Starting phenix.real_space_refine (version: dev) on Sun Sep 4 06:00:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y42_33600/09_2022/7y42_33600_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y42_33600/09_2022/7y42_33600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y42_33600/09_2022/7y42_33600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y42_33600/09_2022/7y42_33600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y42_33600/09_2022/7y42_33600_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y42_33600/09_2022/7y42_33600_updated.pdb" } resolution = 3.45 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= 0.003 sd= 0.048 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 "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B ASP 1118": "OD1" <-> "OD2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "D TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "D TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 457": "NH1" <-> "NH2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 634": "NH1" <-> "NH2" Residue "D PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 985": "OD1" <-> "OD2" Residue "D GLU 988": "OE1" <-> "OE2" Residue "D GLU 990": "OE1" <-> "OE2" Residue "D ASP 1041": "OD1" <-> "OD2" Residue "D GLU 1072": "OE1" <-> "OE2" Residue "D ASP 1118": "OD1" <-> "OD2" Residue "D TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1144": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4709/modules/chem_data/mon_lib" Total number of atoms: 23058 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7538 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 46, 'TRANS': 921} Chain breaks: 15 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 7538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7538 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 46, 'TRANS': 921} Chain breaks: 15 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 7538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 968, 7538 Classifications: {'peptide': 968} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 46, 'TRANS': 921} Chain breaks: 15 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 148 Unusual residues: {'NAG': 9, 'REA': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 148 Unusual residues: {'NAG': 9, 'REA': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 148 Unusual residues: {'NAG': 9, 'REA': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 13.18, per 1000 atoms: 0.57 Number of scatterers: 23058 At special positions: 0 Unit cell: (128.04, 131.92, 177.51, 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 90 16.00 O 4479 8.00 N 3780 7.00 C 14709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " 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 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 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 D 291 " - pdb=" SG CYS D 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 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 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " 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=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 282 " " NAG D1304 " - " ASN D 331 " " NAG D1305 " - " ASN D 343 " " NAG D1306 " - " ASN D 603 " " NAG D1307 " - " ASN D 616 " " NAG D1308 " - " ASN D 657 " " NAG D1309 " - " ASN D 709 " Time building additional restraints: 8.95 Conformation dependent library (CDL) restraints added in 4.0 seconds 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5442 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 48 sheets defined 22.3% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 338 through 341 No H-bonds generated for 'chain 'A' and resid 338 through 341' Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.476A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.612A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 617 through 620 removed outlier: 3.579A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 620' Processing helix chain 'A' and resid 631 through 637 removed outlier: 4.310A pdb=" N TYR A 636 " --> pdb=" O THR A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 747 through 756 removed outlier: 3.874A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 782 removed outlier: 3.909A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 870 through 873 No H-bonds generated for 'chain 'A' and resid 870 through 873' Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.973A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY A 908 " --> pdb=" O TYR A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 920 through 938 removed outlier: 3.801A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 966 removed outlier: 4.106A pdb=" N LYS A 947 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 949 " --> pdb=" O GLY A 946 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 951 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 952 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA A 958 