Starting phenix.real_space_refine on Fri Sep 19 08:44:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfs_44505/09_2025/9bfs_44505.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfs_44505/09_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_44505/09_2025/9bfs_44505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfs_44505/09_2025/9bfs_44505.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfs_44505/09_2025/9bfs_44505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfs_44505/09_2025/9bfs_44505.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.066 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} 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: {'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 4, 'TRP:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} 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: 5.88, per 1000 atoms: 0.24 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: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.50 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: 7.62 Time building geometry restraints manager: 2.49 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: 0.05 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: 10.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.220 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 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:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.510 ------------------------------------------------------------------------------- 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 : 3.02 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.025 0.001 ARG B1549 TYR 0.032 0.003 TYR A 740 PHE 0.067 0.004 PHE B 599 TRP 0.066 0.003 TRP B 861 HIS 0.030 0.002 HIS A 591 Details of bonding type rmsd covalent geometry : bond 0.00714 (24870) covalent geometry : angle 1.25468 (33882) SS BOND : bond 0.00521 ( 20) SS BOND : angle 2.37837 ( 40) hydrogen bonds : bond 0.23318 ( 726) hydrogen bonds : angle 9.50379 ( 2073) link_BETA1-4 : bond 0.00450 ( 4) link_BETA1-4 : angle 1.86897 ( 12) link_BETA1-6 : bond 0.00199 ( 2) link_BETA1-6 : angle 1.25182 ( 6) link_NAG-ASN : bond 0.01522 ( 20) link_NAG-ASN : angle 4.66724 ( 60) *********************** 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 : 0.928 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: 0.2114 time to fit residues: 86.9154 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 : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 50.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 2.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- 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 A1229 HIS A1241 GLN A1244 GLN A1257 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** B 746 HIS 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.192255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120369 restraints weight = 28635.156| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.11 r_work: 0.3302 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 24916 Z= 0.199 Angle : 0.664 9.660 34000 Z= 0.331 Chirality : 0.044 0.191 3790 Planarity : 0.006 0.077 4396 Dihedral : 5.712 56.077 3858 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.75 % Allowed : 6.24 % Favored : 93.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.14), residues: 2996 helix: -1.43 (0.33), residues: 204 sheet: -0.50 (0.14), residues: 1300 loop : -1.43 (0.13), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1075 TYR 0.015 0.002 TYR A1722 PHE 0.025 0.002 PHE B 744 TRP 0.026 0.002 TRP B 688 HIS 0.005 0.001 HIS A1450 Details of bonding type rmsd covalent geometry : bond 0.00468 (24870) covalent geometry : angle 0.65441 (33882) SS BOND : bond 0.00343 ( 20) SS BOND : angle 0.98275 ( 40) hydrogen bonds : bond 0.04199 ( 726) hydrogen bonds : angle 6.45632 ( 2073) link_BETA1-4 : bond 0.00322 ( 4) link_BETA1-4 : angle 2.00318 ( 12) link_BETA1-6 : bond 0.00305 ( 2) link_BETA1-6 : angle 1.54910 ( 6) link_NAG-ASN : bond 0.00481 ( 20) link_NAG-ASN : angle 2.53463 ( 60) *********************** 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 244 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6587 (mtm-85) cc_final: 0.6179 (mtm-85) REVERT: A 339 GLU cc_start: 0.7193 (tt0) cc_final: 0.6294 (tm-30) REVERT: A 462 ARG cc_start: 0.7336 (ttt180) cc_final: 0.6977 (ttt-90) REVERT: A 512 MET cc_start: 0.7223 (ttt) cc_final: 0.6887 (ttt) REVERT: A 513 ILE cc_start: 0.8222 (mt) cc_final: 0.8020 (mm) REVERT: A 728 MET cc_start: 0.6304 (mmt) cc_final: 0.6024 (mmm) REVERT: A 832 LYS cc_start: 0.7258 (mmtt) cc_final: 0.7046 (tptp) REVERT: A 1025 MET cc_start: 0.9219 (ttp) cc_final: 0.8985 (ttp) REVERT: A 1199 MET cc_start: 0.8519 (mtp) cc_final: 0.8226 (mmm) REVERT: A 1239 PHE cc_start: 0.7896 (m-80) cc_final: 0.7680 (m-80) REVERT: A 1433 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7919 (mt-10) REVERT: A 1469 ARG cc_start: 0.8020 (mtm-85) cc_final: 0.7341 (mpt180) REVERT: A 1526 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8424 (tt) REVERT: A 1603 ARG cc_start: 0.7508 (mtm110) cc_final: 0.7222 (ttm170) REVERT: A 1630 ASP cc_start: 0.8533 (p0) cc_final: 0.8112 (p0) REVERT: A 1782 LEU cc_start: 0.7280 (tp) cc_final: 0.6960 (tt) REVERT: B 210 ARG cc_start: 0.6746 (mtm-85) cc_final: 0.6400 (mtm-85) REVERT: B 241 LYS cc_start: 0.7553 (mptt) cc_final: 0.7016 (tttp) REVERT: B 246 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7534 (pt0) REVERT: B 339 