LYS cc_start: 0.7329 (mmtt) cc_final: 0.7118 (tptp) REVERT: B 1025 MET cc_start: 0.9194 (ttp) cc_final: 0.8972 (ttp) REVERT: B 1199 MET cc_start: 0.8535 (mtp) cc_final: 0.8249 (mmm) REVERT: B 1433 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8024 (mt-10) REVERT: B 1469 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7367 (mpt180) REVERT: B 1492 THR cc_start: 0.6181 (m) cc_final: 0.5736 (p) REVERT: B 1597 CYS cc_start: 0.7797 (t) cc_final: 0.7473 (t) REVERT: B 1630 ASP cc_start: 0.8429 (p0) cc_final: 0.8018 (p0) REVERT: B 1749 LEU cc_start: 0.6768 (tp) cc_final: 0.6536 (tp) outliers start: 18 outliers final: 12 residues processed: 238 average time/residue: 0.3842 time to fit residues: 141.3206 Evaluate side-chains 209 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1185 ASP Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1367 ASP Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 1185 ASP Chi-restraints excluded: chain B residue 1263 LEU Chi-restraints excluded: chain B residue 1367 ASP Chi-restraints excluded: chain B residue 1552 SER Chi-restraints excluded: chain B residue 1596 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 193 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 288 optimal weight: 0.7980 chunk 271 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 289 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 HIS A1244 GLN ** A1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1746 GLN B 222 GLN B 746 HIS ** B 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1399 GLN ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1746 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.193495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.123448 restraints weight = 28467.934| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.68 r_work: 0.3253 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24916 Z= 0.144 Angle : 0.586 8.651 34000 Z= 0.289 Chirality : 0.043 0.228 3790 Planarity : 0.005 0.059 4396 Dihedral : 5.246 54.753 3858 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.91 % Allowed : 8.37 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: -1.19 (0.14), residues: 2996 helix: -0.25 (0.36), residues: 204 sheet: -0.42 (0.14), residues: 1314 loop : -1.13 (0.14), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 688 HIS 0.004 0.001 HIS B1427 PHE 0.028 0.001 PHE B 744 TYR 0.010 0.001 TYR A1722 ARG 0.005 0.000 ARG B1075 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 20) link_NAG-ASN : angle 2.27427 ( 60) link_BETA1-4 : bond 0.00380 ( 4) link_BETA1-4 : angle 1.86271 ( 12) hydrogen bonds : bond 0.03547 ( 726) hydrogen bonds : angle 5.78197 ( 2073) link_BETA1-6 : bond 0.00060 ( 2) link_BETA1-6 : angle 1.35024 ( 6) SS BOND : bond 0.00266 ( 20) SS BOND : angle 0.72384 ( 40) covalent geometry : bond 0.00344 (24870) covalent geometry : angle 0.57752 (33882) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6744 (mtm-85) cc_final: 0.6291 (mtm-85) REVERT: A 339 GLU cc_start: 0.7254 (tt0) cc_final: 0.6345 (tm-30) REVERT: A 462 ARG cc_start: 0.7426 (ttt180) cc_final: 0.7118 (ttt-90) REVERT: A 513 ILE cc_start: 0.8276 (mt) cc_final: 0.8057 (mm) REVERT: A 832 LYS cc_start: 0.7298 (mmtt) cc_final: 0.7068 (tptp) REVERT: A 1025 MET cc_start: 0.9202 (ttp) cc_final: 0.8909 (ttp) REVERT: A 1199 MET cc_start: 0.8656 (mtp) cc_final: 0.8390 (mmm) REVERT: A 1433 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8049 (mt-10) REVERT: A 1526 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8422 (tt) REVERT: A 1603 ARG cc_start: 0.7593 (mtm110) cc_final: 0.7270 (ttm170) REVERT: A 1630 ASP cc_start: 0.8459 (p0) cc_final: 0.8040 (p0) REVERT: A 1667 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7986 (tm-30) REVERT: B 210 ARG cc_start: 0.6851 (mtm-85) cc_final: 0.6476 (mtm-85) REVERT: B 241 LYS cc_start: 0.7528 (mptt) cc_final: 0.7011 (tttp) REVERT: B 246 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7627 (pt0) REVERT: B 295 ARG cc_start: 0.8026 (mtt90) cc_final: 0.7647 (mtt90) REVERT: B 339 GLU cc_start: 0.7255 (tt0) cc_final: 0.6348 (tm-30) REVERT: B 565 MET cc_start: 0.6952 (mmp) cc_final: 0.6683 (mmp) REVERT: B 584 GLN cc_start: 0.5268 (tt0) cc_final: 0.5029 (tt0) REVERT: B 728 MET cc_start: 0.6242 (mmm) cc_final: 0.5633 (mmt) REVERT: B 864 GLU cc_start: 0.5842 (tm-30) cc_final: 0.5200 (tm-30) REVERT: B 1025 MET cc_start: 0.9207 (ttp) cc_final: 0.8926 (ttp) REVERT: B 1199 MET cc_start: 0.8644 (mtp) cc_final: 0.8368 (mmm) REVERT: B 1433 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8020 (mt-10) REVERT: B 1469 ARG cc_start: 0.8076 (mtm-85) cc_final: 0.7479 (mpt180) REVERT: B 1492 THR cc_start: 0.6258 (m) cc_final: 0.5880 (p) REVERT: B 1630 ASP cc_start: 0.8454 (p0) cc_final: 0.8063 (p0) REVERT: B 1749 LEU cc_start: 0.6935 (tp) cc_final: 0.6692 (tp) outliers start: 23 outliers final: 14 residues processed: 220 average time/residue: 0.4106 time to fit residues: 139.0453 Evaluate side-chains 208 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 967 