Starting phenix.real_space_refine (version: dev) on Thu Apr 7 19:02:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7chh_30374/04_2022/7chh_30374.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7chh_30374/04_2022/7chh_30374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7chh_30374/04_2022/7chh_30374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7chh_30374/04_2022/7chh_30374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7chh_30374/04_2022/7chh_30374.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7chh_30374/04_2022/7chh_30374.pdb" } resolution = 3.49 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= 0.002 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 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 29029 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 7734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7734 Classifications: {'peptide': 1003} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 52, 'TRANS': 950} Chain breaks: 10 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 7652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7652 Classifications: {'peptide': 994} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 53, 'TRANS': 940} Chain breaks: 10 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 7672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7672 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 53, 'TRANS': 945} Chain breaks: 10 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 84 Chain: "D" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "E" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 103, 'PCIS': 1} Chain: "G" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "H" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 103, 'PCIS': 1} Chain: "J" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "K" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 852 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 103, 'PCIS': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 16.26, per 1000 atoms: 0.56 Number of scatterers: 29029 At special positions: 0 Unit cell: (136.68, 152.76, 227.13, 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 129 16.00 O 5672 8.00 N 4798 7.00 C 18430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 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=2.04 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=2.02 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=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.06 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 93 " 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 616 " " NAG A1302 " - " ASN A 657 " " NAG A1303 " - " ASN A 709 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 234 " " NAG A1313 " - " ASN A 282 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1307 " - " ASN B 801 " " NAG B1310 " - " ASN B1134 " " NAG B1312 " - " ASN B 122 " " NAG B1313 " - " ASN B1074 " " NAG C1301 " - " ASN C1134 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 801 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 616 " " NAG C1311 " - " ASN C 603 " " NAG C1313 " - " ASN C 165 " " NAG F 1 " - " ASN A 717 " " NAG I 1 " - " ASN B 717 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN C1098 " " NAG N 1 " - " ASN C 717 " Time building additional restraints: 12.09 Conformation dependent library (CDL) restraints added in 4.2 seconds 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6854 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 59 sheets defined 20.5% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.692A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.999A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.741A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.913A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 881 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.877A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.054A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.910A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.195A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 295 through 304 removed outlier: 3.564A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.815A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.599A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.534A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.641A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.569A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 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 758 through 783 removed outlier: 3.657A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.566A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.104A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.987A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.024A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.776A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 390' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.821A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.812A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.513A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.829A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.029A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.781A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.958A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 84 through 88 removed outlier: 3.959A pdb=" N VAL H 88 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 84 through 88 removed outlier: 3.959A pdb=" N VAL K 88 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 