GLU cc_start: 0.7201 (tt0) cc_final: 0.6281 (tm-30) REVERT: B 1025 MET cc_start: 0.9216 (ttp) cc_final: 0.9003 (ttp) REVERT: B 1199 MET cc_start: 0.8543 (mtp) cc_final: 0.8233 (mmm) REVERT: B 1433 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7917 (mt-10) REVERT: B 1492 THR cc_start: 0.6084 (m) cc_final: 0.5655 (p) REVERT: B 1630 ASP cc_start: 0.8468 (p0) cc_final: 0.8089 (p0) REVERT: B 1749 LEU cc_start: 0.6661 (tp) cc_final: 0.6405 (tp) outliers start: 19 outliers final: 9 residues processed: 238 average time/residue: 0.1973 time to fit residues: 71.8541 Evaluate side-chains 209 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 199 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 944 LEU 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 1235 LEU 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 86 optimal weight: 0.1980 chunk 184 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 284 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 GLN A 722 HIS A1244 GLN A1450 HIS ** A1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1746 GLN B 222 GLN ** B 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1229 HIS B1450 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.191306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122177 restraints weight = 28704.104| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.57 r_work: 0.3237 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24916 Z= 0.168 Angle : 0.605 9.072 34000 Z= 0.298 Chirality : 0.043 0.235 3790 Planarity : 0.005 0.058 4396 Dihedral : 5.375 54.982 3858 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.10 % Allowed : 8.45 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.14), residues: 2996 helix: -0.35 (0.36), residues: 204 sheet: -0.58 (0.14), residues: 1310 loop : -1.10 (0.14), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1075 TYR 0.009 0.001 TYR A1722 PHE 0.027 0.001 PHE B 744 TRP 0.019 0.001 TRP B 688 HIS 0.005 0.001 HIS A1427 Details of bonding type rmsd covalent geometry : bond 0.00405 (24870) covalent geometry : angle 0.59608 (33882) SS BOND : bond 0.00699 ( 20) SS BOND : angle 0.74316 ( 40) hydrogen bonds : bond 0.03708 ( 726) hydrogen bonds : angle 5.85713 ( 2073) link_BETA1-4 : bond 0.00454 ( 4) link_BETA1-4 : angle 1.96081 ( 12) link_BETA1-6 : bond 0.00082 ( 2) link_BETA1-6 : angle 1.44845 ( 6) link_NAG-ASN : bond 0.00368 ( 20) link_NAG-ASN : angle 2.29106 ( 60) *********************** 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 232 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6608 (mtm-85) cc_final: 0.6198 (mtm-85) REVERT: A 220 CYS cc_start: 0.7155 (t) cc_final: 0.6653 (t) REVERT: A 295 ARG cc_start: 0.7983 (mtt90) cc_final: 0.7745 (mtt90) REVERT: A 339 GLU cc_start: 0.7363 (tt0) cc_final: 0.6327 (tm-30) REVERT: A 462 ARG cc_start: 0.7450 (ttt180) cc_final: 0.7040 (ttt-90) REVERT: A 512 MET cc_start: 0.7367 (ttt) cc_final: 0.7146 (ttt) REVERT: A 515 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8061 (tmtt) REVERT: A 832 LYS cc_start: 0.7250 (mmtt) cc_final: 0.7042 (tptp) REVERT: A 1199 MET cc_start: 0.8659 (mtp) cc_final: 0.8353 (mmm) REVERT: A 1296 ARG cc_start: 0.7645 (mtt180) cc_final: 0.7430 (mtt180) REVERT: A 1433 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7981 (mt-10) REVERT: A 1630 ASP cc_start: 0.8531 (p0) cc_final: 0.8148 (p0) REVERT: A 1667 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: B 210 ARG cc_start: 0.6685 (mtm-85) cc_final: 0.6296 (mtm-85) REVERT: B 220 CYS cc_start: 0.7161 (t) cc_final: 0.6659 (t) REVERT: B 241 LYS cc_start: 0.7507 (mptt) cc_final: 0.6981 (tttp) REVERT: B 246 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7596 (pt0) REVERT: B 295 ARG cc_start: 0.7894 (mtt90) cc_final: 0.7625 (mtt90) REVERT: B 339 GLU cc_start: 0.7348 (tt0) cc_final: 0.6348 (tm-30) REVERT: B 584 GLN cc_start: 0.5323 (tt0) cc_final: 0.5054 (tt0) REVERT: B 728 MET cc_start: 0.6267 (mmm) cc_final: 0.5684 (mmt) REVERT: B 864 GLU cc_start: 0.5863 (tm-30) cc_final: 0.5230 (tm-30) REVERT: B 1199 MET cc_start: 0.8665 (mtp) cc_final: 0.8344 (mmm) REVERT: B 1433 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8004 (mt-10) REVERT: B 1492 THR cc_start: 0.6057 (m) cc_final: 0.5630 (p) REVERT: B 1549 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7759 (mtp85) REVERT: B 1630 ASP cc_start: 0.8496 (p0) cc_final: 0.8112 (p0) REVERT: B 1749 LEU cc_start: 0.6802 (tp) cc_final: 0.6503 (tp) outliers start: 28 outliers final: 18 residues processed: 228 average time/residue: 0.1999 time to fit residues: 69.3392 Evaluate side-chains 212 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1208 LEU 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 1667 GLN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 1105 LEU Chi-restraints excluded: chain B residue 1208 LEU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1263 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 229 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 82 optimal weight: 0.8980 chunk 228 optimal weight: 0.5980 chunk 148 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 245 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.191702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118902 restraints weight = 28693.217| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.08 r_work: 0.3292 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 24916 Z= 0.132 Angle : 0.561 8.597 34000 Z= 0.275 Chirality : 0.042 0.216 3790 