GLU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1589 LEU Chi-restraints excluded: chain A residue 1667 GLN Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1208 LEU Chi-restraints excluded: chain B residue 1263 LEU Chi-restraints excluded: chain B residue 1552 SER Chi-restraints excluded: chain B residue 1589 LEU Chi-restraints excluded: chain B residue 1596 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 140 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 265 optimal weight: 0.0050 chunk 269 optimal weight: 0.4980 chunk 234 optimal weight: 0.5980 chunk 193 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 198 optimal weight: 0.5980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 697 GLN A1450 HIS A1570 GLN A1592 ASN ** B 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.193816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.126127 restraints weight = 28819.091| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.66 r_work: 0.3266 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24916 Z= 0.111 Angle : 0.538 8.258 34000 Z= 0.264 Chirality : 0.041 0.216 3790 Planarity : 0.004 0.057 4396 Dihedral : 4.971 54.310 3858 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.14 % Allowed : 9.75 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: -0.84 (0.15), residues: 2996 helix: 0.53 (0.38), residues: 204 sheet: -0.35 (0.14), residues: 1328 loop : -0.81 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 688 HIS 0.003 0.001 HIS A 445 PHE 0.030 0.001 PHE B 744 TYR 0.013 0.001 TYR B 897 ARG 0.004 0.000 ARG B1075 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 20) link_NAG-ASN : angle 2.15958 ( 60) link_BETA1-4 : bond 0.00420 ( 4) link_BETA1-4 : angle 1.68220 ( 12) hydrogen bonds : bond 0.02937 ( 726) hydrogen bonds : angle 5.36202 ( 2073) link_BETA1-6 : bond 0.00048 ( 2) link_BETA1-6 : angle 1.37466 ( 6) SS BOND : bond 0.00588 ( 20) SS BOND : angle 0.63671 ( 40) covalent geometry : bond 0.00263 (24870) covalent geometry : angle 0.52977 (33882) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6643 (mtm-85) cc_final: 0.6203 (mtm-85) REVERT: A 339 GLU cc_start: 0.7311 (tt0) cc_final: 0.6321 (tm-30) REVERT: A 462 ARG cc_start: 0.7452 (ttt180) cc_final: 0.7060 (ttt-90) REVERT: A 513 ILE cc_start: 0.8205 (mt) cc_final: 0.7870 (mt) REVERT: A 515 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8094 (tmtt) REVERT: A 565 MET cc_start: 0.7235 (mmm) cc_final: 0.6512 (tpt) REVERT: A 1025 MET cc_start: 0.9263 (ttp) cc_final: 0.8968 (ttp) REVERT: A 1105 LEU cc_start: 0.7930 (tp) cc_final: 0.7696 (tt) REVERT: A 1199 MET cc_start: 0.8661 (mtp) cc_final: 0.8370 (mmm) REVERT: A 1433 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8002 (mt-10) REVERT: A 1526 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8401 (tt) REVERT: A 1549 ARG cc_start: 0.8208 (mtp85) cc_final: 0.7919 (mtt90) REVERT: A 1630 ASP cc_start: 0.8420 (p0) cc_final: 0.8054 (p0) REVERT: B 210 ARG cc_start: 0.6731 (mtm-85) cc_final: 0.6323 (mtm-85) REVERT: B 220 CYS cc_start: 0.6996 (t) cc_final: 0.6510 (t) REVERT: B 241 LYS cc_start: 0.7451 (mptt) cc_final: 0.6949 (tttp) REVERT: B 246 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7531 (pt0) REVERT: B 295 ARG cc_start: 0.7932 (mtt90) cc_final: 0.7565 (mtt90) REVERT: B 339 GLU cc_start: 0.7293 (tt0) cc_final: 0.6307 (tm-30) REVERT: B 462 ARG cc_start: 0.6725 (ttt-90) cc_final: 0.5949 (ttp80) REVERT: B 515 LYS cc_start: 0.8304 (tttt) cc_final: 0.8032 (tptt) REVERT: B 864 GLU cc_start: 0.5805 (tm-30) cc_final: 0.5168 (tm-30) REVERT: B 1025 MET cc_start: 0.9246 (ttp) cc_final: 0.8961 (ttp) REVERT: B 1199 MET cc_start: 0.8662 (mtp) cc_final: 0.8355 (mmm) REVERT: B 1248 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8529 (mt) REVERT: B 1433 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8025 (mt-10) REVERT: B 1469 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7481 (mpt180) REVERT: B 1492 THR cc_start: 0.6157 (m) cc_final: 0.5773 (p) REVERT: B 1630 ASP cc_start: 0.8393 (p0) cc_final: 0.8021 (p0) REVERT: B 1749 LEU cc_start: 0.6893 (tp) cc_final: 0.6604 (tp) outliers start: 29 outliers final: 18 residues processed: 226 average time/residue: 0.3947 time to fit residues: 136.6034 Evaluate side-chains 206 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 967 GLU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1589 LEU Chi-restraints excluded: chain A residue 1592 ASN Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 967 GLU Chi-restraints excluded: chain B residue 1208 LEU Chi-restraints excluded: chain B residue 1248 LEU Chi-restraints excluded: chain B residue 1263 LEU Chi-restraints excluded: chain B residue 1426 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1539 ILE Chi-restraints excluded: chain B residue 1552 SER Chi-restraints excluded: chain B residue 1589 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 258 optimal weight: 0.0570 chunk 182 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 216 optimal weight: 9.9990 