7.866A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.026A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.769A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.880A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.260A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.721A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.918A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.757A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.029A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.029A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.343A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.519A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.880A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 200 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.345A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 169 through 172 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.785A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.699A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE B 392 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.699A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 removed outlier: 3.730A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.772A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.772A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 691 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.547A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.539A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 4.692A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.519A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.830A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.720A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.504A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.051A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 6.364A pdb=" N PHE C 392 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.688A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 723 removed outlier: 6.837A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 723 removed outlier: 6.837A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.460A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AF3, first strand: chain 'D' and resid 4 through 8 removed outlier: 4.130A pdb=" N LEU D 20 " --> pdb=" O LEU D 81 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 71 " --> pdb=" O TYR D 80 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.506A pdb=" N THR D 119 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR D 95 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL D 37 " --> pdb=" O TYR D 95 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.628A pdb=" N CYS E 23 " --> pdb=" O PHE E 76 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE E 76 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP E 75 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER E 72 " --> pdb=" O ASP E 75 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.074A pdb=" N GLY E 89 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR E 41 " --> pdb=" O TYR E 92 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU E 42 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU E 51 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR E 54 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN E 58 " --> pdb=" O TYR E 54 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 4 through 8 removed outlier: 4.130A pdb=" N LEU G 20 " --> pdb=" O LEU G 81 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER G 71 " --> pdb=" O TYR G 80 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.505A pdb=" N THR G 119 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR G 95 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL G 37 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET G 34 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.628A pdb=" N CYS H 23 " --> pdb=" O PHE H 76 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE H 76 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP H 75 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER H 72 " --> pdb=" O ASP H 75 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 10 through 13 removed outlier: 4.074A pdb=" N GLY H 89 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR H 41 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU H 42 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU H 51 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR H 54 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN H 58 " --> pdb=" O TYR H 54 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 4 through 8 removed outlier: 4.130A pdb=" N LEU J 20 " --> pdb=" O LEU J 81 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER J 71 " --> pdb=" O TYR J 80 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.506A pdb=" N THR J 119 " --> pdb=" O TYR J 94 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR J 95 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL J 37 " --> pdb=" O TYR J 95 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET J 34 " --> pdb=" O ALA J 50 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.628A pdb=" N CYS K 23 " --> pdb=" O PHE K 76 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE K 76 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP K 75 " --> pdb=" O SER K 72 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER K 72 " --> pdb=" O ASP K 75 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 10 through 13 removed outlier: 4.074A pdb=" N GLY K 89 " --> pdb=" O LEU K 109 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR K 41 " --> pdb=" O TYR K 92 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU K 42 " --> pdb=" O LEU K 51 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU K 51 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N TYR K 54 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN K 58 " --> pdb=" O TYR K 54 " (cutoff:3.500A) 1071 hydrogen bonds defined for protein. 