Starting phenix.real_space_refine (version: dev) on Mon Dec 19 08:17:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjk_23876/12_2022/7mjk_23876.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjk_23876/12_2022/7mjk_23876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjk_23876/12_2022/7mjk_23876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjk_23876/12_2022/7mjk_23876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjk_23876/12_2022/7mjk_23876.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjk_23876/12_2022/7mjk_23876.pdb" } resolution = 2.73 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= 0.032 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 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 34878 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "D" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1581 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Chain: "E" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "G" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "I" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "F" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1581 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Chain: "H" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1581 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Chain: "B" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "C" Number of atoms: 8140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8140 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 56, 'TRANS': 983} Chain breaks: 7 Chain: "J" 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: "K" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 19.12, per 1000 atoms: 0.55 Number of scatterers: 34878 At special positions: 0 Unit cell: (149, 148, 245, 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 144 16.00 O 6870 8.00 N 5721 7.00 C 22143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 194 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG J 1 " - " ASN A 17 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 17 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1074 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 13.99 Conformation dependent library (CDL) restraints added in 5.1 seconds 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8178 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 84 sheets defined 19.8% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.820A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.635A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.082A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.136A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 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: 3.668A 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 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.907A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.533A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.093A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.533A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN D 32 " --> pdb=" O VAL D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 86 through 90 removed outlier: 4.109A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.860A pdb=" N VAL E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.861A pdb=" N VAL G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 126 Processing helix chain 'G' and resid 183 through 188 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.864A pdb=" N VAL I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 126 Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.532A pdb=" N SER F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN F 32 " --> pdb=" O VAL F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 86 through 90 removed outlier: 4.108A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 193 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.542A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 86 through 90 removed outlier: 4.102A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 193 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.816A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.635A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.083A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.135A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 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: 3.666A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.910A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.530A 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 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.091A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.839A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.643A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.085A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 4.135A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.673A 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 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.907A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.533A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.091A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.165A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.289A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.991A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.501A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 163 removed outlier: 5.380A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.639A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.296A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.151A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.009A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.548A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.564A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.564A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.386A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.875A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.130A