chunk 252 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1229 HIS A1257 GLN A1592 ASN B 584 GLN ** B 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.192827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.123341 restraints weight = 28716.792| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.65 r_work: 0.3260 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24916 Z= 0.131 Angle : 0.546 8.427 34000 Z= 0.267 Chirality : 0.042 0.217 3790 Planarity : 0.004 0.068 4396 Dihedral : 4.919 54.454 3858 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.42 % Allowed : 10.46 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: -0.71 (0.15), residues: 2996 helix: 0.84 (0.39), residues: 204 sheet: -0.35 (0.14), residues: 1338 loop : -0.66 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 688 HIS 0.004 0.001 HIS B1427 PHE 0.030 0.001 PHE A 744 TYR 0.014 0.001 TYR A 897 ARG 0.006 0.000 ARG A 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00348 ( 20) link_NAG-ASN : angle 2.14905 ( 60) link_BETA1-4 : bond 0.00367 ( 4) link_BETA1-4 : angle 1.70619 ( 12) hydrogen bonds : bond 0.02978 ( 726) hydrogen bonds : angle 5.28333 ( 2073) link_BETA1-6 : bond 0.00025 ( 2) link_BETA1-6 : angle 1.40472 ( 6) SS BOND : bond 0.00432 ( 20) SS BOND : angle 0.76041 ( 40) covalent geometry : bond 0.00314 (24870) covalent geometry : angle 0.53792 (33882) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 2.375 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6531 (mtm-85) cc_final: 0.6103 (mtm-85) REVERT: A 220 CYS cc_start: 0.6984 (t) cc_final: 0.6498 (t) REVERT: A 317 GLU cc_start: 0.7294 (pt0) cc_final: 0.6887 (mt-10) REVERT: A 339 GLU cc_start: 0.7350 (tt0) cc_final: 0.6334 (tm-30) REVERT: A 462 ARG cc_start: 0.7432 (ttt180) cc_final: 0.7085 (ttt-90) REVERT: A 512 MET cc_start: 0.7274 (ttt) cc_final: 0.6526 (ttp) REVERT: A 515 LYS cc_start: 0.8417 (ttpt) cc_final: 0.8087 (tmtt) REVERT: A 1105 LEU cc_start: 0.7918 (tp) cc_final: 0.7688 (tt) REVERT: A 1199 MET cc_start: 0.8665 (mtp) cc_final: 0.8345 (mmm) REVERT: A 1296 ARG cc_start: 0.7606 (mtt180) cc_final: 0.7259 (mtt180) REVERT: A 1433 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7961 (mt-10) REVERT: A 1526 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8395 (tt) REVERT: A 1630 ASP cc_start: 0.8423 (p0) cc_final: 0.8051 (p0) REVERT: A 1662 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8800 (tt0) REVERT: A 1667 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: B 210 ARG cc_start: 0.6642 (mtm-85) cc_final: 0.6227 (mtm-85) REVERT: B 220 CYS cc_start: 0.6953 (t) cc_final: 0.6474 (t) REVERT: B 241 LYS cc_start: 0.7428 (mptt) cc_final: 0.6914 (tttp) REVERT: B 246 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7493 (pt0) REVERT: B 339 GLU cc_start: 0.7359 (tt0) cc_final: 0.6358 (tm-30) REVERT: B 515 LYS cc_start: 0.8296 (tttt) cc_final: 0.8033 (tptt) REVERT: B 728 MET cc_start: 0.6235 (mmm) cc_final: 0.5648 (mmt) REVERT: B 832 LYS cc_start: 0.7242 (mmtt) cc_final: 0.7032 (tptp) REVERT: B 864 GLU cc_start: 0.5773 (tm-30) cc_final: 0.5140 (tm-30) REVERT: B 1199 MET cc_start: 0.8653 (mtp) cc_final: 0.8339 (mmm) REVERT: B 1248 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8531 (mt) REVERT: B 1433 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7970 (mt-10) REVERT: B 1469 ARG cc_start: 0.8105 (mtm-85) cc_final: 0.7502 (mpt180) REVERT: B 1492 THR cc_start: 0.6044 (m) cc_final: 0.5678 (p) REVERT: B 1630 ASP cc_start: 0.8407 (p0) cc_final: 0.8032 (p0) REVERT: B 1749 LEU cc_start: 0.6795 (tp) cc_final: 0.6578 (tp) outliers start: 36 outliers final: 25 residues processed: 222 average time/residue: 0.3798 time to fit residues: 129.7742 Evaluate side-chains 214 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 4.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 967 GLU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1260 GLN Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1526 LEU Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1589 LEU Chi-restraints excluded: chain A residue 1662 GLU Chi-restraints excluded: chain A residue 1667 GLN Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 967 GLU Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1208 LEU Chi-restraints excluded: chain B residue 1248 LEU Chi-restraints excluded: chain B residue 1260 GLN Chi-restraints excluded: chain B residue 1263 LEU Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1426 VAL Chi-restraints excluded: chain B residue 1539 ILE Chi-restraints excluded: chain B residue 1552 SER Chi-restraints excluded: chain B residue 1589 LEU Chi-restraints excluded: chain B residue 1596 LEU Chi-restraints excluded: chain B residue 1757 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 162 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 192 optimal weight: 30.0000 chunk 274 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 182 optimal weight: 0.0060 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1327 GLN A1592 ASN B 244 ASN B 722 HIS ** B 