Planarity : 0.004 0.057 4396 Dihedral : 5.133 54.630 3858 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.50 % Allowed : 10.02 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.15), residues: 2996 helix: 0.33 (0.38), residues: 204 sheet: -0.60 (0.14), residues: 1348 loop : -0.84 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1075 TYR 0.011 0.001 TYR B 897 PHE 0.028 0.001 PHE B 744 TRP 0.016 0.001 TRP B 688 HIS 0.004 0.001 HIS B1427 Details of bonding type rmsd covalent geometry : bond 0.00316 (24870) covalent geometry : angle 0.55210 (33882) SS BOND : bond 0.00515 ( 20) SS BOND : angle 0.71734 ( 40) hydrogen bonds : bond 0.03091 ( 726) hydrogen bonds : angle 5.52808 ( 2073) link_BETA1-4 : bond 0.00392 ( 4) link_BETA1-4 : angle 1.82230 ( 12) link_BETA1-6 : bond 0.00094 ( 2) link_BETA1-6 : angle 1.41447 ( 6) link_NAG-ASN : bond 0.00360 ( 20) link_NAG-ASN : angle 2.21060 ( 60) *********************** 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 235 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6588 (mtm-85) cc_final: 0.6157 (mtm-85) REVERT: A 220 CYS cc_start: 0.6927 (t) cc_final: 0.6465 (t) REVERT: A 462 ARG cc_start: 0.7386 (ttt180) cc_final: 0.7021 (ttt-90) REVERT: A 515 LYS cc_start: 0.8394 (ttpt) cc_final: 0.8058 (tmtt) REVERT: A 565 MET cc_start: 0.7149 (mmm) cc_final: 0.6467 (tpt) REVERT: A 1150 ARG cc_start: 0.7758 (ttm170) cc_final: 0.7541 (ttp80) REVERT: A 1199 MET cc_start: 0.8613 (mtp) cc_final: 0.8321 (mmm) REVERT: A 1296 ARG cc_start: 0.7633 (mtt180) cc_final: 0.7307 (mtt180) REVERT: A 1433 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7934 (mt-10) REVERT: A 1469 ARG cc_start: 0.7948 (mtm-85) cc_final: 0.7284 (mpt180) REVERT: A 1630 ASP cc_start: 0.8410 (p0) cc_final: 0.8041 (p0) REVERT: A 1667 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: B 210 ARG cc_start: 0.6667 (mtm-85) cc_final: 0.6287 (mtm-85) REVERT: B 220 CYS cc_start: 0.6911 (t) cc_final: 0.6447 (t) REVERT: B 241 LYS cc_start: 0.7471 (mptt) cc_final: 0.6971 (tttp) REVERT: B 246 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7552 (pt0) REVERT: B 339 GLU cc_start: 0.7294 (tt0) cc_final: 0.6328 (tm-30) REVERT: B 555 GLN cc_start: 0.4620 (tm-30) cc_final: 0.4308 (tm-30) REVERT: B 584 GLN cc_start: 0.5313 (tt0) cc_final: 0.5087 (tt0) REVERT: B 864 GLU cc_start: 0.5801 (tm-30) cc_final: 0.5148 (tm-30) REVERT: B 1199 MET cc_start: 0.8631 (mtp) cc_final: 0.8318 (mmm) REVERT: B 1248 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8449 (mt) REVERT: B 1433 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7897 (mt-10) REVERT: B 1469 ARG cc_start: 0.8056 (mtm-85) cc_final: 0.7337 (mpt180) REVERT: B 1492 THR cc_start: 0.6124 (m) cc_final: 0.5756 (p) REVERT: B 1630 ASP cc_start: 0.8400 (p0) cc_final: 0.8028 (p0) REVERT: B 1749 LEU cc_start: 0.6750 (tp) cc_final: 0.6545 (tp) outliers start: 38 outliers final: 21 residues processed: 227 average time/residue: 0.1881 time to fit residues: 66.1285 Evaluate side-chains 213 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLU 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 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 1667 GLN Chi-restraints excluded: chain B residue 234 GLU 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 1208 LEU Chi-restraints excluded: chain B residue 1248 LEU Chi-restraints excluded: chain B residue 1263 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 12 optimal weight: 0.2980 chunk 134 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 301 optimal weight: 0.9990 chunk 296 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 73 optimal weight: 0.0980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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** A1570 GLN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.191871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119737 restraints weight = 28538.815| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.25 r_work: 0.3274 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24916 Z= 0.120 Angle : 0.541 8.429 34000 Z= 0.264 Chirality : 0.041 0.220 3790 Planarity : 0.004 0.061 4396 Dihedral : 4.964 54.289 3858 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.58 % Allowed : 10.69 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.15), residues: 2996 helix: 0.84 (0.39), residues: 204 sheet: -0.50 (0.14), residues: 1348 loop : -0.61 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 295 TYR 0.015 0.001 TYR A 897 PHE 0.030 0.001 PHE A 744 TRP 0.016 0.001 TRP A 688 HIS 0.004 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00290 (24870) covalent geometry : angle 0.53246 (33882) SS BOND : bond 0.00333 ( 20) SS BOND : angle 0.72727 ( 40) hydrogen bonds : bond 0.02903 ( 726) hydrogen bonds : angle 5.27981 ( 2073) link_BETA1-4 : bond 0.00391 ( 4) link_BETA1-4 : angle 1.72689 ( 12) link_BETA1-6 : bond 0.00013 ( 2) link_BETA1-6 : angle 1.42705 ( 6) link_NAG-ASN : bond 0.00332 ( 20) link_NAG-ASN : angle 2.11964 ( 60) *********************** 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 235 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6505 (mtm-85) cc_final: 0.6094 (mtm-85) REVERT: A 220 CYS cc_start: 0.7035 (t) cc_final: 0.6597 (t) REVERT: A 246 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7630 (mm-30) REVERT: A 295 ARG cc_start: 0.7797 (mtt90) cc_final: 0.7504 (mtt90) REVERT: A 317 GLU cc_start: 0.7278 (pt0) cc_final: 0.6866 (mt-10) REVERT: A 462 ARG cc_start: 0.7432 (ttt180) cc_final: 0.6999 (ttt-90) REVERT: A 515 LYS cc_start: 0.8395 (ttpt) cc_final: 0.8067 (tmtt) REVERT: A 1105 LEU cc_start: 0.7888 (tp) cc_final: 0.7659 (tt) REVERT: A 1199 MET cc_start: 0.8643 (mtp) cc_final: 0.8329 (mmm) REVERT: A 1296 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7296 (mtt180) REVERT: A 1433 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7932 (mt-10) REVERT: A 1469 ARG cc_start: 0.7971 (mtm-85) cc_final: 0.7335 (mpt180) REVERT: A 1630 ASP cc_start: 0.8402 (p0) cc_final: 0.8026 (p0) REVERT: A 1662 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8724 (tt0) REVERT: A 1667 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: B 210 ARG cc_start: 0.6635 (mtm-85) cc_final: 0.6228 (mtm-85) REVERT: B 220 CYS cc_start: 0.6953 (t) cc_final: 0.6504 (t) REVERT: B 241 LYS cc_start: 0.7484 (mptt) cc_final: 0.6959 (tttp) REVERT: B 246 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7540 (pt0) REVERT: B 295 ARG cc_start: 0.7800 (mtt90) cc_final: 0.7475 (mtt90) REVERT: B 339 GLU cc_start: 0.7429 (tt0) cc_final: 0.6958 (tm-30) REVERT: B 515 LYS cc_start: 0.8268 (tttt) cc_final: 0.7998 (tptt) REVERT: B 555 GLN cc_start: 0.4516 (tm-30) cc_final: 0.4198 (tm-30) REVERT: B 728 MET cc_start: 0.6240 (mmm) cc_final: 0.5574 (mmt) REVERT: B 864 GLU cc_start: 0.5769 (tm-30) cc_final: 0.5131 (tm-30) REVERT: B 1199 MET cc_start: 0.8618 (mtp) cc_final: 0.8298 (mmm) REVERT: B 1433 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7930 (mt-10) REVERT: B 1469 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7366 (mpt180) REVERT: B 1492 THR cc_start: 0.6123 (m) cc_final: 0.5750 (p) REVERT: B 1597 CYS cc_start: 0.7850 (t) cc_final: 0.7600 (t) REVERT: B 1630 ASP cc_start: 0.8391 (p0) cc_final: 0.8023 (p0) REVERT: B 1749 LEU cc_start: 0.6746 (tp) cc_final: 0.6528 (tp) outliers start: 40 outliers final: 29 residues processed: 227 average time/residue: 0.1962 time to fit residues: 67.3532 Evaluate side-chains 216 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 GLU 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 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 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 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 1342 VAL Chi-restraints excluded: chain B residue 1526 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 14 optimal weight: 0.0040 chunk 292 optimal weight: 0.0870 chunk 90 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 267 optimal weight: 0.9990 chunk 238 optimal weight: 0.9980 chunk 273 optimal weight: 0.9990 chunk 196 optimal weight: 0.0980 overall best weight: 0.4370 ------------------------------------------------------------------------------- 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** A1592 ASN B 584 GLN ** B 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1592 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.192506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120992 restraints weight = 28496.094| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.25 r_work: 0.3282 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24916 Z= 0.102 Angle : 0.523 8.195 34000 Z= 0.256 Chirality : 0.041 0.215 3790 Planarity : 0.004 0.058 4396 Dihedral : 4.846 54.130 3858 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.66 % Allowed : 10.89 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.15), residues: 2996 helix: 1.10 (0.40), residues: 204 sheet: -0.44 (0.14), residues: 1356 loop : -0.50 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 295 TYR 0.013 0.001 TYR B 897 PHE 0.029 0.001 PHE A 744 TRP 0.015 0.001 TRP B 688 HIS 0.004 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00245 (24870) covalent geometry : angle 0.51468 (33882) SS BOND : bond 0.00238 ( 20) SS BOND : angle 0.66796 ( 40) hydrogen bonds : bond 0.02711 ( 726) hydrogen bonds : angle 5.13057 ( 2073) link_BETA1-4 : bond 0.00371 ( 4) link_BETA1-4 : angle 1.62027 ( 12) link_BETA1-6 : bond 0.00054 ( 2) link_BETA1-6 : angle 1.39628 ( 6) link_NAG-ASN : bond 0.00336 ( 20) link_NAG-ASN : angle 2.07135 ( 60) *********************** 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 232 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6535 (mtm-85) cc_final: 0.6122 (mtm-85) REVERT: A 220 CYS cc_start: 0.7010 (t) cc_final: 0.6583 (t) REVERT: A 246 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: A 317 GLU cc_start: 0.7226 (pt0) cc_final: 0.6830 (mt-10) REVERT: A 462 ARG cc_start: 0.7446 (ttt180) cc_final: 0.7026 (ttt-90) REVERT: A 515 LYS cc_start: 0.8383 (ttpt) cc_final: 0.8055 (tmtt) REVERT: A 565 MET cc_start: 0.7152 (mmm) cc_final: 0.6635 (tpt) REVERT: A 1105 LEU cc_start: 0.7908 (tp) cc_final: 0.7696 (tt) REVERT: A 1199 MET cc_start: 0.8640 (mtp) cc_final: 0.8325 (mmm) REVERT: A 1239 PHE cc_start: 0.7971 (m-80) cc_final: 0.7760 (m-80) REVERT: A 1433 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7925 (mt-10) REVERT: A 1469 ARG cc_start: 0.7935 (mtm-85) cc_final: 0.7320 (mpt180) REVERT: A 1630 ASP cc_start: 0.8375 (p0) cc_final: 0.7988 (p0) REVERT: A 1662 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8738 (tt0) REVERT: A 1667 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: B 210 ARG cc_start: 0.6671 (mtm-85) cc_final: 0.6260 (mtm-85) REVERT: B 220 CYS cc_start: 0.6949 (t) cc_final: 0.6502 (t) REVERT: B 241 LYS cc_start: 0.7493 (mptt) cc_final: 0.6971 (tttp) REVERT: B 246 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7489 (pt0) REVERT: B 295 