pdb=" N TYR D 33 " --> pdb=" O GLY D 98 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.861A pdb=" N TYR D 99 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE D 104 " --> pdb=" O TYR D 99 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 124 through 128 removed outlier: 6.098A pdb=" N TYR D 180 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 124 through 128 removed outlier: 6.098A pdb=" N TYR D 180 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 198 through 204 removed outlier: 4.072A pdb=" N TYR D 198 " --> pdb=" O VAL D 215 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 4 through 7 removed outlier: 5.951A pdb=" N THR E 69 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 10.593A pdb=" N GLN E 27 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N SER E 67 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 11.615A pdb=" N VAL E 29 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N SER E 65 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 10 through 13 removed outlier: 5.991A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 13 removed outlier: 5.991A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 114 through 118 removed outlier: 5.877A pdb=" N SER E 131 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU E 181 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL E 133 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N LEU E 179 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU E 135 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER E 177 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN E 137 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU E 175 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 145 through 150 Processing sheet with id=AD4, first strand: chain 'G' and resid 4 through 7 removed outlier: 5.951A pdb=" N THR G 69 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N GLN G 27 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N SER G 67 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 11.614A pdb=" N VAL G 29 " --> pdb=" O SER G 65 " (cutoff:3.500A) removed outlier: 11.596A pdb=" N SER G 65 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 13 removed outlier: 5.990A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 13 removed outlier: 5.990A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 114 through 118 removed outlier: 5.838A pdb=" N SER G 131 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU G 181 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL G 133 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N LEU G 179 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU G 135 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER G 177 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN G 137 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU G 175 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 145 through 150 Processing sheet with id=AD9, first strand: chain 'I' and resid 4 through 7 removed outlier: 5.985A pdb=" N THR I 69 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N GLN I 27 " --> pdb=" O SER I 67 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N SER I 67 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 11.586A pdb=" N VAL I 29 " --> pdb=" O SER I 65 " (cutoff:3.500A) removed outlier: 11.561A pdb=" N SER I 65 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.983A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.983A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 114 through 118 removed outlier: 5.868A pdb=" N SER I 131 " --> pdb=" O LEU I 181 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU I 181 " --> pdb=" O SER I 131 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL I 133 " --> pdb=" O LEU I 179 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LEU I 179 " --> pdb=" O VAL I 133 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU I 135 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N SER I 177 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASN I 137 " --> pdb=" O LEU I 175 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU I 175 " --> pdb=" O ASN I 137 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 145 through 150 Processing sheet with id=AE5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'F' and resid 11 through 12 removed outlier: 4.130A pdb=" N TYR F 33 " --> pdb=" O GLY F 98 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.860A pdb=" N TYR F 99 " --> pdb=" O PHE F 104 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE F 104 " --> pdb=" O TYR F 99 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 124 through 128 removed outlier: 6.093A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 124 through 128 removed outlier: 6.093A pdb=" N TYR F 180 " --> pdb=" O ASP F 148 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 198 through 204 removed outlier: 4.054A pdb=" N TYR F 198 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.138A pdb=" N TYR H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.517A pdb=" N TYR H 106 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR H 99 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE H 104 " --> pdb=" O TYR H 99 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.082A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 124 through 128 removed outlier: 6.082A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 198 through 204 removed outlier: 