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1229 HIS B1327 GLN B1450 HIS ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.189417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116093 restraints weight = 28532.163| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.08 r_work: 0.3251 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 24916 Z= 0.210 Angle : 0.610 9.150 34000 Z= 0.297 Chirality : 0.043 0.212 3790 Planarity : 0.005 0.067 4396 Dihedral : 5.139 55.455 3858 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.70 % Allowed : 10.81 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: -0.76 (0.15), residues: 2996 helix: 0.80 (0.39), residues: 204 sheet: -0.40 (0.14), residues: 1314 loop : -0.68 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 688 HIS 0.005 0.001 HIS B1427 PHE 0.030 0.002 PHE B 744 TYR 0.013 0.002 TYR A 897 ARG 0.007 0.000 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 20) link_NAG-ASN : angle 2.24032 ( 60) link_BETA1-4 : bond 0.00320 ( 4) link_BETA1-4 : angle 1.93286 ( 12) hydrogen bonds : bond 0.03318 ( 726) hydrogen bonds : angle 5.40850 ( 2073) link_BETA1-6 : bond 0.00294 ( 2) link_BETA1-6 : angle 1.58290 ( 6) SS BOND : bond 0.00313 ( 20) SS BOND : angle 0.91018 ( 40) covalent geometry : bond 0.00511 (24870) covalent geometry : angle 0.60153 (33882) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 2.433 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6508 (mtm-85) cc_final: 0.6105 (mtm-85) REVERT: A 220 CYS cc_start: 0.7111 (t) cc_final: 0.6649 (t) REVERT: A 317 GLU cc_start: 0.7248 (pt0) cc_final: 0.6871 (mt-10) REVERT: A 462 ARG cc_start: 0.7360 (ttt180) cc_final: 0.7008 (ttt-90) REVERT: A 512 MET cc_start: 0.7247 (ttt) cc_final: 0.6580 (ttp) REVERT: A 515 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8139 (tmtt) REVERT: A 565 MET cc_start: 0.7313 (mmm) cc_final: 0.6876 (tpt) REVERT: A 728 MET cc_start: 0.6000 (mmm) cc_final: 0.5695 (mmm) REVERT: A 1199 MET cc_start: 0.8616 (mtp) cc_final: 0.8296 (mmm) REVERT: A 1248 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8550 (mt) REVERT: A 1433 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7911 (mt-10) REVERT: A 1630 ASP cc_start: 0.8530 (p0) cc_final: 0.8130 (p0) REVERT: A 1662 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8747 (tt0) REVERT: A 1667 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7792 (tm-30) REVERT: B 210 ARG cc_start: 0.6611 (mtm-85) cc_final: 0.6242 (mtm-85) REVERT: B 220 CYS cc_start: 0.7094 (t) cc_final: 0.6646 (t) REVERT: B 241 LYS cc_start: 0.7474 (mptt) cc_final: 0.7014 (tttp) REVERT: B 246 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7566 (pt0) REVERT: B 295 ARG cc_start: 0.7801 (mtt90) cc_final: 0.7570 (mtt90) REVERT: B 515 LYS cc_start: 0.8325 (tttt) cc_final: 0.8090 (tptt) REVERT: B 864 GLU cc_start: 0.5764 (tm-30) cc_final: 0.5131 (tm-30) REVERT: B 1150 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7607 (ttp80) REVERT: B 1199 MET cc_start: 0.8614 (mtp) cc_final: 0.8303 (mmm) REVERT: B 1248 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8515 (mt) REVERT: B 1433 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7909 (mt-10) REVERT: B 1492 THR cc_start: 0.6175 (m) cc_final: 0.5785 (p) REVERT: B 1597 CYS cc_start: 0.7843 (t) cc_final: 0.7597 (t) REVERT: B 1630 ASP cc_start: 0.8478 (p0) cc_final: 0.8117 (p0) REVERT: B 1749 LEU cc_start: 0.6810 (tp) cc_final: 0.6564 (tp) outliers start: 43 outliers final: 26 residues processed: 216 average time/residue: 0.4199 time to fit residues: 137.6114 Evaluate side-chains 205 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 967 GLU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1260 GLN Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1589 LEU Chi-restraints excluded: chain A residue 1592 ASN Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1662 GLU Chi-restraints excluded: chain A residue 1667 GLN Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 967 GLU Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1208 LEU Chi-restraints excluded: chain B residue 1248 LEU Chi-restraints excluded: chain B residue 1260 GLN Chi-restraints excluded: chain B residue 1263 LEU Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1426 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1539 ILE Chi-restraints excluded: chain B residue 1552 SER Chi-restraints excluded: chain B residue 1589 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 40 optimal weight: 5.9990 chunk 149 optimal weight: 0.8980 chunk 271 optimal weight: 0.0870 chunk 147 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 287 optimal weight: 0.8980 chunk 68 optimal weight: 0.0770 chunk 148 optimal weight: 4.9990 chunk 252 optimal weight: 0.9980 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1592 ASN ** 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 = 0.4251 r_free = 0.4251 target = 0.191352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118599 restraints weight = 28576.464| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.10 