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7458 (mtt90) REVERT: B 339 GLU cc_start: 0.7443 (tt0) cc_final: 0.6999 (tm-30) REVERT: B 515 LYS cc_start: 0.8248 (tttt) cc_final: 0.8027 (tptt) REVERT: B 555 GLN cc_start: 0.4469 (tm-30) cc_final: 0.4095 (tm-30) REVERT: B 584 GLN cc_start: 0.4860 (tt0) cc_final: 0.4565 (tm-30) REVERT: B 728 MET cc_start: 0.6429 (mmm) cc_final: 0.5815 (mmt) REVERT: B 864 GLU cc_start: 0.5778 (tm-30) cc_final: 0.5142 (tm-30) REVERT: B 1199 MET cc_start: 0.8605 (mtp) cc_final: 0.8300 (mmm) REVERT: B 1433 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7937 (mt-10) REVERT: B 1469 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7371 (mpt180) REVERT: B 1492 THR cc_start: 0.6093 (m) cc_final: 0.5751 (p) REVERT: B 1630 ASP cc_start: 0.8355 (p0) cc_final: 0.7984 (p0) REVERT: B 1662 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8886 (tt0) REVERT: B 1749 LEU cc_start: 0.6763 (tp) cc_final: 0.6542 (tp) outliers start: 42 outliers final: 33 residues processed: 221 average time/residue: 0.1876 time to fit residues: 63.8347 Evaluate side-chains 222 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 GLU 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 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 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 950 VAL Chi-restraints excluded: chain B residue 967 GLU Chi-restraints excluded: chain B residue 1020 ASN 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 1342 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 Chi-restraints excluded: chain B residue 1592 ASN Chi-restraints excluded: chain B residue 1659 GLU Chi-restraints excluded: chain B residue 1662 GLU Chi-restraints excluded: chain B residue 1757 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 64 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 257 optimal weight: 0.0370 chunk 103 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 145 optimal weight: 0.0770 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1592 ASN B 722 HIS ** B 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.190623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.122096 restraints weight = 28466.649| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.58 r_work: 0.3224 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24916 Z= 0.164 Angle : 0.558 8.660 34000 Z= 0.272 Chirality : 0.042 0.211 3790 Planarity : 0.004 0.058 4396 Dihedral : 4.915 54.784 3858 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.97 % Allowed : 11.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.15), residues: 2996 helix: 1.04 (0.40), residues: 204 sheet: -0.45 (0.14), residues: 1346 loop : -0.48 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 295 TYR 0.012 0.001 TYR A 897 PHE 0.029 0.001 PHE A 744 TRP 0.015 0.001 TRP B 688 HIS 0.004 0.001 HIS B 445 Details of bonding type rmsd covalent geometry : bond 0.00398 (24870) covalent geometry : angle 0.54928 (33882) SS BOND : bond 0.00318 ( 20) SS BOND : angle 0.87306 ( 40) hydrogen bonds : bond 0.02958 ( 726) hydrogen bonds : angle 5.18634 ( 2073) link_BETA1-4 : bond 0.00356 ( 4) link_BETA1-4 : angle 1.75485 ( 12) link_BETA1-6 : bond 0.00193 ( 2) link_BETA1-6 : angle 1.47756 ( 6) link_NAG-ASN : bond 0.00344 ( 20) link_NAG-ASN : angle 2.12126 ( 60) *********************** 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 229 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 179 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6585 (mtm-85) cc_final: 0.6171 (mtm-85) REVERT: A 220 CYS cc_start: 0.7163 (t) cc_final: 0.6728 (t) REVERT: A 246 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7688 (mm-30) REVERT: A 317 GLU cc_start: 0.7280 (pt0) cc_final: 0.6883 (mt-10) REVERT: A 462 ARG cc_start: 0.7504 (ttt180) cc_final: 0.7049 (ttt-90) REVERT: A 515 LYS cc_start: 0.8426 (ttpt) cc_final: 0.8115 (tmtt) REVERT: A 565 MET cc_start: 0.7214 (mmm) cc_final: 0.6778 (tpt) REVERT: A 641 MET cc_start: 0.1964 (mmm) cc_final: 0.1419 (mpp) REVERT: A 1199 MET cc_start: 0.8694 (mtp) cc_final: 0.8378 (mmm) REVERT: A 1296 ARG cc_start: 0.7582 (mtt180) cc_final: 0.7237 (mtt180) REVERT: A 1433 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7997 (mt-10) REVERT: A 1630 ASP cc_start: 0.8487 (p0) cc_final: 0.8105 (p0) REVERT: A 1662 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8757 (tt0) REVERT: A 1667 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.7969 (tm-30) REVERT: B 210 ARG cc_start: 0.6664 (mtm-85) cc_final: 0.6264 (mtm-85) REVERT: B 220 CYS cc_start: 0.7096 (t) cc_final: 0.6660 (t) REVERT: B 241 LYS cc_start: 0.7553 (mptt) cc_final: 0.7027 (tttp) REVERT: B 246 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7618 (pt0) REVERT: B 339 GLU cc_start: 0.7539 (tt0) cc_final: 0.7071 (tm-30) REVERT: B 515 LYS cc_start: 0.8273 (tttt) cc_final: 0.8055 (tptt) REVERT: B 555 GLN cc_start: 0.4330 (tm-30) cc_final: 0.3996 (tm-30) REVERT: B 584 GLN cc_start: 0.4831 (tt0) cc_final: 0.4548 (tm-30) REVERT: B 864 GLU cc_start: 0.5781 (tm-30) cc_final: 0.5160 (tm-30) REVERT: B 1102 SER cc_start: 0.7193 (p) cc_final: 0.6920 (t) REVERT: B 1199 MET cc_start: 0.8681 (mtp) cc_final: 0.8356 (mmm) REVERT: B 1433 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7982 (mt-10) REVERT: B 1492 THR cc_start: 0.6060 (m) cc_final: 0.5702 (p) REVERT: B 1597 CYS cc_start: 0.7984 (t) cc_final: 0.7772 (t) REVERT: B 1630 ASP cc_start: 0.8467 (p0) cc_final: 0.8102 (p0) REVERT: B 1662 