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A 959 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN A 965 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1031 removed outlier: 4.446A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A1025 " --> pdb=" O SER A1021 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A1027 " --> pdb=" O ASN A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.877A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 338 through 341 No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 365 through 367 No H-bonds generated for 'chain 'B' and resid 365 through 367' Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.476A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.612A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 617 through 620 removed outlier: 3.579A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 617 through 620' Processing helix chain 'B' and resid 631 through 637 removed outlier: 4.310A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 756 removed outlier: 3.874A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.909A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 823 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 870 through 873 No H-bonds generated for 'chain 'B' and resid 870 through 873' Processing helix chain 'B' and resid 898 through 908 removed outlier: 3.974A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 917 Processing helix chain 'B' and resid 920 through 938 removed outlier: 3.801A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 966 removed outlier: 4.106A pdb=" N LYS B 947 " --> pdb=" O ALA B 944 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN B 949 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 951 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B 952 " --> pdb=" O GLN B 949 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA B 958 " --> pdb=" O ASN B 955 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU B 959 " --> pdb=" O ALA B 956 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN B 965 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1031 removed outlier: 4.446A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B1003 " --> pdb=" O GLY B 999 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B1025 " --> pdb=" O SER B1021 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B1027 " --> pdb=" O ASN B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.878A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 303 Processing helix chain 'D' and resid 338 through 341 No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.477A pdb=" N ASN D 388 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 3.612A pdb=" N VAL D 407 " --> pdb=" O GLY D 404 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 545 No H-bonds generated for 'chain 'D' and resid 543 through 545' Processing helix chain 'D' and resid 617 through 620 removed outlier: 3.579A pdb=" N VAL D 620 " --> pdb=" O CYS D 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 617 through 620' Processing helix chain 'D' and resid 631 through 637 removed outlier: 4.310A pdb=" N TYR D 636 " --> pdb=" O THR D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 742 Processing helix chain 'D' and resid 747 through 756 removed outlier: 3.874A pdb=" N ASN D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR D 756 " --> pdb=" O LEU D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 759 through 782 removed outlier: 3.909A pdb=" N ASN D 764 " --> pdb=" O CYS D 760 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU D 767 " --> pdb=" O LEU D 763 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 823 Processing helix chain 'D' and resid 849 through 855 Processing helix chain 'D' and resid 870 through 873 No H-bonds generated for 'chain 'D' and resid 870 through 873' Processing helix chain 'D' and resid 898 through 908 removed outlier: 3.974A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY D 908 " --> pdb=" O TYR D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 917 Processing helix chain 'D' and resid 920 through 938 removed outlier: 3.801A pdb=" N SER D 929 " --> pdb=" O ASN D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 966 removed outlier: 4.106A pdb=" N LYS D 947 " --> pdb=" O ALA D 944 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN D 949 " --> pdb=" O GLY D 946 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 951 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL D 952 " --> pdb=" O GLN D 949 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA D 958 " --> pdb=" O ASN D 955 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU D 959 " --> pdb=" O ALA D 956 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLN D 965 " --> pdb=" O LEU D 962 " (cutoff:3.500A) Processing helix chain 'D' and resid 977 through 983 Processing helix chain 'D' and resid 986 through 1031 removed outlier: 4.446A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY D 999 " --> pdb=" O ARG D 995 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN D1002 " --> pdb=" O THR D 998 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER D1003 " --> pdb=" O GLY D 999 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA D1025 " --> pdb=" O SER D1021 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D1026 " --> pdb=" O ALA D1022 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR D1027 " --> pdb=" O ASN D1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1145 removed outlier: 3.878A pdb=" N GLU D1144 " --> pdb=" O PRO D1140 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 Processing sheet with id= B, first strand: chain 'A' and resid 54 through 56 removed outlier: 3.979A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 91 through 93 removed outlier: 4.332A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 104 through 107 Processing sheet with id= E, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.505A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 395 through 403 Processing sheet with id= G, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= H, first strand: chain 'A' and resid 538 through 541 removed outlier: 3.556A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.360A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 711 through 713 Processing sheet with id= K, first strand: chain 'A' and resid 717 through 722 removed outlier: 6.052A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 725 through 728 Processing sheet with id= M, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.532A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= O, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id= P, first strand: chain 'A' and resid 275 through 279 removed outlier: 3.821A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 28 through 30 Processing sheet with id= R, first strand: chain 'B' and resid 54 through 56 removed outlier: 3.979A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'B' and resid 91 through 93 removed outlier: 4.332A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 104 through 107 Processing sheet with id= U, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.505A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 395 through 403 Processing sheet with id= W, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= X, first strand: chain 'B' and resid 538 through 541 removed outlier: 3.556A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 691 through 696 removed outlier: 6.360A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 711 through 713 Processing sheet with id= AA, first strand: chain 'B' and resid 717 through 722 removed outlier: 6.052A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 725 through 728 Processing sheet with id= AC, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.533A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= AE, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id= AF, first strand: chain 'B' and resid 275 through 279 removed outlier: 3.821A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 28 through 30 Processing sheet with id= AH, first strand: chain 'D' and resid 54 through 56 removed outlier: 3.979A pdb=" N PHE D 55 " --> pdb=" O GLN D 271 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D 271 " --> pdb=" O PHE D 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'D' and resid 91 through 93 removed outlier: 4.332A pdb=" N GLY D 268 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA D 93 " --> pdb=" O TYR D 266 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'D' and resid 104 through 107 Processing sheet with id= AK, first strand: chain 'D' and resid 311 through 313 removed outlier: 3.504A pdb=" N TYR D 313 " --> pdb=" O VAL D 597 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'D' and resid 395 through 403 Processing sheet with id= AM, first strand: chain 'D' and resid 452 through 454 Processing sheet with id= AN, first strand: chain 'D' and resid 538 through 541 removed outlier: 3.555A pdb=" N GLY D 548 " --> pdb=" O PHE D 541 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'D' and resid 691 through 696 removed outlier: 6.360A pdb=" N ALA D 672 " --> pdb=" O PRO D 665 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'D' and resid 711 through 713 Processing sheet with id= AQ, first strand: chain 'D' and resid 717 through 722 removed outlier: 6.052A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'D' and resid 725 through 728 Processing sheet with id= AS, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.533A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'D' and resid 1088 through 1090 Processing sheet with id= AU, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id= AV, first strand: chain 'D' and resid 275 through 279 removed outlier: 3.821A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1440 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: 8.23 Time building geometry restraints manager: 9.