r_work: 0.3290 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24916 Z= 0.117 Angle : 0.547 10.601 34000 Z= 0.266 Chirality : 0.042 0.210 3790 Planarity : 0.004 0.070 4396 Dihedral : 4.971 54.593 3858 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.54 % Allowed : 11.37 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: -0.64 (0.15), residues: 2996 helix: 1.08 (0.39), residues: 204 sheet: -0.43 (0.14), residues: 1344 loop : -0.50 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 688 HIS 0.004 0.001 HIS A 445 PHE 0.031 0.001 PHE A 744 TYR 0.013 0.001 TYR A 897 ARG 0.005 0.000 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00338 ( 20) link_NAG-ASN : angle 2.07698 ( 60) link_BETA1-4 : bond 0.00404 ( 4) link_BETA1-4 : angle 1.69727 ( 12) hydrogen bonds : bond 0.02835 ( 726) hydrogen bonds : angle 5.18864 ( 2073) link_BETA1-6 : bond 0.00072 ( 2) link_BETA1-6 : angle 1.43427 ( 6) SS BOND : bond 0.00265 ( 20) SS BOND : angle 0.72248 ( 40) covalent geometry : bond 0.00282 (24870) covalent geometry : angle 0.53951 (33882) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 2.671 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6512 (mtm-85) cc_final: 0.6125 (mtm-85) REVERT: A 220 CYS cc_start: 0.6890 (t) cc_final: 0.6441 (t) REVERT: A 317 GLU cc_start: 0.7177 (pt0) cc_final: 0.6822 (mt-10) REVERT: A 462 ARG cc_start: 0.7421 (ttt180) cc_final: 0.6985 (ttt-90) REVERT: A 512 MET cc_start: 0.7165 (ttt) cc_final: 0.6591 (ttp) REVERT: A 515 LYS cc_start: 0.8407 (ttpt) cc_final: 0.8104 (tmtt) REVERT: A 565 MET cc_start: 0.7262 (mmm) cc_final: 0.6856 (tpt) REVERT: A 641 MET cc_start: 0.2102 (mmm) cc_final: 0.1606 (mpp) REVERT: A 1105 LEU cc_start: 0.7889 (tp) cc_final: 0.7673 (tt) REVERT: A 1199 MET cc_start: 0.8609 (mtp) cc_final: 0.8300 (mmm) REVERT: A 1433 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7892 (mt-10) REVERT: A 1630 ASP cc_start: 0.8414 (p0) cc_final: 0.8015 (p0) REVERT: A 1662 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8771 (tt0) REVERT: A 1667 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: B 210 ARG cc_start: 0.6601 (mtm-85) cc_final: 0.6230 (mtm-85) REVERT: B 220 CYS cc_start: 0.6863 (t) cc_final: 0.6421 (t) REVERT: B 241 LYS cc_start: 0.7473 (mptt) cc_final: 0.6981 (tttp) REVERT: B 246 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7520 (pt0) REVERT: B 295 ARG cc_start: 0.7714 (mtt90) cc_final: 0.7466 (mtt90) REVERT: B 515 LYS cc_start: 0.8286 (tttt) cc_final: 0.8071 (tptt) REVERT: B 864 GLU cc_start: 0.5732 (tm-30) cc_final: 0.5097 (tm-30) REVERT: B 1102 SER cc_start: 0.7137 (p) cc_final: 0.6876 (t) REVERT: B 1199 MET cc_start: 0.8586 (mtp) cc_final: 0.8265 (mmm) REVERT: B 1248 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8500 (mt) REVERT: B 1433 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7860 (mt-10) REVERT: B 1492 THR cc_start: 0.6095 (m) cc_final: 0.5755 (p) REVERT: B 1630 ASP cc_start: 0.8372 (p0) cc_final: 0.8000 (p0) REVERT: B 1749 LEU cc_start: 0.6721 (tp) cc_final: 0.6495 (tp) outliers start: 39 outliers final: 31 residues processed: 211 average time/residue: 0.4189 time to fit residues: 134.8841 Evaluate side-chains 207 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 967 GLU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1260 GLN Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1589 LEU Chi-restraints excluded: chain A residue 1592 ASN Chi-restraints excluded: chain A residue 1662 GLU Chi-restraints excluded: chain A residue 1667 GLN Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 967 GLU Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1208 LEU Chi-restraints excluded: chain B residue 1248 LEU Chi-restraints excluded: chain B residue 1260 GLN Chi-restraints excluded: chain B residue 1263 LEU Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1426 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1539 ILE Chi-restraints excluded: chain B residue 1552 SER Chi-restraints excluded: chain B residue 1589 LEU Chi-restraints excluded: chain B residue 1596 LEU Chi-restraints excluded: chain B residue 1659 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 162 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 211 optimal weight: 20.0000 chunk 183 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 281 optimal weight: 0.1980 chunk 259 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1592 ASN ** B 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.190247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.120574 restraints weight = 28550.709| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.63 r_work: 0.3229 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24916 Z= 0.154 Angle : 0.566 10.076 34000 Z= 0.274 Chirality : 0.042 0.197 3790 Planarity : 0.004 0.063 4396 Dihedral : 4.971 54.780 3858 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.66 % Allowed : 11.37 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: -0.60 (0.15), residues: 2996 helix: 1.09 (0.39), residues: 