Starting phenix.real_space_refine (version: dev) on Sun May 15 18:37:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8y_22735/05_2022/7k8y_22735.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8y_22735/05_2022/7k8y_22735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8y_22735/05_2022/7k8y_22735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8y_22735/05_2022/7k8y_22735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8y_22735/05_2022/7k8y_22735.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8y_22735/05_2022/7k8y_22735.pdb" } resolution = 4.4 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 ------------------------------------------------------------------------------- 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= 0.012 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 25560 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "D" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "E" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'CIS': 2, 'TRANS': 950} Chain breaks: 7 Chain: "G" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'CIS': 1, 'TRANS': 121} Chain: "I" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 778 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'CIS': 1, 'TRANS': 101} Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "D" 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 chiralities: 8 Chain: "E" 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 chiralities: 8 Time building chain proxies: 13.70, per 1000 atoms: 0.54 Number of scatterers: 25560 At special positions: 0 Unit cell: (141.284, 144.628, 204.82, 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 116 16.00 O 4941 8.00 N 4219 7.00 C 16284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.04 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.04 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=1, symmetry=0 Links applied NAG-ASN " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG D1301 " - " ASN D 282 " " NAG D1302 " - " ASN D 331 " " NAG D1303 " - " ASN D 603 " " NAG D1304 " - " ASN D 616 " " NAG D1305 " - " ASN D 709 " " NAG D1306 " - " ASN D 717 " " NAG D1307 " - " ASN D 801 " " NAG D1308 " - " ASN D1134 " " NAG E1301 " - " ASN E 122 " " NAG E1302 " - " ASN E 282 " " NAG E1303 " - " ASN E 331 " " NAG E1304 " - " ASN E 616 " " NAG E1305 " - " ASN E 709 " " NAG E1306 " - " ASN E 717 " " NAG E1307 " - " ASN E 801 " " NAG E1308 " - " ASN E1074 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.25 Conformation dependent library (CDL) restraints added in 3.7 seconds 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6048 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 50 sheets defined 24.3% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.962A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.522A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.522A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 760 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.627A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.353A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.314A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.996A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.618A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 366 through 371 Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.859A pdb=" N LEU D 387 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 388' Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.848A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE D 410 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.822A pdb=" N GLN D 506 " --> pdb=" O VAL D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 744 removed outlier: 3.563A pdb=" N GLY D 744 " --> pdb=" O MET D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.988A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 Processing helix chain 'D' and resid 866 through 884 Processing helix chain 'D' and resid 886 through 891 removed outlier: 3.733A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 Processing helix chain 'D' and resid 912 through 941 removed outlier: 4.351A pdb=" N LEU D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 944 No H-bonds generated for 'chain 'D' and resid 942 through 944' Processing helix chain 'D' and resid 945 through 966 removed outlier: 4.344A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 984 removed outlier: 4.134A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1033 removed outlier: 4.856A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) Processing helix chain 'D' and resid 1116 through 1118 No H-bonds generated for 'chain 'D' and resid 1116 through 1118' Processing helix chain 'D' and resid 1140 through 1147 removed outlier: 3.976A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 342 Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.312A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 747 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 Processing helix chain 'E' and resid 816 through 825 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 886 through 891 removed