4.055A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AF9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.172A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.987A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.728A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 154 through 163 removed outlier: 9.411A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 11.462A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.147A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.640A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 325 through 326 removed outlier: 5.299A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AG7, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.154A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AG9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AH1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.013A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.548A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.393A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AH7, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AH8, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.154A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.988A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.727A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 154 through 163 removed outlier: 9.414A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 11.463A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.149A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.640A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AI5, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.148A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AI7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AI8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.018A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.553A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.553A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.389A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'C' and resid 1120 through 1122 1533 hydrogen bonds defined for protein. 4029 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: 18.79 Time building geometry restraints manager: 15.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10141 1.34 - 1.46: 7771 1.46 - 1.58: 17584 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 35676 Sorted by residual: bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.55e+00 bond pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 1.335 1.361 -0.025 1.36e-02 5.41e+03 3.50e+00 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.335 1.361 -0.025 1.36e-02 5.41e+03 3.43e+00 bond pdb=" C SER E 94 " pdb=" N PRO E 95 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.91e+00 bond pdb=" C SER G 94 " pdb=" N PRO G 95 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.86e+00 ... (remaining 35671 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.32: 1059 106.32 - 113.27: 19288 113.27 - 120.22: 12362 120.22 - 127.17: 15516 127.17 - 134.12: 342 Bond angle restraints: 48567 Sorted by residual: angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.04 -5.34 1.22e+00 6.72e-01 1.92e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.03 -5.33 1.22e+00 6.72e-01 1.91e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.01 -5.31 1.22e+00 6.72e-01 1.90e+01 angle pdb=" N GLN B1010 " pdb=" CA GLN B1010 " pdb=" CB GLN B1010 " ideal model delta sigma weight residual 110.39 116.39 -6.00 1.66e+00 3.63e-01 1.31e+01 angle pdb=" CA PRO B 986 " pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 117.93 122.24 -4.31 1.20e+00 6.94e-01 1.29e+01 ... (remaining 48562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 19580 17.87 - 35.75: 1252 35.75 - 53.62: 207 53.62 - 71.50: 61 71.50 - 89.37: 44 Dihedral angle restraints: 21144 sinusoidal: 8397 harmonic: 12747 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.61 -59.61 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.44 -59.44 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 152.36 -59.36 1 1.00e+01 1.00e-02 4.71e+01 ... (remaining 21141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 5139 0.094 - 0.189: 495 0.189 - 0.283: 25 0.283 - 0.377: 5 0.377 - 0.472: 3 Chirality restraints: 5667 Sorted by residual: chirality pdb=" CB VAL D 63 " pdb=" CA VAL D 63 " pdb=" CG1 VAL D 63 " pdb=" CG2 VAL D 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CB VAL F 63 " pdb=" CA VAL F 63 " pdb=" CG1 VAL F 63 " pdb=" CG2 VAL F 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" CB VAL H 63 " pdb=" CA VAL H 63 " pdb=" CG1 VAL H 63 " pdb=" CG2 VAL H 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.46 2.00e-01 2.50e+01 5.40e+00 ... (remaining 5664 not shown) Planarity restraints: 6231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 203 " -0.074 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO E 204 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO E 204 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO E 204 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER I 203 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO I 204 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO I 204 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO I 204 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 203 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO G 204 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO G 204 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO G 204 " -0.059 5.00e-02 4.00e+02 ... (remaining 6228 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 10042 2.83 - 3.34: 28741 3.34 - 3.86: 59634 3.86 - 4.38: 68274 4.38 - 4.90: 118506 Nonbonded interactions: 285197 Sorted by model distance: nonbonded pdb=" OG SER F 56 " pdb=" OD2 ASP B 420 " model vdw 2.307 2.440 nonbonded pdb=" OD2 ASP A 420 " pdb=" OG SER D 56 " model vdw 2.308 2.440 