Starting phenix.real_space_refine on Sat Dec 16 11:57:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjk_23876/12_2023/7mjk_23876.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjk_23876/12_2023/7mjk_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_2023/7mjk_23876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjk_23876/12_2023/7mjk_23876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjk_23876/12_2023/7mjk_23876.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjk_23876/12_2023/7mjk_23876.pdb" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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 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. 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 17.01, per 1000 atoms: 0.49 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: 12.27 Conformation dependent library (CDL) restraints added in 5.8 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: 5.29 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: 19.71 Time building geometry restraints manager: 13.42 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=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.75e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.69e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.67e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.60e+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: 20384 17.87 - 35.75: 1318 35.75 - 53.62: 234 53.62 - 71.50: 64 71.50 - 89.37: 44 Dihedral angle restraints: 22044 sinusoidal: 9297 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 22041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 5109 0.094 - 0.189: 525 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 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 15.390 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 92.960 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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= 0.291 Angle : 0.792 10.178 48567 Z= 0.422 Chirality : 0.055 0.472 5667 Planarity : 0.008 0.111 6189 Dihedral : 12.845 89.373 13704 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 886 HIS 0.004 0.001 HIS A 66 PHE 0.035 0.002 PHE C 275 TYR 0.024 0.002 TYR A 495 ARG 0.019 0.001 ARG E 211 *********************** 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 : 3.963 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 3 residues processed: 286 average time/residue: 1.6548 time to fit residues: 560.8046 Evaluate side-chains 108 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 105 time to evaluate : 4.043 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 5.3225 ------------------------------------------------------------------------------- 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: 0.8120 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 35676 Z= 0.328 Angle : 0.603 10.668 48567 Z= 0.313 Chirality : 0.045 0.197 5667 Planarity : 0.005 0.074 6189 Dihedral : 5.800 52.870 5973 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.94 % Allowed : 5.87 % Favored : 93.19 % 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: -0.03 (0.12), residues: 4323 helix: 1.45 (0.20), residues: 678 sheet: 0.32 (0.14), residues: 1311 loop : -0.64 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.006 0.001 HIS H 72 PHE 0.021 0.002 PHE C 275 TYR 0.018 0.002 TYR A 265 ARG 0.008 0.001 ARG B 346 *********************** 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 168 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 4.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 13 residues processed: 159 average time/residue: 1.4383 time to fit residues: 281.7181 Evaluate side-chains 112 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 4.199 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 2 average time/residue: 0.9148 time to fit residues: 7.6341 ------------------------------------------------------------------------------- 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: 1.9990 chunk 123 optimal weight: 8.9990 chunk 331 optimal weight: 4.9990 chunk 270 optimal weight: 0.2980 chunk 109 optimal weight: 20.0000 chunk 398 optimal weight: 0.9990 chunk 430 optimal weight: 0.9990 chunk 354 optimal weight: 4.9990 chunk 395 optimal weight: 0.8980 chunk 135 optimal weight: 30.0000 chunk 319 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35676 Z= 0.154 Angle : 0.515 8.747 48567 Z= 0.266 Chirality : 0.043 0.225 5667 Planarity : 0.004 0.074 6189 Dihedral : 5.114 53.607 5973 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.26 % Allowed : 7.62 % Favored : 91.12 % 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: 1.75 (0.20), residues: 702 sheet: 0.43 (0.14), residues: 1308 loop : -0.47 (0.12), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 107 HIS 0.005 0.001 HIS B 207 PHE 0.014 0.001 PHE B 565 TYR 0.019 0.001 TYR A1067 ARG 0.004 0.000 ARG F 19 *********************** 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 163 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 115 time to evaluate : 3.897 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 11 residues processed: 153 average time/residue: 1.2290 time to fit residues: 238.2020 Evaluate side-chains 107 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 3.993 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.8336 time to fit residues: 7.5531 ------------------------------------------------------------------------------- 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: 2.9990 chunk 206 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 190 optimal weight: 1.9990 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: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN B 824 ASN C 824 ASN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 35676 Z= 0.501 Angle : 0.650 9.852 48567 Z= 0.333 Chirality : 0.047 