outlier: 3.830A pdb=" N ALA E 890 " --> pdb=" O TRP E 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 909 Processing helix chain 'E' and resid 913 through 919 Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 966 removed outlier: 4.152A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.726A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.529A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1147 removed outlier: 3.874A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.598A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 29 removed outlier: 6.758A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.623A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.925A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.306A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.731A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.334A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.690A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.961A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.689A pdb=" N ALA B 701 " --> pdb=" O ILE D 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.472A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.472A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.368A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 28 through 29 removed outlier: 6.519A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.994A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'D' and resid 141 through 142 removed outlier: 6.392A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 311 through 313 Processing sheet with id=AC4, first strand: chain 'D' and resid 325 through 328 removed outlier: 5.356A pdb=" N ASP D 574 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 575 " --> pdb=" O GLY D 566 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE D 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.644A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 654 through 655 removed outlier: 5.921A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 701 through 702 removed outlier: 7.081A pdb=" N ALA D 701 " --> pdb=" O ILE E 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 711 through 715 Processing sheet with id=AD2, first strand: chain 'D' and resid 718 through 728 removed outlier: 6.839A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 734 through 735 Processing sheet with id=AD4, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.377A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS D1088 " --> pdb=" O ILE D1081 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE D1081 " --> pdb=" O HIS D1088 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 28 through 31 removed outlier: 3.723A pdb=" N SER E 60 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 47 through 55 removed outlier: 4.049A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.021A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 84 through 85 removed outlier: 5.784A pdb=" N ALA E 243 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE E 101 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.475A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AE3, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.079A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA E 672 " --> pdb=" O PRO E 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 712 through 728 removed outlier: 6.837A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.315A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AF4, first strand: chain 'I' and resid 9 through 13 removed outlier: 6.490A pdb=" N TRP I 35 " --> pdb=" O MET I 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 19 through 24 1096 hydrogen bonds defined for protein. 2979 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: 12.52 Time building geometry restraints manager: 11.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8199 1.35 - 1.47: 6559 1.47 - 1.59: 11225 1.59 - 1.72: 1 1.72 - 1.84: 146 Bond restraints: 26130 Sorted by residual: bond pdb=" CA PHE I 98 " pdb=" C PHE I 98 " ideal model delta sigma weight residual 1.525 1.595 -0.070 1.25e-02 6.40e+03 3.14e+01 bond pdb=" CA VAL I 97 " pdb=" C VAL I 97 " ideal model delta sigma weight residual 1.523 1.592 -0.069 1.27e-02 6.20e+03 2.93e+01 bond pdb=" N PHE I 98 " pdb=" CA PHE I 98 " ideal model delta sigma weight residual 1.458 1.521 -0.063 1.42e-02 4.96e+03 1.96e+01 bond pdb=" N VAL I 97 " pdb=" CA VAL I 97 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.41e+01 bond pdb=" C VAL I 97 " pdb=" N PHE I 98 " ideal model delta sigma weight residual 1.328 1.360 -0.032 1.23e-02 6.61e+03 6.77e+00 ... (remaining 26125 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.87: 748 106.87 - 113.68: 14252 113.68 - 120.49: 9734 120.49 - 127.30: 10594 127.30 - 134.11: 223 Bond angle restraints: 35551 Sorted by residual: angle pdb=" N PHE I 98 " pdb=" CA PHE I 98 " pdb=" C PHE I 98 " ideal model delta sigma weight residual 108.24 125.89 -17.65 1.32e+00 5.74e-01 1.79e+02 angle pdb=" C PHE I 98 " pdb=" N GLY I 99 " pdb=" CA GLY I 99 " ideal model delta sigma weight residual 121.96 