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7332 1.34 - 1.46: 5714 1.46 - 1.58: 10378 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 23538 Sorted by residual: bond pdb=" C7 REA B1310 " pdb=" C8 REA B1310 " ideal model delta sigma weight residual 1.342 1.468 -0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C7 REA D1310 " pdb=" C8 REA D1310 " ideal model delta sigma weight residual 1.342 1.468 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C7 REA A1310 " pdb=" C8 REA A1310 " ideal model delta sigma weight residual 1.342 1.468 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C11 REA D1310 " pdb=" C12 REA D1310 " ideal model delta sigma weight residual 1.349 1.472 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C11 REA A1310 " pdb=" C12 REA A1310 " ideal model delta sigma weight residual 1.349 1.472 -0.123 2.00e-02 2.50e+03 3.79e+01 ... (remaining 23533 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.49: 613 106.49 - 113.40: 13068 113.40 - 120.32: 8327 120.32 - 127.23: 9798 127.23 - 134.15: 195 Bond angle restraints: 32001 Sorted by residual: angle pdb=" N ASN A 370 " pdb=" CA ASN A 370 " pdb=" C ASN A 370 " ideal model delta sigma weight residual 114.56 107.66 6.90 1.27e+00 6.20e-01 2.96e+01 angle pdb=" N ASN D 370 " pdb=" CA ASN D 370 " pdb=" C ASN D 370 " ideal model delta sigma weight residual 114.56 107.67 6.89 1.27e+00 6.20e-01 2.94e+01 angle pdb=" N ASN B 370 " pdb=" CA ASN B 370 " pdb=" C ASN B 370 " ideal model delta sigma weight residual 114.56 107.68 6.88 1.27e+00 6.20e-01 2.94e+01 angle pdb=" N VAL B 130 " pdb=" CA VAL B 130 " pdb=" C VAL B 130 " ideal model delta sigma weight residual 112.17 107.61 4.56 9.50e-01 1.11e+00 2.30e+01 angle pdb=" N VAL A 130 " pdb=" CA VAL A 130 " pdb=" C VAL A 130 " ideal model delta sigma weight residual 112.17 107.62 4.55 9.50e-01 1.11e+00 2.30e+01 ... (remaining 31996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 12537 17.54 - 35.08: 1047 35.08 - 52.62: 246 52.62 - 70.16: 45 70.16 - 87.70: 33 Dihedral angle restraints: 13908 sinusoidal: 5481 harmonic: 8427 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -173.70 87.70 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -173.70 87.70 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS D 291 " pdb=" SG CYS D 291 " pdb=" SG CYS D 301 " pdb=" CB CYS D 301 " ideal model delta sinusoidal sigma weight residual -86.00 -173.68 87.68 1 1.00e+01 1.00e-02 9.21e+01 ... (remaining 13905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2140 0.033 - 0.067: 1012 0.067 - 0.100: 426 0.100 - 0.133: 141 0.133 - 0.167: 22 Chirality restraints: 3741 Sorted by residual: chirality pdb=" CA VAL B 267 " pdb=" N VAL B 267 " pdb=" C VAL B 267 " pdb=" CB VAL B 267 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA VAL A 267 " pdb=" N VAL A 267 " pdb=" C VAL A 267 " pdb=" CB VAL A 267 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA VAL D 267 " pdb=" N VAL D 267 " pdb=" C VAL D 267 " pdb=" CB VAL D 267 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 3738 not shown) Planarity restraints: 4116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 REA B1310 " -0.380 2.00e-02 2.50e+03 2.25e-01 6.32e+02 pdb=" C11 REA B1310 " 0.272 2.00e-02 2.50e+03 pdb=" C19 REA B1310 " -0.012 2.00e-02 2.50e+03 pdb=" C8 REA B1310 " 0.177 2.00e-02 2.50e+03 pdb=" C9 REA B1310 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 REA A1310 " 0.380 2.00e-02 2.50e+03 2.25e-01 6.31e+02 pdb=" C11 REA A1310 " -0.272 2.00e-02 2.50e+03 pdb=" C19 REA A1310 " 0.012 2.00e-02 2.50e+03 pdb=" C8 REA A1310 " -0.177 2.00e-02 2.50e+03 pdb=" C9 REA A1310 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 REA D1310 " 0.379 2.00e-02 2.50e+03 2.25e-01 6.30e+02 pdb=" C11 REA D1310 " -0.271 2.00e-02 2.50e+03 pdb=" C19 REA D1310 " 0.012 2.00e-02 2.50e+03 pdb=" C8 REA D1310 " -0.177 2.00e-02 2.50e+03 pdb=" C9 REA D1310 " 0.057 2.00e-02 2.50e+03 ... (remaining 4113 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 595 2.68 - 3.23: 22534 3.23 - 3.79: 33714 3.79 - 4.34: 45154 4.34 - 4.90: 75371 Nonbonded interactions: 177368 Sorted by model distance: nonbonded pdb=" OG SER D 116 " pdb=" O VAL D 130 " model vdw 2.121 2.440 nonbonded pdb=" OG SER B 116 " pdb=" O VAL B 130 " model vdw 2.121 2.440 nonbonded pdb=" OG SER A 116 " pdb=" O VAL A 130 " model vdw 2.121 2.440 nonbonded pdb=" O ASN D 99 " pdb=" NH1 ARG D 102 " model vdw 2.151 2.520 nonbonded pdb=" O ASN A 99 " pdb=" NH1 ARG A 102 " model vdw 2.152 2.520 ... (remaining 177363 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 'A' selection = chain 'B' selection = chain 'D' } 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 90 5.16 5 C 14709 2.51 5 N 3780 2.21 5 O 4479 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 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.710 Check model and map are aligned: 0.330 Convert atoms to be neutral: 0.200 Process input model: 59.280 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.006 0.126 23538 Z= 0.415 Angle : 0.827 9.302 32001 Z= 0.476 Chirality : 0.047 0.167 3741 Planarity : 0.010 0.225 4089 Dihedral : 14.453 84.498 8394 