2931 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: 14.79 Time building geometry restraints manager: 13.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 9318 1.35 - 1.48: 8012 1.48 - 1.62: 12165 1.62 - 1.75: 2 1.75 - 1.89: 163 Bond restraints: 29660 Sorted by residual: bond pdb=" CA TRP J 109 " pdb=" C TRP J 109 " ideal model delta sigma weight residual 1.522 1.571 -0.049 1.72e-02 3.38e+03 8.16e+00 bond pdb=" CB ARG D 43 " pdb=" CG ARG D 43 " ideal model delta sigma weight residual 1.520 1.604 -0.084 3.00e-02 1.11e+03 7.87e+00 bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.426 1.515 -0.089 3.20e-02 9.77e+02 7.81e+00 bond pdb=" CB ARG J 43 " pdb=" CG ARG J 43 " ideal model delta sigma weight residual 1.520 1.604 -0.084 3.00e-02 1.11e+03 7.81e+00 bond pdb=" CA TRP G 109 " pdb=" C TRP G 109 " ideal model delta sigma weight residual 1.522 1.570 -0.048 1.72e-02 3.38e+03 7.75e+00 ... (remaining 29655 not shown) Histogram of bond angle deviations from ideal: 95.66 - 103.39: 310 103.39 - 111.12: 11035 111.12 - 118.85: 12378 118.85 - 126.58: 16273 126.58 - 134.31: 371 Bond angle restraints: 40367 Sorted by residual: angle pdb=" C2 NAG B1303 " pdb=" N2 NAG B1303 " pdb=" C7 NAG B1303 " ideal model delta sigma weight residual 123.12 134.06 -10.94 1.28e+00 6.08e-01 7.27e+01 angle pdb=" C2 NAG C1311 " pdb=" N2 NAG C1311 " pdb=" C7 NAG C1311 " ideal model delta sigma weight residual 123.12 134.06 -10.94 1.28e+00 6.08e-01 7.26e+01 angle pdb=" C2 NAG C1308 " pdb=" N2 NAG C1308 " pdb=" C7 NAG C1308 " ideal model delta sigma weight residual 123.12 134.00 -10.88 1.28e+00 6.08e-01 7.19e+01 angle pdb=" C2 NAG A1313 " pdb=" N2 NAG A1313 " pdb=" C7 NAG A1313 " ideal model delta sigma weight residual 123.12 133.99 -10.87 1.28e+00 6.08e-01 7.18e+01 angle pdb=" C2 NAG B1312 " pdb=" N2 NAG B1312 " pdb=" C7 NAG B1312 " ideal model delta sigma weight residual 123.12 133.96 -10.84 1.28e+00 6.08e-01 7.14e+01 ... (remaining 40362 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.40: 15843 19.40 - 38.80: 1326 38.80 - 58.20: 289 58.20 - 77.60: 53 77.60 - 97.00: 17 Dihedral angle restraints: 17528 sinusoidal: 6839 harmonic: 10689 Sorted by residual: dihedral pdb=" CA LEU B 293 " pdb=" C LEU B 293 " pdb=" N ASP B 294 " pdb=" CA ASP B 294 " ideal model delta harmonic sigma weight residual -180.00 -117.24 -62.76 0 5.00e+00 4.00e-02 1.58e+02 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.81 -85.19 1 1.00e+01 1.00e-02 8.80e+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 93.00 177.64 -84.64 1 1.00e+01 1.00e-02 8.70e+01 ... (remaining 17525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3960 0.082 - 0.164: 653 0.164 - 0.246: 61 0.246 - 0.327: 10 0.327 - 0.409: 10 Chirality restraints: 4694 Sorted by residual: chirality pdb=" CB ILE A 119 " pdb=" CA ILE A 119 " pdb=" CG1 ILE A 119 " pdb=" CG2 ILE A 119 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CB ILE C 666 " pdb=" CA ILE C 666 " pdb=" CG1 ILE C 666 " pdb=" CG2 ILE C 666 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" C2 NAG C1308 " pdb=" C1 NAG C1308 " pdb=" C3 NAG C1308 " pdb=" N2 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.87e+00 ... (remaining 4691 not shown) Planarity restraints: 5215 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 29 " 0.025 2.00e-02 2.50e+03 3.54e-02 2.19e+01 pdb=" CG PHE J 29 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE J 29 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE J 29 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE J 29 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE J 29 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE J 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 29 " -0.025 2.00e-02 2.50e+03 3.53e-02 2.18e+01 pdb=" CG PHE D 29 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE D 29 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE D 29 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE D 29 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 29 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 29 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 29 " -0.025 2.00e-02 2.50e+03 3.51e-02 2.16e+01 pdb=" CG PHE G 29 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE G 29 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE G 29 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE G 29 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE G 29 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 29 " -0.000 2.00e-02 2.50e+03 ... (remaining 5212 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1627 2.73 - 3.27: 26607 3.27 - 3.81: 47275 3.81 - 4.36: 54094 4.36 - 4.90: 95682 Nonbonded interactions: 225285 Sorted by model distance: nonbonded pdb=" O GLY D 116 " pdb=" OG SER E 48 " model vdw 2.182 2.440 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 2.253 2.520 nonbonded pdb=" O SER D 85 " pdb=" OG SER D 85 " model vdw 2.257 2.440 nonbonded pdb=" O SER G 85 " pdb=" OG SER G 85 " model vdw 2.257 2.440 nonbonded pdb=" O SER J 85 " pdb=" OG SER J 85 " model vdw 2.257 2.440 ... (remaining 225280 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' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 66 or resid 81 through 95 or (resi \ d 99 through 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) or \ resid 103 through 104 or (resid 105 and (name N or name CA or name C or name O \ or name CB )) or resid 106 through 128 or (resid 129 and (name N or name CA or n \ ame