204 sheet: -0.41 (0.14), residues: 1334 loop : -0.46 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 688 HIS 0.004 0.001 HIS B1427 PHE 0.031 0.001 PHE A 744 TYR 0.012 0.001 TYR B 897 ARG 0.004 0.000 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 20) link_NAG-ASN : angle 2.10936 ( 60) link_BETA1-4 : bond 0.00384 ( 4) link_BETA1-4 : angle 1.77608 ( 12) hydrogen bonds : bond 0.02957 ( 726) hydrogen bonds : angle 5.18475 ( 2073) link_BETA1-6 : bond 0.00084 ( 2) link_BETA1-6 : angle 1.55200 ( 6) SS BOND : bond 0.00336 ( 20) SS BOND : angle 0.92414 ( 40) covalent geometry : bond 0.00377 (24870) covalent geometry : angle 0.55794 (33882) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 2.418 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6530 (mtm-85) cc_final: 0.6139 (mtm-85) REVERT: A 220 CYS cc_start: 0.7056 (t) cc_final: 0.6602 (t) REVERT: A 317 GLU cc_start: 0.7250 (pt0) cc_final: 0.6893 (mt-10) REVERT: A 462 ARG cc_start: 0.7526 (ttt180) cc_final: 0.7068 (ttt-90) REVERT: A 512 MET cc_start: 0.7199 (ttt) cc_final: 0.6689 (ttp) REVERT: A 515 LYS cc_start: 0.8413 (ttpt) cc_final: 0.8107 (tmtt) REVERT: A 565 MET cc_start: 0.7248 (mmm) cc_final: 0.6943 (tpt) REVERT: A 1199 MET cc_start: 0.8670 (mtp) cc_final: 0.8347 (mmm) REVERT: A 1433 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7961 (mt-10) REVERT: A 1597 CYS cc_start: 0.7819 (t) cc_final: 0.7532 (t) REVERT: A 1630 ASP cc_start: 0.8457 (p0) cc_final: 0.8079 (p0) REVERT: A 1662 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8795 (tt0) REVERT: A 1667 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: B 210 ARG cc_start: 0.6600 (mtm-85) cc_final: 0.6210 (mtm-85) REVERT: B 220 CYS cc_start: 0.6996 (t) cc_final: 0.6541 (t) REVERT: B 241 LYS cc_start: 0.7505 (mptt) cc_final: 0.6975 (tttp) REVERT: B 246 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7540 (pt0) REVERT: B 295 ARG cc_start: 0.7762 (mtt90) cc_final: 0.7497 (mtt90) REVERT: B 515 LYS cc_start: 0.8246 (tttt) cc_final: 0.8009 (tptt) REVERT: B 728 MET cc_start: 0.6296 (mmm) cc_final: 0.5453 (mmt) REVERT: B 864 GLU cc_start: 0.5799 (tm-30) cc_final: 0.5210 (tm-30) REVERT: B 943 GLU cc_start: 0.7863 (pm20) cc_final: 0.7392 (pm20) REVERT: B 1102 SER cc_start: 0.7118 (p) cc_final: 0.6876 (t) REVERT: B 1199 MET cc_start: 0.8649 (mtp) cc_final: 0.8314 (mmm) REVERT: B 1248 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8564 (mt) REVERT: B 1433 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7950 (mt-10) REVERT: B 1492 THR cc_start: 0.6034 (m) cc_final: 0.5667 (p) REVERT: B 1630 ASP cc_start: 0.8465 (p0) cc_final: 0.8104 (p0) REVERT: B 1749 LEU cc_start: 0.6865 (tp) cc_final: 0.6609 (tp) outliers start: 42 outliers final: 35 residues processed: 205 average time/residue: 0.3982 time to fit residues: 124.6926 Evaluate side-chains 206 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 967 GLU Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1260 GLN Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1589 LEU Chi-restraints excluded: chain A residue 1592 ASN Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1662 GLU Chi-restraints excluded: chain A residue 1667 GLN Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 967 GLU Chi-restraints excluded: chain B residue 1020 ASN Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1208 LEU Chi-restraints excluded: chain B residue 1248 LEU Chi-restraints excluded: chain B residue 1260 GLN Chi-restraints excluded: chain B residue 1263 LEU Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1426 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1539 ILE Chi-restraints excluded: chain B residue 1552 SER Chi-restraints excluded: chain B residue 1589 LEU Chi-restraints excluded: chain B residue 1596 LEU Chi-restraints excluded: chain B residue 1659 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 221 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 84 optimal weight: 0.0270 chunk 100 optimal weight: 0.6980 chunk 279 optimal weight: 0.0040 chunk 244 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 219 optimal weight: 0.0270 chunk 36 optimal weight: 4.9990 overall best weight: 0.3108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1592 ASN ** B 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.192355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.120410 restraints weight = 28636.545| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.25 r_work: 0.3285 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24916 Z= 0.093 Angle : 0.530 9.725 34000 Z= 0.256 Chirality : 0.041 0.197 3790 Planarity : 0.004 0.057 4396 Dihedral : 4.812 54.137 3858 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.70 % Allowed : 11.44 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: -0.45 (0.15), residues: 2996 helix: 1.40 (0.40), residues: 204 sheet: -0.35 (0.14), residues: 1346 loop : -0.37 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 688 HIS 0.004 0.001 HIS A 445 PHE 0.033 0.001 PHE A 744 TYR 0.014 0.001 TYR