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.15), residues: 2814 helix: -1.29 (0.20), residues: 684 sheet: -2.01 (0.21), residues: 555 loop : -2.38 (0.14), residues: 1575 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 211 average time/residue: 0.3332 time to fit residues: 111.7627 Evaluate side-chains 165 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 2.878 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4509 time to fit residues: 6.9527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 168 optimal weight: 0.1980 chunk 261 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B1071 GLN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1071 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 23538 Z= 0.264 Angle : 0.608 9.749 32001 Z= 0.312 Chirality : 0.044 0.176 3741 Planarity : 0.005 0.059 4089 Dihedral : 7.209 89.120 3270 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.15), residues: 2814 helix: -0.83 (0.20), residues: 684 sheet: -1.72 (0.22), residues: 552 loop : -2.27 (0.14), residues: 1578 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 189 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 19 residues processed: 201 average time/residue: 0.3068 time to fit residues: 101.9495 Evaluate side-chains 182 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 2.695 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2019 time to fit residues: 10.8492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 chunk 283 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 210 optimal weight: 0.4980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 23538 Z= 0.181 Angle : 0.544 9.798 32001 Z= 0.276 Chirality : 0.043 0.153 3741 Planarity : 0.004 0.055 4089 Dihedral : 6.858 89.731 3270 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.15), residues: 2814 helix: -0.60 (0.21), residues: 693 sheet: -1.57 (0.21), residues: 579 loop : -2.11 (0.15), residues: 1542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 197 time to evaluate : 2.920 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 210 average time/residue: 0.2953 time to fit residues: 104.0305 Evaluate side-chains 155 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 2.677 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2090 time to fit residues: 5.1181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 chunk 135 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 249 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.080 23538 Z= 0.563 Angle : 0.713 9.800 32001 Z= 0.364 Chirality : 0.049 0.150 3741 Planarity : 0.005 0.056 4089 Dihedral : 7.103 89.260 3270 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.15), residues: 2814 helix: -1.18 (0.19), residues: 726 sheet: -1.83 (0.21), residues: 555 loop : -2.26 (0.14), residues: 1533 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 171 time to evaluate : 2.840 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 32 residues processed: 202 average time/residue: 0.2898 time to fit residues: 99.9880 Evaluate side-chains 187 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 2.642 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2038 time to fit residues: 15.9427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 10.0000 chunk 158 optimal weight: 0.0070 chunk 4 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 23538 Z= 0.192 Angle : 0.542 9.700 32001 Z= 0.279 Chirality : 0.046 0.706 3741 Planarity : 0.004 0.055 4089 Dihedral : 6.728 86.920 3270 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.15), residues: 2814 helix: -0.64 (0.21), residues: 696 sheet: -1.52 (0.21), residues: 552 loop : -2.02 (0.15), residues: 1566 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 184 time to evaluate : 2.908 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 201 average time/residue: 0.3109 time to fit residues: 104.0623 Evaluate side-chains 173 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 163 time to evaluate : 2.634 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2136 time to fit residues: 7.8545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 0.8980 chunk 250 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 163 optimal weight: 10.0000 chunk 68 optimal weight: 0.0050 chunk 278 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 23538 Z= 0.151 Angle : 0.518 9.695 32001 Z= 0.263 Chirality : 0.049 1.095 3741 Planarity : 0.004 0.054 4089 Dihedral : 6.346 80.908 3270 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.15), residues: 2814 helix: -0.42 (0.21), residues: 696 sheet: -1.43 (0.21), residues: 582 loop : -1.87 (0.15), residues: 1536 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 2.717 Fit side-chains outliers start: 25 outliers final: 15 residues processed: 213 average time/residue: 0.3175 time to fit residues: 112.5195 Evaluate side-chains 177 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 2.865 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2060 time to fit residues: 9.2950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 203 optimal