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8898 (tt0) REVERT: B 1749 LEU cc_start: 0.6895 (tp) cc_final: 0.6647 (tp) outliers start: 50 outliers final: 36 residues processed: 221 average time/residue: 0.1994 time to fit residues: 67.6694 Evaluate side-chains 216 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 GLU 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 1526 LEU Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1589 LEU 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 234 GLU 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 1342 VAL Chi-restraints excluded: chain B residue 1515 GLU Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1526 LEU 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 1596 LEU Chi-restraints excluded: chain B residue 1659 GLU Chi-restraints excluded: chain B residue 1662 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 61 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 281 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 296 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 253 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** B1592 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.190662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121706 restraints weight = 28417.283| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.62 r_work: 0.3220 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2758 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= 0.143 Angle : 0.553 11.214 34000 Z= 0.268 Chirality : 0.042 0.202 3790 Planarity : 0.004 0.051 4396 Dihedral : 4.899 54.818 3858 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.85 % Allowed : 11.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.15), residues: 2996 helix: 1.08 (0.39), residues: 204 sheet: -0.44 (0.14), residues: 1346 loop : -0.41 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 295 TYR 0.013 0.001 TYR B 897 PHE 0.032 0.001 PHE A 744 TRP 0.015 0.001 TRP A 688 HIS 0.004 0.001 HIS A1427 Details of bonding type rmsd covalent geometry : bond 0.00346 (24870) covalent geometry : angle 0.54491 (33882) SS BOND : bond 0.00283 ( 20) SS BOND : angle 0.78009 ( 40) hydrogen bonds : bond 0.02847 ( 726) hydrogen bonds : angle 5.13877 ( 2073) link_BETA1-4 : bond 0.00365 ( 4) link_BETA1-4 : angle 1.69512 ( 12) link_BETA1-6 : bond 0.00175 ( 2) link_BETA1-6 : angle 1.46320 ( 6) link_NAG-ASN : bond 0.00336 ( 20) link_NAG-ASN : angle 2.05085 ( 60) *********************** 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 226 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 210 ARG cc_start: 0.6685 (mtm-85) cc_final: 0.6287 (mtm-85) REVERT: A 220 CYS cc_start: 0.7164 (t) cc_final: 0.6740 (t) REVERT: A 246 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7760 (mm-30) REVERT: A 317 GLU cc_start: 0.7327 (pt0) cc_final: 0.6965 (mt-10) REVERT: A 462 ARG cc_start: 0.7538 (ttt180) cc_final: 0.7105 (ttt-90) REVERT: A 515 LYS cc_start: 0.8426 (ttpt) cc_final: 0.8141 (tmtt) REVERT: A 565 MET cc_start: 0.7075 (mmm) cc_final: 0.6767 (tpt) REVERT: A 1153 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7793 (mtm110) REVERT: A 1199 MET cc_start: 0.8713 (mtp) cc_final: 0.8420 (mmm) REVERT: A 1296 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7341 (mtt180) REVERT: A 1433 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8032 (mt-10) REVERT: A 1630 ASP cc_start: 0.8464 (p0) cc_final: 0.8069 (p0) REVERT: A 1662 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8736 (tt0) REVERT: A 1667 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: B 210 ARG cc_start: 0.6778 (mtm-85) cc_final: 0.6383 (mtm-85) REVERT: B 220 CYS cc_start: 0.7071 (t) cc_final: 0.6629 (t) REVERT: B 241 LYS cc_start: 0.7549 (mptt) cc_final: 0.7040 (tttp) REVERT: B 246 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7623 (pt0) REVERT: B 339 GLU cc_start: 0.7614 (tt0) cc_final: 0.7135 (tm-30) REVERT: B 555 GLN cc_start: 0.4467 (tm-30) cc_final: 0.4159 (tm-30) REVERT: B 584 GLN cc_start: 0.5125 (tt0) cc_final: 0.4841 (tm-30) REVERT: B 728 MET cc_start: 0.6321 (mmm) cc_final: 0.5446 (mmt) REVERT: B 864 GLU cc_start: 0.5806 (tm-30) cc_final: 0.5174 (tm-30) REVERT: B 1102 SER cc_start: 0.7166 (p) cc_final: 0.6894 (t) REVERT: B 1150 ARG cc_start: 0.7830 (ttm170) cc_final: 0.7600 (ttp80) REVERT: B 1199 MET cc_start: 0.8709 (mtp) cc_final: 0.8403 (mmm) REVERT: B 1433 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8014 (mt-10) REVERT: B 1492 THR cc_start: 0.6182 (m) cc_final: 0.5814 (p) REVERT: B 1597 CYS cc_start: 0.7998 (t) cc_final: 0.7764 (t) REVERT: B 1630 ASP cc_start: 0.8452 (p0) cc_final: 0.8081 (p0) REVERT: B 1662 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8887 (tt0) REVERT: B 1749 LEU cc_start: 0.6979 (tp) cc_final: 0.6740 (tp) outliers start: 47 outliers final: 39 residues processed: 215 average time/residue: 0.2036 time to fit residues: 66.9867 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 : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 GLU 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 1526 LEU Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1575 LEU 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 A residue 1678 ASN 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 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 1342 VAL Chi-restraints excluded: chain B residue 1515 GLU Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1526 LEU 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 