130.85 -8.89 1.38e+00 5.25e-01 4.15e+01 angle pdb=" N THR G 104 " pdb=" CA THR G 104 " pdb=" C THR G 104 " ideal model delta sigma weight residual 113.17 106.20 6.97 1.26e+00 6.30e-01 3.06e+01 angle pdb=" N TYR G 115 " pdb=" CA TYR G 115 " pdb=" C TYR G 115 " ideal model delta sigma weight residual 108.38 114.73 -6.35 1.35e+00 5.49e-01 2.22e+01 angle pdb=" C2 NAG D1305 " pdb=" N2 NAG D1305 " pdb=" C7 NAG D1305 " ideal model delta sigma weight residual 123.12 129.04 -5.92 1.28e+00 6.08e-01 2.13e+01 ... (remaining 35546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.11: 14908 22.11 - 44.21: 515 44.21 - 66.32: 49 66.32 - 88.43: 23 88.43 - 110.53: 4 Dihedral angle restraints: 15499 sinusoidal: 6089 harmonic: 9410 Sorted by residual: dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 760 " pdb=" CB CYS E 760 " ideal model delta sinusoidal sigma weight residual 93.00 4.25 88.75 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 5.04 87.96 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual -86.00 -173.52 87.52 1 1.00e+01 1.00e-02 9.18e+01 ... (remaining 15496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 4077 0.123 - 0.246: 23 0.246 - 0.369: 7 0.369 - 0.491: 2 0.491 - 0.614: 2 Chirality restraints: 4111 Sorted by residual: chirality pdb=" C1 NAG E1305 " pdb=" ND2 ASN E 709 " pdb=" C2 NAG E1305 " pdb=" O5 NAG E1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.43e+00 chirality pdb=" C1 NAG D1302 " pdb=" ND2 ASN D 331 " pdb=" C2 NAG D1302 " pdb=" O5 NAG D1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" C1 NAG E1306 " pdb=" ND2 ASN E 717 " pdb=" C2 NAG E1306 " pdb=" O5 NAG E1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.86 0.46 2.00e-01 2.50e+01 5.36e+00 ... (remaining 4108 not shown) Planarity restraints: 4594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 717 " -0.034 2.00e-02 2.50e+03 8.07e-02 8.14e+01 pdb=" CG ASN E 717 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN E 717 " 0.081 2.00e-02 2.50e+03 pdb=" ND2 ASN E 717 " -0.124 2.00e-02 2.50e+03 pdb=" C1 NAG E1306 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 122 " 0.046 2.00e-02 2.50e+03 5.41e-02 3.66e+01 pdb=" CG ASN E 122 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN E 122 " -0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN E 122 " -0.086 2.00e-02 2.50e+03 pdb=" C1 NAG E1301 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 282 " -0.045 2.00e-02 2.50e+03 5.15e-02 3.31e+01 pdb=" CG ASN D 282 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN D 282 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 282 " 0.086 2.00e-02 2.50e+03 pdb=" C1 NAG D1301 " -0.060 2.00e-02 2.50e+03 ... (remaining 4591 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 22 1.89 - 2.64: 521 2.64 - 3.39: 33951 3.39 - 4.15: 61462 4.15 - 4.90: 108946 Nonbonded interactions: 204902 Sorted by model distance: nonbonded pdb=" O ALA D 713 " pdb=" CG LEU E 894 " model vdw 1.137 3.470 nonbonded pdb=" O ALA D 713 " pdb=" CD1 LEU E 894 " model vdw 1.340 3.460 nonbonded pdb=" OE2 GLU B 516 " pdb=" OH TYR D 200 " model vdw 1.368 2.440 nonbonded pdb=" CE1 PHE D 559 " pdb=" CD2 PHE E 43 " model vdw 1.370 3.640 nonbonded pdb=" CH2 TRP G 47 " pdb=" OG SER I 95 " model vdw 1.387 3.340 ... (remaining 204897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 27 through 1147 or resid 1301 through 1307)) selection = (chain 'E' and (resid 27 through 1147 or resid 1301 through 1307)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 16284 2.51 5 N 4219 2.21 5 O 4941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 22.030 Check model and map are aligned: 0.390 Convert atoms to be neutral: 0.220 Process input model: 68.780 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 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 : 0.002 0.070 26130 Z= 0.149 Angle : 0.527 17.652 35551 Z= 0.312 Chirality : 0.046 0.614 4111 Planarity : 0.004 0.048 4571 Dihedral : 10.711 110.534 9334 Min Nonbonded Distance : 1.137 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.79 % Favored : 96.96 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.13), residues: 3190 helix: -0.03 (0.19), residues: 641 sheet: -0.91 (0.17), residues: 767 loop : -2.22 (0.12), residues: 1782 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 274 average time/residue: 0.4049 time to fit residues: 171.7327 Evaluate side-chains 146 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 2.944 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2119 time to fit residues: 4.4823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 252 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 153 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 292 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN B 314 GLN B 394 ASN B 437 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 777 ASN B 953 ASN B 965 GLN B1002 GLN D 66 HIS ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN D 762 GLN ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 GLN D 935 GLN E 450 ASN E 542 ASN E 675 GLN ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 965 GLN G 39 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 26130 Z= 0.203 Angle : 0.526 11.604 35551 Z= 0.275 Chirality : 0.042 0.193 4111 Planarity : 0.004 0.048 4571 Dihedral : 4.828 111.336 3604 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.26 % Favored : 96.55 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 3190 helix: 1.40 (0.21), residues: 652 sheet: -0.62 (0.17), residues: 770 loop : -1.67 (0.13), residues: 1768 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 171 time to evaluate : 3.