C or name O or name CB )) or resid 130 through 140 or (resid 157 through 160 \ and (name N or name CA or name C or name O or name CB )) or resid 161 through 1 \ 87 or (resid 188 and (name N or name CA or name C or name O or name CB )) or res \ id 189 through 194 or (resid 195 through 198 and (name N or name CA or name C or \ name O or name CB )) or resid 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 209 or resid 217 through 236 or ( \ resid 237 and (name N or name CA or name C or name O or name CB )) or resid 238 \ or (resid 239 and (name N or name CA or name C or name O or name CB )) or resid \ 240 through 243 or resid 264 through 516 or resid 521 through 620 or resid 641 t \ hrough 1146 or resid 1301 through 1311)) selection = (chain 'B' and (resid 27 through 95 or resid 99 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 140 or ( \ resid 157 through 160 and (name N or name CA or name C or name O or name CB )) o \ r resid 161 through 175 or (resid 176 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 or (resid 190 and (name N or name CA or \ name C or name O or name CB )) or resid 191 through 236 or (resid 237 and (name \ N or name CA or name C or name O or name CB )) or resid 238 or (resid 239 and (n \ ame N or name CA or name C or name O or name CB )) or resid 240 through 289 or ( \ resid 290 and (name N or name CA or name C or name O or name CB )) or resid 291 \ through 328 or resid 334 through 527 or (resid 528 through 529 and (name N or na \ me CA or name C or name O or name CB )) or resid 530 through 620 or resid 641 th \ rough 1146 or resid 1301 through 1313)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 59 or (resid 60 and (name N or nam \ e CA or name C or name O or name CB )) or resid 61 through 66 or resid 81 throug \ h 95 or (resid 99 through 100 and (name N or name CA or name C or name O or name \ CB )) or resid 101 through 104 or (resid 105 and (name N or name CA or name C o \ r name O or name CB )) or resid 106 through 187 or (resid 188 and (name N or nam \ e CA or name C or name O or name CB )) or resid 189 through 199 or (resid 200 an \ d (name N or name CA or name C or name O or name CB )) or resid 201 through 209 \ or resid 217 through 243 or resid 264 through 328 or resid 334 through 516 or re \ sid 521 through 1146 or resid 1301 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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 129 5.16 5 C 18430 2.51 5 N 4798 2.21 5 O 5672 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: 3.480 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: 15.960 Check model and map are aligned: 0.460 Convert atoms to be neutral: 0.250 Process input model: 78.630 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.250 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0183 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.089 29660 Z= 0.463 Angle : 1.089 15.643 40367 Z= 0.599 Chirality : 0.062 0.409 4694 Planarity : 0.007 0.085 5183 Dihedral : 15.081 97.001 10542 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.03 (0.12), residues: 3626 helix: -1.01 (0.18), residues: 665 sheet: -0.57 (0.17), residues: 843 loop : -1.85 (0.12), residues: 2118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 233 time to evaluate : 3.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 58 residues processed: 338 average time/residue: 0.3992 time to fit residues: 215.6606 Evaluate side-chains 188 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 130 time to evaluate : 3.187 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.3011 time to fit residues: 34.7747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 309 optimal weight: 3.9990 chunk 278 optimal weight: 50.0000 chunk 154 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 187 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 chunk 287 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 214 optimal weight: 0.9990 chunk 333 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 965 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN B 563 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 901 GLN C 954 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1106 GLN K 31 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0521 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 29660 Z= 0.221 Angle : 0.674 12.895 40367 Z= 0.357 Chirality : 0.046 0.254 4694 Planarity : 0.006 0.091 5183 Dihedral : 6.004 102.384 4211 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.55 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.37 (0.13), residues: 3626 helix: 0.23 (0.20), residues: 664 sheet: -0.46 (0.17), residues: 882 loop : -1.52 (0.13), residues: 2080 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 17 residues processed: 182 average time/residue: 0.4152 time to fit residues: 123.3953 Evaluate side-chains 142 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 2.982 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3968 time to fit residues: 15.6266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 185 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 277 optimal weight: 10.0000 chunk 226 optimal weight: 0.9980 chunk 91 optimal weight: 0.0770 chunk 333 optimal weight: 20.0000 chunk 360 optimal weight: 5.9990 chunk 297 optimal weight: 3.9990 chunk 331 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 267 optimal weight: 6.