B 897 ARG 0.006 0.000 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 20) link_NAG-ASN : angle 1.96763 ( 60) link_BETA1-4 : bond 0.00398 ( 4) link_BETA1-4 : angle 1.55291 ( 12) hydrogen bonds : bond 0.02595 ( 726) hydrogen bonds : angle 4.97701 ( 2073) link_BETA1-6 : bond 0.00034 ( 2) link_BETA1-6 : angle 1.38599 ( 6) SS BOND : bond 0.00246 ( 20) SS BOND : angle 0.70354 ( 40) covalent geometry : bond 0.00225 (24870) covalent geometry : angle 0.52250 (33882) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 2.786 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6515 (mtm-85) cc_final: 0.6128 (mtm-85) REVERT: A 220 CYS cc_start: 0.6908 (t) cc_final: 0.6465 (t) REVERT: A 317 GLU cc_start: 0.7199 (pt0) cc_final: 0.6879 (mt-10) REVERT: A 462 ARG cc_start: 0.7466 (ttt180) cc_final: 0.7095 (ttt-90) REVERT: A 515 LYS cc_start: 0.8406 (ttpt) cc_final: 0.8104 (tmtt) REVERT: A 565 MET cc_start: 0.7181 (mmm) cc_final: 0.6926 (tpt) REVERT: A 1105 LEU cc_start: 0.7866 (tp) cc_final: 0.7647 (tt) REVERT: A 1199 MET cc_start: 0.8648 (mtp) cc_final: 0.8338 (mmm) REVERT: A 1433 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7915 (mt-10) REVERT: A 1469 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7361 (mpt180) REVERT: A 1597 CYS cc_start: 0.7759 (t) cc_final: 0.7459 (t) REVERT: A 1630 ASP cc_start: 0.8334 (p0) cc_final: 0.7949 (p0) REVERT: A 1662 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8706 (tt0) REVERT: A 1667 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: B 210 ARG cc_start: 0.6598 (mtm-85) cc_final: 0.6215 (mtm-85) REVERT: B 220 CYS cc_start: 0.6877 (t) cc_final: 0.6435 (t) REVERT: B 241 LYS cc_start: 0.7472 (mptt) cc_final: 0.6955 (tttp) REVERT: B 246 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7453 (pt0) REVERT: B 295 ARG cc_start: 0.7665 (mtt90) cc_final: 0.7382 (mtt90) REVERT: B 515 LYS cc_start: 0.8242 (tttt) cc_final: 0.8026 (tptt) REVERT: B 728 MET cc_start: 0.6390 (mmm) cc_final: 0.5721 (mmt) REVERT: B 864 GLU cc_start: 0.5736 (tm-30) cc_final: 0.5106 (tm-30) REVERT: B 1102 SER cc_start: 0.7125 (p) cc_final: 0.6803 (t) REVERT: B 1199 MET cc_start: 0.8632 (mtp) cc_final: 0.8308 (mmm) REVERT: B 1433 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7867 (mt-10) REVERT: B 1469 ARG cc_start: 0.8155 (mtm-85) cc_final: 0.7397 (mpt180) REVERT: B 1492 THR cc_start: 0.6120 (m) cc_final: 0.5750 (p) REVERT: B 1630 ASP cc_start: 0.8343 (p0) cc_final: 0.7977 (p0) REVERT: B 1749 LEU cc_start: 0.6787 (tp) cc_final: 0.6551 (tp) outliers start: 43 outliers final: 32 residues processed: 208 average time/residue: 0.3994 time to fit residues: 128.6845 Evaluate side-chains 207 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1208 LEU Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1260 GLN Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1589 LEU Chi-restraints excluded: chain A residue 1592 ASN Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1662 GLU Chi-restraints excluded: chain A residue 1667 GLN Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1208 LEU Chi-restraints excluded: chain B residue 1248 LEU Chi-restraints excluded: chain B residue 1260 GLN Chi-restraints excluded: chain B residue 1263 LEU Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1426 VAL Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1539 ILE Chi-restraints excluded: chain B residue 1552 SER Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1589 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 269 optimal weight: 0.5980 chunk 242 optimal weight: 0.6980 chunk 288 optimal weight: 0.6980 chunk 129 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 0.0370 chunk 165 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1592 ASN ** B 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1570 GLN B1592 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.191822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120382 restraints weight = 28489.502| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.43 r_work: 0.3267 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24916 Z= 0.116 Angle : 0.542 10.951 34000 Z= 0.262 Chirality : 0.041 0.190 3790 Planarity : 0.004 0.057 4396 Dihedral : 4.767 54.320 3858 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.50 % Allowed : 11.88 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: -0.41 (0.15), residues: 2996 helix: 1.42 (0.40), residues: 204 sheet: -0.31 (0.14), residues: 1346 loop : -0.33 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 688 HIS 0.003 0.001 HIS A 445 PHE 0.032 0.001 PHE A 744 TYR 0.013 0.001 TYR B 897 ARG 0.006 0.000 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 20) link_NAG-ASN : angle 2.01711 ( 60) link_BETA1-4 : bond 0.00350 ( 4) link_BETA1-4 : angle 1.59212 ( 12) hydrogen bonds : bond 0.02670 ( 726) hydrogen bonds : angle 4.92032 ( 2073) link_BETA1-6 : bond 0.00022 ( 2) link_BETA1-6 : angle 1.42556 ( 6) SS BOND : bond 0.00251 ( 20) SS BOND : angle 0.71498 ( 40) covalent geometry : bond 0.00282 (24870) covalent geometry : angle 0.53500 (33882) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5992 Ramachandran restraints generated. 