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 172 average time/residue: 0.3966 time to fit residues: 109.1364 Evaluate side-chains 115 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.068 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 199 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 292 optimal weight: 10.0000 chunk 316 optimal weight: 0.9990 chunk 260 optimal weight: 7.9990 chunk 290 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 235 optimal weight: 20.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN E1002 GLN E1119 ASN I 6 GLN I 39 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 26130 Z= 0.166 Angle : 0.499 9.478 35551 Z= 0.261 Chirality : 0.042 0.192 4111 Planarity : 0.004 0.041 4571 Dihedral : 4.827 110.941 3604 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.35 % Favored : 96.46 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3190 helix: 1.85 (0.21), residues: 650 sheet: -0.47 (0.17), residues: 763 loop : -1.38 (0.14), residues: 1777 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.3828 time to fit residues: 97.9602 Evaluate side-chains 109 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.972 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 8.9990 chunk 220 optimal weight: 0.0970 chunk 152 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 196 optimal weight: 2.9990 chunk 293 optimal weight: 6.9990 chunk 311 optimal weight: 40.0000 chunk 153 optimal weight: 0.9980 chunk 278 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 777 ASN B 953 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN ** E1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 26130 Z= 0.139 Angle : 0.491 10.935 35551 Z= 0.255 Chirality : 0.042 0.198 4111 Planarity : 0.004 0.084 4571 Dihedral : 4.869 110.643 3604 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.35 % Favored : 96.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3190 helix: 2.01 (0.21), residues: 648 sheet: -0.24 (0.18), residues: 750 loop : -1.21 (0.14), residues: 1792 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.3889 time to fit residues: 96.0427 Evaluate side-chains 107 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.974 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 0.8980 chunk 176 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 265 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 158 optimal weight: 8.9990 chunk 279 optimal weight: 0.0170 chunk 78 optimal weight: 8.9990 overall best weight: 3.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 GLN D 965 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN E 804 GLN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 935 GLN I 6 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 26130 Z= 0.254 Angle : 0.577 8.650 35551 Z= 0.304 Chirality : 0.043 0.231 4111 Planarity : 0.004 0.074 4571 Dihedral : 5.195 110.775 3604 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.33 % Favored : 95.55 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 3190 helix: 1.72 (0.21), residues: 669 sheet: -0.45 (0.17), residues: 791 loop : -1.14 (0.14), residues: 1730 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 3.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.3655 time to fit residues: 80.6289 Evaluate side-chains 90 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 3.035 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 4.9990 chunk 280 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 311 optimal weight: 8.9990 chunk 258 optimal weight: 0.9980 chunk 144 optimal weight: 0.3980 chunk 25 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN B 955 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 784 GLN ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 26130 Z= 0.151 Angle : 0.512 9.196 35551 Z= 0.266 Chirality : 0.043 0.249 4111 Planarity : 0.004 0.046 4571 Dihedral : 5.054 109.985 3604 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.73 % Favored : 96.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3190 helix: 1.91 (0.21), residues: 675 sheet: -0.33 (0.18), residues: 784 loop : -1.10 (0.14), residues: 1731 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 3.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3696 time to fit residues: 84.6301 Evaluate side-chains 93 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 3.084 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 262 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 310 optimal weight: 20.0000 chunk 194 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1005 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 ASN ** D1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN ** E 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 777 ASN E 907 ASN E 953 ASN E 955 ASN E 965 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.096 26130 Z= 0.307 Angle : 0.644 11.203 35551 Z= 0.339 Chirality : 0.044 0.235 4111 Planarity : 0.005 0.104 4571 Dihedral : 5.554 109.783 3604 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.58 % Favored : 94.