0.200 5667 Planarity : 0.005 0.079 6189 Dihedral : 5.269 52.637 5973 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.75 % Allowed : 8.61 % Favored : 89.63 % 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: 0.07 (0.12), residues: 4323 helix: 1.37 (0.20), residues: 723 sheet: 0.23 (0.14), residues: 1353 loop : -0.45 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 886 HIS 0.006 0.001 HIS H 72 PHE 0.026 0.002 PHE C 275 TYR 0.023 0.002 TYR A 904 ARG 0.005 0.001 ARG B1014 *********************** 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: 67 poor density : 95 time to evaluate : 4.304 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 25 residues processed: 146 average time/residue: 1.3409 time to fit residues: 245.2080 Evaluate side-chains 105 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 80 time to evaluate : 4.070 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 22 residues processed: 3 average time/residue: 1.0821 time to fit residues: 9.4344 ------------------------------------------------------------------------------- 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: 1.9990 chunk 240 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 315 optimal weight: 2.9990 chunk 174 optimal weight: 30.0000 chunk 361 optimal weight: 4.9990 chunk 292 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 216 optimal weight: 3.9990 chunk 380 optimal weight: 10.0000 chunk 106 optimal weight: 0.1980 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN B 907 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 907 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35676 Z= 0.208 Angle : 0.523 8.916 48567 Z= 0.271 Chirality : 0.043 0.197 5667 Planarity : 0.004 0.077 6189 Dihedral : 4.914 52.965 5973 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.41 % Allowed : 9.64 % Favored : 88.95 % 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: 0.27 (0.13), residues: 4323 helix: 1.92 (0.20), residues: 705 sheet: 0.30 (0.14), residues: 1263 loop : -0.38 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 50 HIS 0.004 0.001 HIS B 207 PHE 0.027 0.001 PHE D 67 TYR 0.020 0.001 TYR A 904 ARG 0.006 0.000 ARG E 24 *********************** 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 150 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 96 time to evaluate : 3.958 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 21 residues processed: 142 average time/residue: 1.3410 time to fit residues: 238.9033 Evaluate side-chains 101 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 3.689 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 0.2837 time to fit residues: 5.9820 ------------------------------------------------------------------------------- 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: 4.9990 chunk 381 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 423 optimal weight: 3.9990 chunk 351 optimal weight: 9.9990 chunk 196 optimal weight: 30.0000 chunk 35 optimal weight: 10.0000 chunk 140 optimal weight: 0.0170 chunk 222 optimal weight: 8.9990 overall best weight: 2.7624 ------------------------------------------------------------------------------- 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** ** D 76 ASN ** 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 199 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN F 203 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 35676 Z= 0.360 Angle : 0.571 9.324 48567 Z= 0.293 Chirality : 0.044 0.197 5667 Planarity : 0.004 0.077 6189 Dihedral : 4.976 53.268 5973 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.05 % Allowed : 10.60 % Favored : 88.35 % 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: 0.20 (0.13), residues: 4323 helix: 1.61 (0.20), residues: 744 sheet: 0.24 (0.14), residues: 1320 loop : -0.38 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP I 50 HIS 0.005 0.001 HIS H 72 PHE 0.027 0.002 PHE D 67 TYR 0.025 0.001 TYR A 904 ARG 0.009 0.000 ARG E 24 *********************** 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 133 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 93 time to evaluate : 3.980 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 21 residues processed: 124 average time/residue: 1.6033 time to fit residues: 246.4422 Evaluate side-chains 102 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 3.954 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 1.4056 time to fit residues: 6.9537 ------------------------------------------------------------------------------- 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: 0.8980 chunk 47 optimal weight: 0.8980 chunk 241 optimal weight: 0.4980 chunk 309 optimal weight: 0.7980 chunk 239 optimal weight: 0.9990 chunk 356 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 422 optimal weight: 0.7980 chunk 264 optimal weight: 9.9990 chunk 257 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35676 Z= 0.153 Angle : 0.508 8.920 48567 Z= 0.262 Chirality : 0.043 0.212 5667 Planarity : 0.004 0.077 6189 Dihedral : 4.716 53.071 5973 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.92 % Allowed : 11.00 % Favored : 88.09 % 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: 0.38 (0.13), residues: 4323 helix: 2.01 (0.20), residues: 723 sheet: 0.33 (0.14), residues: 1281 loop : -0.32 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 50 HIS 0.004 0.001 HIS H 72 PHE 0.042 0.001 PHE D 67 TYR 0.020 0.001 TYR A 904 ARG 0.014 0.000 ARG C 983 *********************** 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 131 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 96 time to evaluate : 3.