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 658 ASN A 913 GLN A 955 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 501 ASN B 901 GLN B 913 GLN B 957 GLN B1058 HIS B1101 HIS C 751 ASN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0916 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.194 29660 Z= 0.276 Angle : 0.728 13.364 40367 Z= 0.383 Chirality : 0.049 0.269 4694 Planarity : 0.006 0.094 5183 Dihedral : 5.946 100.628 4211 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % 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: -1.42 (0.13), residues: 3626 helix: 0.07 (0.20), residues: 661 sheet: -0.59 (0.17), residues: 966 loop : -1.48 (0.13), residues: 1999 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 144 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 23 residues processed: 178 average time/residue: 0.3776 time to fit residues: 114.1612 Evaluate side-chains 147 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 3.040 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3063 time to fit residues: 17.2662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 329 optimal weight: 50.0000 chunk 251 optimal weight: 0.9990 chunk 173 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 335 optimal weight: 20.0000 chunk 354 optimal weight: 0.4980 chunk 175 optimal weight: 0.9980 chunk 317 optimal weight: 50.0000 chunk 95 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN B1064 HIS B1106 GLN C 343 ASN C 784 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1019 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.119 29660 Z= 0.237 Angle : 0.654 11.960 40367 Z= 0.343 Chirality : 0.047 0.326 4694 Planarity : 0.005 0.084 5183 Dihedral : 5.738 100.037 4211 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.52 % Favored : 95.45 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.54 % 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: -1.35 (0.13), residues: 3626 helix: 0.23 (0.20), residues: 666 sheet: -0.52 (0.17), residues: 949 loop : -1.49 (0.13), residues: 2011 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 130 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 171 average time/residue: 0.3799 time to fit residues: 109.7359 Evaluate side-chains 133 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 3.173 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2717 time to fit residues: 14.2499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 295 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 302 optimal weight: 0.7980 chunk 245 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 318 optimal weight: 40.0000 chunk 89 optimal weight: 0.7980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 409 GLN B 895 GLN B 907 ASN B 949 GLN B1058 HIS B1108 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 957 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1341 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.145 29660 Z= 0.335 Angle : 0.818 21.268 40367 Z= 0.432 Chirality : 0.053 0.508 4694 Planarity : 0.006 0.092 5183 Dihedral : 6.369 97.193 4211 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.51 % Favored : 93.44 % Rotamer Outliers : 3.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.75 (0.13), residues: 3626 helix: -0.32 (0.20), residues: 648 sheet: -0.71 (0.16), residues: 961 loop : -1.69 (0.13), residues: 2017 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 129 time to evaluate : 3.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 45 residues processed: 215 average time/residue: 0.3916 time to fit residues: 139.5608 Evaluate side-chains 161 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 116 time to evaluate : 3.210 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2853 time to fit residues: 28.9590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 119 optimal weight: 0.5980 chunk 319 optimal weight: 20.0000 chunk 70 optimal weight: 0.0970 chunk 208 optimal weight: 0.0270 chunk 87 optimal weight: 1.9990 chunk 355 optimal weight: 6.9990 chunk 294 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 186 optimal weight: 0.8980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS B 949 GLN B1058 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1333 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.737 29660 Z= 0.552 Angle : 1.081 106.100 40367 Z= 0.517 Chirality : 0.051 0.502 4694 Planarity : 0.006 0.084 5183 Dihedral : 6.361 98.878 4211 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.54 % Favored : 93.44 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.77 (0.13), residues: 3626 helix: -0.33 (0.20), residues: 648 sheet: -0.73 (0.16), residues: 959 loop : -1.71 (0.13), residues: 2019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 119 time to evaluate : 3.301 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 135 average time/residue: 0.4148 time to fit residues: 93.3405 Evaluate side-chains 125 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 3.149 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2571 time to fit residues: 9.7743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 342 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 202 optimal weight: 0.0470 chunk 259 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 298 optimal weight: 0.0030 chunk 198 optimal weight: 4.9990 chunk 353 optimal weight: 0.7980 chunk 221 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 163 optimal weight: 0.1980 overall best weight: 0.3888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B1058 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1338 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.269 29660 Z= 0.817 Angle : 1.127 106.100 40367 Z= 0.555 Chirality : 0.051 0.502 4694 Planarity : 0.006 0.084 5183 Dihedral : 6.361 98.878 4211 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.54 % Favored : 93.