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3190 helix: 1.23 (0.20), residues: 687 sheet: -0.65 (0.17), residues: 764 loop : -1.15 (0.14), residues: 1739 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.3581 time to fit residues: 71.3196 Evaluate side-chains 76 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 3.660 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 0.0870 chunk 123 optimal weight: 40.0000 chunk 185 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 211 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 282 optimal weight: 0.5980 overall best weight: 1.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 HIS D 321 GLN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1023 ASN D1048 HIS ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 784 GLN E 953 ASN E 955 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 26130 Z= 0.167 Angle : 0.535 10.751 35551 Z= 0.278 Chirality : 0.043 0.206 4111 Planarity : 0.004 0.037 4571 Dihedral : 5.269 109.390 3604 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.11 % Favored : 95.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3190 helix: 1.62 (0.21), residues: 687 sheet: -0.57 (0.18), residues: 747 loop : -1.07 (0.14), residues: 1756 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.3378 time to fit residues: 74.6115 Evaluate side-chains 88 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 3.013 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 0.0980 chunk 271 optimal weight: 4.9990 chunk 289 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 227 optimal weight: 0.0570 chunk 88 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 273 optimal weight: 0.9990 chunk 288 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 overall best weight: 2.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.569 26130 Z= 0.261 Angle : 0.678 66.058 35551 Z= 0.326 Chirality : 0.043 0.284 4111 Planarity : 0.004 0.082 4571 Dihedral : 5.257 109.354 3604 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3190 helix: 1.68 (0.21), residues: 687 sheet: -0.55 (0.18), residues: 751 loop : -1.06 (0.15), residues: 1752 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3502 time to fit residues: 71.8062 Evaluate side-chains 88 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 2.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 30.0000 chunk 186 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 320 optimal weight: 30.0000 chunk 295 optimal weight: 8.9990 chunk 255 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 202 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 26130 Z= 0.191 Angle : 0.542 9.212 35551 Z= 0.284 Chirality : 0.043 0.223 4111 Planarity : 0.004 0.107 4571 Dihedral : 5.268 109.031 3604 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.92 % Favored : 94.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.15), residues: 3190 helix: 1.71 (0.21), residues: 685 sheet: -0.54 (0.18), residues: 761 loop : -1.00 (0.15), residues: 1744 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6380 Ramachandran restraints generated. 3190 Oldfield, 0 Emsley, 3190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 3.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3430 time to fit residues: 72.4640 Evaluate side-chains 88 residues out of total 2818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 3.031 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 235 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 32 optimal weight: 0.0000 chunk 47 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN ** D 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 965 GLN ** D1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** 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 = 0.3279 r_free = 0.3279 target = 0.065052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.050263 restraints weight = 215003.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.051215 restraints weight = 132109.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.051901 restraints weight = 93846.953| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 26130 Z= 0.132 Angle : 0.516 9.657 35551 Z= 0.267 Chirality : 0.043 0.202 4111 Planarity : 0.004 0.102 4571 Dihedral : 5.095 108.696 3604 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.73 % Favored : 96.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3190 helix: 1.84 (0.21), residues: 687 sheet: -0.34 (0.18), residues: 762 loop : -0.98 (0.15), residues: 1741 =============================================================================== Job complete usr+sys time: 3914.49 seconds wall clock time: 74 minutes 1.07 seconds (4441.07 seconds total)