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 126 average time/residue: 1.4235 time to fit residues: 223.5812 Evaluate side-chains 103 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 3.789 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 0 time to fit residues: 5.0705 ------------------------------------------------------------------------------- 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: 7.9990 chunk 168 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 127 optimal weight: 30.0000 chunk 82 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 268 optimal weight: 40.0000 chunk 287 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 331 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 35676 Z= 0.414 Angle : 0.586 7.808 48567 Z= 0.300 Chirality : 0.045 0.190 5667 Planarity : 0.004 0.084 6189 Dihedral : 4.984 53.094 5973 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.07 % Allowed : 11.36 % Favored : 87.56 % 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: 1.86 (0.20), residues: 720 sheet: 0.21 (0.14), residues: 1317 loop : -0.31 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 50 HIS 0.003 0.001 HIS H 72 PHE 0.023 0.002 PHE D 67 TYR 0.031 0.002 TYR A 904 ARG 0.010 0.001 ARG E 24 *********************** 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 127 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 86 time to evaluate : 4.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 23 residues processed: 120 average time/residue: 1.5267 time to fit residues: 225.3420 Evaluate side-chains 103 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 3.907 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 2 average time/residue: 0.9345 time to fit residues: 7.6619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 0.9980 chunk 404 optimal weight: 0.9980 chunk 368 optimal weight: 9.9990 chunk 393 optimal weight: 0.7980 chunk 236 optimal weight: 0.0970 chunk 171 optimal weight: 30.0000 chunk 308 optimal weight: 0.6980 chunk 120 optimal weight: 20.0000 chunk 355 optimal weight: 20.0000 chunk 372 optimal weight: 7.9990 chunk 392 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35676 Z= 0.156 Angle : 0.514 10.130 48567 Z= 0.264 Chirality : 0.043 0.210 5667 Planarity : 0.004 0.084 6189 Dihedral : 4.734 53.081 5973 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.81 % Allowed : 11.55 % Favored : 87.64 % 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: 0.41 (0.13), residues: 4323 helix: 1.94 (0.20), residues: 741 sheet: 0.34 (0.14), residues: 1263 loop : -0.26 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP I 50 HIS 0.003 0.001 HIS H 72 PHE 0.020 0.001 PHE D 67 TYR 0.021 0.001 TYR A 904 ARG 0.008 0.000 ARG C 983 *********************** REFINEMENT MACRO_CYCLE 9 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 124 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 93 time to evaluate : 4.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 22 residues processed: 121 average time/residue: 1.6013 time to fit residues: 240.6214 Evaluate side-chains 106 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 84 time to evaluate : 4.397 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 0.3441 time to fit residues: 5.3039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 3.9990 chunk 415 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 289 optimal weight: 7.9990 chunk 436 optimal weight: 0.0070 chunk 401 optimal weight: 5.9990 chunk 347 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 213 optimal weight: 30.0000 overall best weight: 3.2006 ------------------------------------------------------------------------------- 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** ** 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** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 35676 Z= 0.399 Angle : 0.586 9.330 48567 Z= 0.300 Chirality : 0.045 0.188 5667 Planarity : 0.004 0.091 6189 Dihedral : 4.954 53.169 5973 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.73 % Allowed : 11.70 % Favored : 87.56 % 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: 0.31 (0.13), residues: 4323 helix: 1.95 (0.20), residues: 738 sheet: 0.22 (0.14), residues: 1302 loop : -0.33 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP I 50 HIS 0.003 0.001 HIS C1048 PHE 0.022 0.002 PHE C 565 TYR 0.033 0.002 TYR A 904 ARG 0.013 0.001 ARG A 983 ********************** REFINEMENT MACRO_CYCLE 10 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 112 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 22 residues processed: 111 average time/residue: 1.4393 time to fit residues: 200.6787 Evaluate side-chains 100 residues out of total 3819 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 4.282 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 1 average time/residue: 0.6485 time to fit residues: 6.4589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 9.9990 chunk 370 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 320 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 348 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 357 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.115678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.069385 restraints weight = 109145.932| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.78 r_work: 0.2982 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35676 Z= 0.164 Angle : 0.510 10.142 48567 Z= 0.261 Chirality : 0.043 0.206 5667 Planarity : 0.004 0.089 6189 Dihedral : 4.742 52.935 5973 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.73 % Allowed : 11.70 % Favored : 87.56 % 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: 0.44 (0.13), residues: 4323 helix: 2.00 (0.20), residues: 741 sheet: 0.26 (0.14), residues: 1281 loop : -0.20 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 50 HIS 0.003 0.001 HIS C 207 PHE 0.022 0.001 PHE C 565 TYR 0.023 0.001 TYR A 904 ARG 0.011 0.000 ARG A 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8791.07 seconds wall clock time: 160 minutes 0.39 seconds (9600.39 seconds total)