weight: 0.3980 chunk 157 optimal weight: 1.9990 chunk 234 optimal weight: 0.0000 chunk 155 optimal weight: 7.9990 chunk 277 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.8946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 23538 Z= 0.168 Angle : 0.515 9.721 32001 Z= 0.263 Chirality : 0.049 0.918 3741 Planarity : 0.004 0.053 4089 Dihedral : 6.113 84.307 3270 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.15), residues: 2814 helix: -0.30 (0.21), residues: 696 sheet: -1.36 (0.20), residues: 582 loop : -1.81 (0.15), residues: 1536 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 177 time to evaluate : 2.655 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 196 average time/residue: 0.3085 time to fit residues: 101.7998 Evaluate side-chains 178 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 163 time to evaluate : 2.894 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2434 time to fit residues: 10.2095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 137 optimal weight: 8.9990 chunk 25 optimal weight: 0.0770 chunk 218 optimal weight: 3.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 23538 Z= 0.206 Angle : 0.522 9.804 32001 Z= 0.264 Chirality : 0.046 0.778 3741 Planarity : 0.004 0.053 4089 Dihedral : 6.033 84.143 3270 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.15), residues: 2814 helix: -0.26 (0.21), residues: 696 sheet: -1.29 (0.20), residues: 579 loop : -1.82 (0.15), residues: 1539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 165 time to evaluate : 2.685 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 176 average time/residue: 0.3010 time to fit residues: 89.4626 Evaluate side-chains 162 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 2.672 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2252 time to fit residues: 5.1569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 chunk 155 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 233 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 23538 Z= 0.373 Angle : 0.605 9.828 32001 Z= 0.309 Chirality : 0.050 0.900 3741 Planarity : 0.005 0.053 4089 Dihedral : 6.347 84.616 3270 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.15), residues: 2814 helix: -0.51 (0.21), residues: 681 sheet: -1.47 (0.20), residues: 558 loop : -1.92 (0.15), residues: 1575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 169 time to evaluate : 2.799 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 175 average time/residue: 0.2975 time to fit residues: 88.6400 Evaluate side-chains 176 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 167 time to evaluate : 2.876 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2235 time to fit residues: 7.0740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 166 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 190 optimal weight: 0.7980 chunk 286 optimal weight: 6.9990 chunk 264 optimal weight: 0.7980 chunk 228 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 23538 Z= 0.195 Angle : 0.522 9.592 32001 Z= 0.264 Chirality : 0.045 0.652 3741 Planarity : 0.004 0.053 4089 Dihedral : 6.041 84.694 3270 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.15), residues: 2814 helix: -0.32 (0.21), residues: 684 sheet: -1.34 (0.21), residues: 558 loop : -1.84 (0.15), residues: 1572 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 177 time to evaluate : 2.517 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 182 average time/residue: 0.3107 time to fit residues: 96.0649 Evaluate side-chains 164 residues out of total 2535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 161 time to evaluate : 2.922 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1919 time to fit residues: 4.6422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 1.9990 chunk 243 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 234 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.135580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.105212 restraints weight = 41932.238| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.98 r_work: 0.3370 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work: 0.3335 rms_B_bonded: 2.75 restraints_weight: 0.1250 r_work: 0.3316 rms_B_bonded: 2.88 restraints_weight: 0.0625 r_work: 0.3294 rms_B_bonded: 3.08 restraints_weight: 0.0312 r_work: 0.3268 rms_B_bonded: 3.38 restraints_weight: 0.0156 r_work: 0.3238 rms_B_bonded: 3.78 restraints_weight: 0.0078 r_work: 0.3202 rms_B_bonded: 4.32 restraints_weight: 0.0039 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 23538 Z= 0.202 Angle : 0.529 9.692 32001 Z= 0.265 Chirality : 0.045 0.541 3741 Planarity : 0.004 0.052 4089 Dihedral : 6.039 87.603 3270 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.15), residues: 2814 helix: -0.18 (0.21), residues: 693 sheet: -1.32 (0.20), residues: 558 loop : -1.84 (0.15), residues: 1563 =============================================================================== Job complete usr+sys time: 3392.14 seconds wall clock time: 64 minutes 1.84 seconds (3841.84 seconds total)