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.77 (0.13), residues: 3626 helix: -0.33 (0.20), residues: 648 sheet: -0.73 (0.16), residues: 959 loop : -1.71 (0.13), residues: 2019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.164 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.4238 time to fit residues: 82.3379 Evaluate side-chains 115 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.110 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 218 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 69 optimal weight: 0.0470 chunk 68 optimal weight: 0.9990 chunk 224 optimal weight: 9.9990 chunk 240 optimal weight: 10.0000 chunk 174 optimal weight: 0.9990 chunk 32 optimal weight: 0.0030 chunk 278 optimal weight: 1.9990 overall best weight: 0.5690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B1058 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1338 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.269 29660 Z= 0.817 Angle : 1.127 106.100 40367 Z= 0.555 Chirality : 0.051 0.502 4694 Planarity : 0.006 0.084 5183 Dihedral : 6.361 98.878 4211 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.54 % Favored : 93.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.77 (0.13), residues: 3626 helix: -0.33 (0.20), residues: 648 sheet: -0.73 (0.16), residues: 959 loop : -1.71 (0.13), residues: 2019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.400 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.4264 time to fit residues: 83.1304 Evaluate side-chains 115 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.070 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 321 optimal weight: 0.0170 chunk 338 optimal weight: 0.4980 chunk 309 optimal weight: 3.9990 chunk 329 optimal weight: 50.0000 chunk 198 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 101 optimal weight: 0.0870 chunk 297 optimal weight: 0.6980 chunk 311 optimal weight: 50.0000 chunk 328 optimal weight: 5.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B1058 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1338 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.269 29660 Z= 0.817 Angle : 1.127 106.100 40367 Z= 0.555 Chirality : 0.051 0.502 4694 Planarity : 0.006 0.084 5183 Dihedral : 6.361 98.878 4211 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.54 % Favored : 93.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.77 (0.13), residues: 3626 helix: -0.33 (0.20), residues: 648 sheet: -0.73 (0.16), residues: 959 loop : -1.71 (0.13), residues: 2019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.166 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.4207 time to fit residues: 81.0321 Evaluate side-chains 115 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 2.985 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 216 optimal weight: 0.9980 chunk 348 optimal weight: 0.9980 chunk 212 optimal weight: 8.9990 chunk 165 optimal weight: 0.1980 chunk 242 optimal weight: 6.9990 chunk 365 optimal weight: 0.9990 chunk 336 optimal weight: 10.0000 chunk 291 optimal weight: 40.0000 chunk 30 optimal weight: 0.0970 chunk 224 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B1058 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1338 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.269 29660 Z= 0.817 Angle : 1.127 106.100 40367 Z= 0.555 Chirality : 0.051 0.502 4694 Planarity : 0.006 0.084 5183 Dihedral : 6.361 98.878 4211 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.54 % Favored : 93.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.77 (0.13), residues: 3626 helix: -0.33 (0.20), residues: 648 sheet: -0.73 (0.16), residues: 959 loop : -1.71 (0.13), residues: 2019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.135 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.4142 time to fit residues: 80.1578 Evaluate side-chains 115 residues out of total 3200 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 3.067 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.5462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 367 random chunks: chunk 231 optimal weight: 0.8980 chunk 310 optimal weight: 50.0000 chunk 89 optimal weight: 0.9990 chunk 268 optimal weight: 50.0000 chunk 42 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 291 optimal weight: 40.0000 chunk 122 optimal weight: 0.5980 chunk 299 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B1058 HIS ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5340 r_free = 0.5340 target = 0.299631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.294964 restraints weight = 68851.297| |-----------------------------------------------------------------------------| r_work (start): 0.5288 rms_B_bonded: 0.86 r_work: 0.5280 rms_B_bonded: 0.75 restraints_weight: 0.5000 r_work: 0.5276 rms_B_bonded: 0.82 restraints_weight: 0.2500 r_work: 0.5269 rms_B_bonded: 0.99 restraints_weight: 0.1250 r_work: 0.5260 rms_B_bonded: 1.27 restraints_weight: 0.0625 r_work: 0.5246 rms_B_bonded: 1.71 restraints_weight: 0.0312 r_work: 0.5226 rms_B_bonded: 2.45 restraints_weight: 0.0156 r_work: 0.5190 rms_B_bonded: 3.77 restraints_weight: 0.0078 r_work (final): 0.5190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1215 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.269 29660 Z= 0.817 Angle : 1.127 106.100 40367 Z= 0.555 Chirality : 0.051 0.502 4694 Planarity : 0.006 0.084 5183 Dihedral : 6.361 98.878 4211 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.54 % Favored : 93.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.77 (0.13), residues: 3626 helix: -0.33 (0.20), residues: 648 sheet: -0.73 (0.16), residues: 959 loop : -1.71 (0.13), residues: 2019 =============================================================================== Job complete usr+sys time: 4147.36 seconds wall clock time: 78 minutes 17.86 seconds (4697.86 seconds total)