2996 Oldfield, 0 Emsley, 2996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 2.712 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6505 (mtm-85) cc_final: 0.6110 (mtm-85) REVERT: A 220 CYS cc_start: 0.6949 (t) cc_final: 0.6505 (t) REVERT: A 317 GLU cc_start: 0.7224 (pt0) cc_final: 0.6900 (mt-10) REVERT: A 462 ARG cc_start: 0.7445 (ttt180) cc_final: 0.7001 (ttt-90) REVERT: A 515 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8108 (tmtt) REVERT: A 565 MET cc_start: 0.7168 (mmm) cc_final: 0.6939 (tpt) REVERT: A 832 LYS cc_start: 0.7150 (mmtt) cc_final: 0.6946 (tptp) REVERT: A 1199 MET cc_start: 0.8657 (mtp) cc_final: 0.8342 (mmm) REVERT: A 1433 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7934 (mt-10) REVERT: A 1469 ARG cc_start: 0.8167 (mtm-85) cc_final: 0.7442 (mpt180) REVERT: A 1597 CYS cc_start: 0.7792 (t) cc_final: 0.7490 (t) REVERT: A 1630 ASP cc_start: 0.8397 (p0) cc_final: 0.8005 (p0) REVERT: A 1667 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: B 210 ARG cc_start: 0.6601 (mtm-85) cc_final: 0.6211 (mtm-85) REVERT: B 220 CYS cc_start: 0.6931 (t) cc_final: 0.6486 (t) REVERT: B 241 LYS cc_start: 0.7480 (mptt) cc_final: 0.7009 (tttp) REVERT: B 246 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7466 (pt0) REVERT: B 295 ARG cc_start: 0.7680 (mtt90) cc_final: 0.7398 (mtt90) REVERT: B 515 LYS cc_start: 0.8291 (tttt) cc_final: 0.8053 (tptt) REVERT: B 728 MET cc_start: 0.6440 (mmm) cc_final: 0.5803 (mmt) REVERT: B 864 GLU cc_start: 0.5745 (tm-30) cc_final: 0.5168 (tm-30) REVERT: B 1102 SER cc_start: 0.7091 (p) cc_final: 0.6760 (t) REVERT: B 1199 MET cc_start: 0.8618 (mtp) cc_final: 0.8295 (mmm) REVERT: B 1433 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7925 (mt-10) REVERT: B 1492 THR cc_start: 0.6126 (m) cc_final: 0.5763 (p) REVERT: B 1630 ASP cc_start: 0.8383 (p0) cc_final: 0.8014 (p0) REVERT: B 1749 LEU cc_start: 0.6817 (tp) cc_final: 0.6568 (tp) outliers start: 38 outliers final: 31 residues processed: 205 average time/residue: 0.3992 time to fit residues: 125.7413 Evaluate side-chains 202 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1245 THR Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1260 GLN Chi-restraints excluded: chain A residue 1263 LEU Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1589 LEU Chi-restraints excluded: chain A residue 1592 ASN Chi-restraints excluded: chain A residue 1659 GLU Chi-restraints excluded: chain A residue 1667 GLN Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 950 VAL Chi-restraints excluded: chain B residue 1132 VAL Chi-restraints excluded: chain B residue 1146 LEU Chi-restraints excluded: chain B residue 1248 LEU Chi-restraints excluded: chain B residue 1260 GLN Chi-restraints excluded: chain B residue 1263 LEU Chi-restraints excluded: chain B residue 1265 LEU Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1426 VAL Chi-restraints excluded: chain B residue 1515 GLU Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1539 ILE Chi-restraints excluded: chain B residue 1552 SER Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1589 LEU Chi-restraints excluded: chain B residue 1592 ASN Chi-restraints excluded: chain B residue 1659 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 46 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 170 optimal weight: 0.3980 chunk 145 optimal weight: 0.9980 chunk 180 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1592 ASN B1592 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.191353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119168 restraints weight = 28570.857| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.29 r_work: 0.3267 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24916 Z= 0.132 Angle : 0.548 12.289 34000 Z= 0.265 Chirality : 0.042 0.188 3790 Planarity : 0.004 0.056 4396 Dihedral : 4.782 54.505 3858 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.50 % Allowed : 11.88 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % 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: -0.41 (0.15), residues: 2996 helix: 1.40 (0.40), residues: 204 sheet: -0.31 (0.14), residues: 1344 loop : -0.34 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 688 HIS 0.004 0.001 HIS B1427 PHE 0.032 0.001 PHE A 744 TYR 0.011 0.001 TYR A 897 ARG 0.006 0.000 ARG B 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 20) link_NAG-ASN : angle 2.01240 ( 60) link_BETA1-4 : bond 0.00331 ( 4) link_BETA1-4 : angle 1.61692 ( 12) hydrogen bonds : bond 0.02730 ( 726) hydrogen bonds : angle 4.92761 ( 2073) link_BETA1-6 : bond 0.00045 ( 2) link_BETA1-6 : angle 1.45999 ( 6) SS BOND : bond 0.00264 ( 20) SS BOND : angle 0.73346 ( 40) covalent geometry : bond 0.00323 (24870) covalent geometry : angle 0.54100 (33882) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17898.49 seconds wall clock time: 308 minutes 39.05 seconds (18519.05 seconds total)