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.308 2.440 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.311 2.440 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.314 2.440 ... (remaining 285192 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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 144 5.16 5 C 22143 2.51 5 N 5721 2.21 5 O 6870 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: 3.190 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: 16.440 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.260 Process input model: 94.240 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.004 0.077 35676 Z= 0.253 Angle : 0.766 10.178 48567 Z= 0.419 Chirality : 0.054 0.472 5667 Planarity : 0.008 0.111 6189 Dihedral : 12.926 89.373 12804 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.12), residues: 4323 helix: -0.04 (0.18), residues: 684 sheet: -0.04 (0.14), residues: 1329 loop : -1.01 (0.11), residues: 2310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 3.946 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 3 residues processed: 286 average time/residue: 1.5267 time to fit residues: 522.6140 Evaluate side-chains 108 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 3.948 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 5.2861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 10.0000 chunk 331 optimal weight: 0.9990 chunk 184 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 223 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 343 optimal weight: 0.1980 chunk 132 optimal weight: 40.0000 chunk 208 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 chunk 397 optimal weight: 1.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 926 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN H 72 HIS ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 926 GLN C 115 GLN C 926 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 35676 Z= 0.328 Angle : 0.600 10.469 48567 Z= 0.314 Chirality : 0.044 0.209 5667 Planarity : 0.005 0.076 6189 Dihedral : 5.044 23.067 5073 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.12), residues: 4323 helix: 1.39 (0.20), residues: 678 sheet: 0.33 (0.14), residues: 1317 loop : -0.64 (0.12), residues: 2328 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 132 time to evaluate : 3.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 13 residues processed: 160 average time/residue: 1.3139 time to fit residues: 262.8782 Evaluate side-chains 110 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 4.238 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 1 average time/residue: 0.4848 time to fit residues: 6.2620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 331 optimal weight: 2.9990 chunk 270 optimal weight: 0.2980 chunk 109 optimal weight: 20.0000 chunk 398 optimal weight: 0.6980 chunk 430 optimal weight: 0.0770 chunk 354 optimal weight: 4.9990 chunk 395 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 319 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN E 38 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN F 39 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 HIS ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 35676 Z= 0.146 Angle : 0.510 8.843 48567 Z= 0.266 Chirality : 0.043 0.246 5667 Planarity : 0.004 0.075 6189 Dihedral : 4.715 18.282 5073 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.13), residues: 4323 helix: 1.77 (0.20), residues: 699 sheet: 0.46 (0.13), residues: 1407 loop : -0.51 (0.13), residues: 2217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 110 time to evaluate : 3.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 11 residues processed: 148 average time/residue: 1.1959 time to fit residues: 228.6745 Evaluate side-chains 104 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 4.073 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.8880 time to fit residues: 7.8630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 5.9990 chunk 299 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 399 optimal weight: 4.9990 chunk 423 optimal weight: 3.9990 chunk 208 optimal weight: 20.0000 chunk 379 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A 957 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** H 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B 957 GLN C 824 ASN C1002 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.078 35676 Z= 0.651 Angle : 0.725 11.886 48567 Z= 0.376 Chirality : 0.049 0.231 5667 Planarity : 0.005 0.078 6189 Dihedral : 5.191 22.915 5073 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.12), residues: 4323 helix: 1.33 (0.19), residues: 702 sheet: 0.08 (0.14), residues: 1365 loop : -0.46 (0.13), residues: 2256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 97 time to evaluate : 4.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 20 residues processed: 149 average time/residue: 1.2989 time to fit residues: 243.3949 Evaluate side-chains 104 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 3.899 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 1.3291 time to fit residues: 6.8817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 315 optimal weight: 1.9990 chunk 174 optimal weight: 30.0000 chunk 361 optimal weight: 4.9990 chunk 292 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 216 optimal weight: 3.9990 chunk 380 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN H 203 ASN B 907 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 35676 Z= 0.208 Angle : 0.525 9.050 48567 Z= 0.275 Chirality : 0.043 0.234 5667 Planarity : 0.004 0.078 6189 Dihedral : 4.795 21.281 5073 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 4323 helix: 1.85 (0.20), residues: 702 sheet: 0.20 (0.14), residues: 1287 loop : -0.43 (0.12), residues: 2334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 95 time to evaluate : 3.