1596 LEU Chi-restraints excluded: chain B residue 1659 GLU Chi-restraints excluded: chain B residue 1662 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 62 optimal weight: 2.9990 chunk 249 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 266 optimal weight: 0.8980 chunk 235 optimal weight: 0.7980 chunk 184 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 262 optimal weight: 0.5980 chunk 112 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 B1020 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.190725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119285 restraints weight = 28590.735| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.62 r_work: 0.3240 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2806 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 : 0.549 9.497 34000 Z= 0.265 Chirality : 0.042 0.198 3790 Planarity : 0.004 0.050 4396 Dihedral : 4.859 54.606 3858 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.78 % Allowed : 11.76 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.15), residues: 2996 helix: 1.17 (0.39), residues: 204 sheet: -0.42 (0.14), residues: 1346 loop : -0.37 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 295 TYR 0.012 0.001 TYR B 897 PHE 0.031 0.001 PHE A 744 TRP 0.015 0.001 TRP A 688 HIS 0.004 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00319 (24870) covalent geometry : angle 0.54125 (33882) SS BOND : bond 0.00268 ( 20) SS BOND : angle 0.72449 ( 40) hydrogen bonds : bond 0.02791 ( 726) hydrogen bonds : angle 5.08879 ( 2073) link_BETA1-4 : bond 0.00348 ( 4) link_BETA1-4 : angle 1.67672 ( 12) link_BETA1-6 : bond 0.00069 ( 2) link_BETA1-6 : angle 1.47107 ( 6) link_NAG-ASN : bond 0.00315 ( 20) link_NAG-ASN : angle 2.03076 ( 60) *********************** 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 222 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 1.051 Fit side-chains REVERT: A 210 ARG cc_start: 0.6481 (mtm-85) cc_final: 0.6079 (mtm-85) REVERT: A 220 CYS cc_start: 0.6984 (t) cc_final: 0.6542 (t) REVERT: A 246 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7708 (mm-30) REVERT: A 317 GLU cc_start: 0.7257 (pt0) cc_final: 0.6876 (mt-10) REVERT: A 462 ARG cc_start: 0.7464 (ttt180) cc_final: 0.6996 (ttt-90) REVERT: A 515 LYS cc_start: 0.8392 (ttpt) cc_final: 0.8071 (tmtt) REVERT: A 565 MET cc_start: 0.7038 (mmm) cc_final: 0.6825 (tpt) REVERT: A 832 LYS cc_start: 0.7137 (mmtt) cc_final: 0.6925 (tptp) REVERT: A 1199 MET cc_start: 0.8663 (mtp) cc_final: 0.8334 (mmm) REVERT: A 1296 ARG cc_start: 0.7583 (mtt180) cc_final: 0.7234 (mtt180) REVERT: A 1433 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7937 (mt-10) REVERT: A 1597 CYS cc_start: 0.7835 (t) cc_final: 0.7542 (t) REVERT: A 1630 ASP cc_start: 0.8445 (p0) cc_final: 0.8077 (p0) REVERT: A 1662 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8849 (tt0) REVERT: A 1667 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: B 210 ARG cc_start: 0.6562 (mtm-85) cc_final: 0.6168 (mtm-85) REVERT: B 220 CYS cc_start: 0.6978 (t) cc_final: 0.6533 (t) REVERT: B 241 LYS cc_start: 0.7510 (mptt) cc_final: 0.6975 (tttp) REVERT: B 246 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7516 (pt0) REVERT: B 339 GLU cc_start: 0.7603 (tt0) cc_final: 0.7071 (tm-30) REVERT: B 555 GLN cc_start: 0.4331 (tm-30) cc_final: 0.4052 (tm-30) REVERT: B 728 MET cc_start: 0.6359 (mmm) cc_final: 0.5644 (mmt) REVERT: B 864 GLU cc_start: 0.5708 (tm-30) cc_final: 0.5147 (tm-30) REVERT: B 1102 SER cc_start: 0.7186 (p) cc_final: 0.6900 (t) REVERT: B 1199 MET cc_start: 0.8661 (mtp) cc_final: 0.8313 (mmm) REVERT: B 1433 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7929 (mt-10) REVERT: B 1492 THR cc_start: 0.6041 (m) cc_final: 0.5659 (p) REVERT: B 1597 CYS cc_start: 0.7934 (t) cc_final: 0.7680 (t) REVERT: B 1630 ASP cc_start: 0.8439 (p0) cc_final: 0.8067 (p0) REVERT: B 1662 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8871 (tt0) REVERT: B 1749 LEU cc_start: 0.6813 (tp) cc_final: 0.6561 (tp) outliers start: 45 outliers final: 40 residues processed: 212 average time/residue: 0.1964 time to fit residues: 63.8939 Evaluate side-chains 218 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 GLU 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 1526 LEU Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1575 LEU 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 A residue 1678 ASN 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 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 1515 GLU Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1526 LEU 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 1596 LEU Chi-restraints excluded: chain B residue 1659 GLU Chi-restraints excluded: chain B residue 1662 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 254 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 HIS ** A 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1592 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.190370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120394 restraints weight = 28434.476| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.64 r_work: 0.3224 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24916 Z= 0.145 Angle : 0.559 10.891 34000 Z= 0.271 Chirality : 0.042 0.193 3790 Planarity : 0.004 0.050 4396 Dihedral : 4.864 54.703 3858 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.82 % Allowed : 11.76 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.15), residues: 