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 22 residues processed: 141 average time/residue: 1.3720 time to fit residues: 243.4200 Evaluate side-chains 97 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 4.403 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 0 time to fit residues: 5.7820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 30.0000 chunk 381 optimal weight: 0.3980 chunk 83 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 423 optimal weight: 4.9990 chunk 351 optimal weight: 7.9990 chunk 196 optimal weight: 30.0000 chunk 35 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 222 optimal weight: 8.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.006 0.053 35676 Z= 0.411 Angle : 0.584 8.984 48567 Z= 0.304 Chirality : 0.045 0.220 5667 Planarity : 0.004 0.079 6189 Dihedral : 4.879 21.631 5073 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.13), residues: 4323 helix: 1.72 (0.20), residues: 720 sheet: 0.13 (0.14), residues: 1320 loop : -0.42 (0.13), residues: 2283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 90 time to evaluate : 4.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 25 residues processed: 129 average time/residue: 1.3264 time to fit residues: 216.1766 Evaluate side-chains 105 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 80 time to evaluate : 4.133 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 1 average time/residue: 1.4598 time to fit residues: 7.0220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 0.9990 chunk 47 optimal weight: 0.0770 chunk 241 optimal weight: 0.9980 chunk 309 optimal weight: 0.5980 chunk 239 optimal weight: 2.9990 chunk 356 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 422 optimal weight: 0.9980 chunk 264 optimal weight: 10.0000 chunk 257 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 35676 Z= 0.155 Angle : 0.505 9.142 48567 Z= 0.262 Chirality : 0.043 0.235 5667 Planarity : 0.004 0.079 6189 Dihedral : 4.619 20.120 5073 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.13), residues: 4323 helix: 1.80 (0.20), residues: 738 sheet: 0.26 (0.14), residues: 1284 loop : -0.34 (0.13), residues: 2301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 92 time to evaluate : 4.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 24 residues processed: 128 average time/residue: 1.3193 time to fit residues: 212.1655 Evaluate side-chains 102 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 78 time to evaluate : 4.061 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.5189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 287 optimal weight: 0.5980 chunk 208 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 331 optimal weight: 6.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 35676 Z= 0.399 Angle : 0.574 8.080 48567 Z= 0.298 Chirality : 0.044 0.216 5667 Planarity : 0.004 0.083 6189 Dihedral : 4.774 23.048 5073 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.13), residues: 4323 helix: 1.88 (0.20), residues: 720 sheet: 0.17 (0.14), residues: 1326 loop : -0.34 (0.13), residues: 2277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8646 Ramachandran restraints generated. 4323 Oldfield, 0 Emsley, 4323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 89 time to evaluate : 4.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 26 residues processed: 126 average time/residue: 1.4471 time to fit residues: 228.2844 Evaluate side-chains 106 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 80 time to evaluate : 4.079 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 26 residues processed: 0 time to fit residues: 5.2416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.4364 > 50: distance: 12 - 152: 28.657 distance: 15 - 149: 22.179 distance: 21 - 148: 3.335 distance: 72 - 81: 17.654 distance: 81 - 82: 17.395 distance: 82 - 83: 50.168 distance: 82 - 85: 23.506 distance: 83 - 84: 41.553 distance: 83 - 90: 22.890 distance: 85 - 86: 9.299 distance: 87 - 88: 4.850 distance: 90 - 91: 28.218 distance: 91 - 92: 48.001 distance: 91 - 94: 44.111 distance: 92 - 93: 43.202 distance: 92 - 98: 67.436 distance: 94 - 95: 26.336 distance: 95 - 96: 33.505 distance: 95 - 97: 32.075 distance: 98 - 99: 43.259 distance: 98 - 104: 43.758 distance: 99 - 100: 26.046 distance: 99 - 102: 16.348 distance: 100 - 101: 26.755 distance: 100 - 105: 26.097 distance: 102 - 103: 18.282 distance: 103 - 104: 17.979 distance: 105 - 106: 14.506 distance: 106 - 107: 12.780 distance: 106 - 109: 12.507 distance: 107 - 108: 27.683 distance: 107 - 113: 11.177 distance: 109 - 110: 9.182 distance: 110 - 111: 9.928 distance: 110 - 112: 8.786 distance: 113 - 114: 3.001 distance: 114 - 115: 7.611 distance: 114 - 117: 24.526 distance: 115 - 116: 26.928 distance: 115 - 121: 6.596 distance: 117 - 118: 3.421 distance: 118 - 119: 12.284 distance: 118 - 120: 11.663 distance: 121 - 122: 10.475 distance: 122 - 123: 10.418 distance: 122 - 125: 8.122 distance: 123 - 124: 31.212 distance: 123 - 132: 13.358 distance: 125 - 126: 5.646 distance: 126 - 127: 5.606 distance: 126 - 128: 3.655 distance: 127 - 129: 9.018 distance: 128 - 130: 4.603 distance: 132 - 133: 4.417 distance: 133 - 134: 11.474 distance: 133 - 136: 5.210 distance: 134 - 135: 14.614 distance: 134 - 139: 6.954 distance: 136 - 137: 9.424 distance: 139 - 140: 13.042 distance: 140 - 141: 24.788 distance: 141 - 142: 40.318 distance: 141 - 143: 12.957 distance: 143 - 144: 11.398 distance: 143 - 204: 9.227 distance: 144 - 145: 17.562 distance: 144 - 147: 20.679 distance: 145 - 146: 33.115 distance: 145 - 149: 28.535 distance: 146 - 201: 18.842 distance: 147 - 148: 17.438 distance: 149 - 150: 28.090 distance: 150 - 151: 33.034 distance: 150 - 153: 48.682 distance: 151 - 152: 43.159 distance: 151 - 156: 22.110 distance: 153 - 154: 18.248 distance: 153 - 155: 26.416