2996 helix: 1.17 (0.39), residues: 204 sheet: -0.43 (0.14), residues: 1348 loop : -0.36 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 295 TYR 0.012 0.001 TYR B 897 PHE 0.032 0.001 PHE A 744 TRP 0.019 0.001 TRP A 623 HIS 0.004 0.001 HIS B1427 Details of bonding type rmsd covalent geometry : bond 0.00352 (24870) covalent geometry : angle 0.55198 (33882) SS BOND : bond 0.00276 ( 20) SS BOND : angle 0.74840 ( 40) hydrogen bonds : bond 0.02824 ( 726) hydrogen bonds : angle 5.08337 ( 2073) link_BETA1-4 : bond 0.00358 ( 4) link_BETA1-4 : angle 1.69352 ( 12) link_BETA1-6 : bond 0.00104 ( 2) link_BETA1-6 : angle 1.49274 ( 6) link_NAG-ASN : bond 0.00314 ( 20) link_NAG-ASN : angle 2.02470 ( 60) ********************** 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 217 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 0.945 Fit side-chains REVERT: A 210 ARG cc_start: 0.6518 (mtm-85) cc_final: 0.6115 (mtm-85) REVERT: A 220 CYS cc_start: 0.7050 (t) cc_final: 0.6601 (t) REVERT: A 317 GLU cc_start: 0.7269 (pt0) cc_final: 0.6900 (mt-10) REVERT: A 515 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8106 (tmtt) REVERT: A 832 LYS cc_start: 0.7181 (mmtt) cc_final: 0.6969 (tptp) REVERT: A 943 GLU cc_start: 0.7829 (pm20) cc_final: 0.7396 (pm20) REVERT: A 1199 MET cc_start: 0.8656 (mtp) cc_final: 0.8326 (mmm) REVERT: A 1296 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7267 (mtt180) REVERT: A 1433 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7939 (mt-10) REVERT: A 1597 CYS cc_start: 0.7826 (t) cc_final: 0.7538 (t) REVERT: A 1630 ASP cc_start: 0.8473 (p0) cc_final: 0.8105 (p0) REVERT: A 1662 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8855 (tt0) REVERT: A 1667 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: B 210 ARG cc_start: 0.6592 (mtm-85) cc_final: 0.6204 (mtm-85) REVERT: B 220 CYS cc_start: 0.7007 (t) cc_final: 0.6566 (t) REVERT: B 241 LYS cc_start: 0.7526 (mptt) cc_final: 0.7002 (tttp) REVERT: B 246 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7539 (pt0) REVERT: B 555 GLN cc_start: 0.4383 (tm-30) cc_final: 0.4085 (tm-30) REVERT: B 728 MET cc_start: 0.6390 (mmm) cc_final: 0.5701 (mmt) REVERT: B 864 GLU cc_start: 0.5760 (tm-30) cc_final: 0.5188 (tm-30) REVERT: B 943 GLU cc_start: 0.7799 (pm20) cc_final: 0.7348 (pm20) REVERT: B 1102 SER cc_start: 0.7154 (p) cc_final: 0.6834 (t) REVERT: B 1199 MET cc_start: 0.8653 (mtp) cc_final: 0.8308 (mmm) REVERT: B 1433 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7939 (mt-10) REVERT: B 1492 THR cc_start: 0.6068 (m) cc_final: 0.5696 (p) REVERT: B 1597 CYS cc_start: 0.7955 (t) cc_final: 0.7703 (t) REVERT: B 1630 ASP cc_start: 0.8452 (p0) cc_final: 0.8089 (p0) REVERT: B 1662 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8884 (tt0) REVERT: B 1749 LEU cc_start: 0.6843 (tp) cc_final: 0.6592 (tp) outliers start: 46 outliers final: 41 residues processed: 207 average time/residue: 0.1917 time to fit residues: 61.1452 Evaluate side-chains 213 residues out of total 2590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 1526 LEU Chi-restraints excluded: chain A residue 1539 ILE Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1575 LEU 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 A residue 1678 ASN 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 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 1342 VAL Chi-restraints excluded: chain B residue 1515 GLU Chi-restraints excluded: chain B residue 1517 VAL Chi-restraints excluded: chain B residue 1526 LEU 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 1596 LEU Chi-restraints excluded: chain B residue 1659 GLU Chi-restraints excluded: chain B residue 1662 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 209 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 290 optimal weight: 0.0670 chunk 37 optimal weight: 0.0980 chunk 281 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 157 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 164 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- 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 B1257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.189770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119680 restraints weight = 28518.821| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.63 r_work: 0.3217 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24916 Z= 0.162 Angle : 0.567 11.971 34000 Z= 0.274 Chirality : 0.042 0.186 3790 Planarity : 0.004 0.049 4396 Dihedral : 4.904 54.890 3858 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.82 % Allowed : 11.68 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.15), residues: 2996 helix: 1.08 (0.39), residues: 206 sheet: -0.45 (0.14), residues: 1352 loop : -0.36 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 295 TYR 0.011 0.001 TYR A 897 PHE 0.031 0.001 PHE A 744 TRP 0.015 0.001 TRP A 688 HIS 0.004 0.001 HIS B1427 Details of bonding type rmsd covalent geometry : bond 0.00394 (24870) covalent geometry : angle 0.55941 (33882) SS BOND : bond 0.00294 ( 20) SS BOND : angle 0.76419 ( 40) hydrogen bonds : bond 0.02899 ( 726) hydrogen bonds : angle 5.10321 ( 2073) link_BETA1-4 : bond 0.00326 ( 4) link_BETA1-4 : angle 1.73154 ( 12) link_BETA1-6 : bond 0.00182 ( 2) link_BETA1-6 : angle 1.51242 ( 6) link_NAG-ASN : bond 0.00316 ( 20) link_NAG-ASN : angle 2.03540 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9362.40 seconds wall clock time: 159 minutes 57.88 seconds (9597.88 seconds total)