Starting phenix.real_space_refine on Sat Dec 16 06:23:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whd_32499/12_2023/7whd_32499.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whd_32499/12_2023/7whd_32499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whd_32499/12_2023/7whd_32499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whd_32499/12_2023/7whd_32499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whd_32499/12_2023/7whd_32499.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whd_32499/12_2023/7whd_32499.pdb" } resolution = 2.65 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 147 5.16 5 C 21677 2.51 5 N 5644 2.21 5 O 6741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 220": "OE1" <-> "OE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J GLU 82": "OE1" <-> "OE2" Residue "J GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 34209 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7870 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "D" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "G" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "H" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "J" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "K" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 18.56, per 1000 atoms: 0.54 Number of scatterers: 34209 At special positions: 0 Unit cell: (175.664, 164.685, 252.517, 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 147 16.00 O 6741 8.00 N 5644 7.00 C 21677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 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=2.02 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=2.02 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=2.02 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 B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.04 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=2.49 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=2.04 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 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 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 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 148 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.08 Simple disulfide: pdb=" SG CYS J 148 " - pdb=" SG CYS J 204 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG 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-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 282 " " NAG A1403 " - " ASN A 603 " " NAG A1404 " - " ASN A 616 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A 165 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 282 " " NAG B1403 " - " ASN B 603 " " NAG B1404 " - " ASN B 616 " " NAG B1405 " - " ASN B 657 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 234 " " NAG C1404 " - " ASN C 282 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 165 " " NAG F 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 709 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1074 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 14.02 Conformation dependent library (CDL) restraints added in 6.8 seconds 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8054 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 80 sheets defined 18.5% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.85 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.969A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.349A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 4.492A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 removed outlier: 4.178A pdb=" N THR A 572 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.528A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.552A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) 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 760 through 783 removed outlier: 4.005A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.999A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.667A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.522A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.469A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.892A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.456A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.692A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.531A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.545A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.577A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.115A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (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 982 removed outlier: 3.786A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.714A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.547A pdb=" N GLU B1144 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1141 through 1145' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.229A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.859A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 411 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.520A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 737 through 743 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: 3.786A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.117A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.613A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 4.028A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 983 removed outlier: 3.622A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.439A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.936A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.055A pdb=" N SER E 127 " --> pdb=" O GLN E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 153 Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.577A pdb=" N GLN G 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.850A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 126 Processing helix chain 'H' and resid 150 through 153 Processing helix chain 'H' and resid 183 through 187 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.800A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 126 Processing helix chain 'K' and resid 182 through 188 removed outlier: 3.525A pdb=" N GLU K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS K 188 " --> pdb=" O ALA K 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 8.153A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.708A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.555A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.859A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN A 125 " --> pdb=" O ASN A 122 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.936A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 357 removed outlier: 3.694A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.587A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.123A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.536A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.536A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.181A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.661A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.126A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 51 through 55 removed outlier: 3.602A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.102A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 225 through 229 removed outlier: 6.757A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 114 through 116 removed outlier: 4.248A pdb=" N THR B 114 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 133 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 127 through 128 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.409A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 323 through 326 removed outlier: 5.703A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 542 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC9, first strand: chain 'B' and resid 395 through 402 Processing sheet with id=AD1, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 567 through 568 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.565A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.837A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.810A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.810A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.436A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.238A pdb=" N GLY C 89 " --> pdb=" O LEU C 270 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 50 through 55 removed outlier: 7.474A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.651A pdb=" N LEU C 241 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 134 through 135 removed outlier: 6.633A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 310 through 319 removed outlier: 5.453A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.714A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.163A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.176A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.828A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.828A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.978A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 57 through 60 removed outlier: 5.071A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL D 110 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 57 through 60 removed outlier: 5.071A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 92 " --> pdb=" O VAL D 117 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 68 through 73 Processing sheet with id=AF8, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.594A pdb=" N GLY D 147 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS D 151 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU D 186 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.594A pdb=" N GLY D 147 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 158 through 162 removed outlier: 3.861A pdb=" N THR D 159 " --> pdb=" O ASN D 207 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 215 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.608A pdb=" N SER E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS E 23 " --> pdb=" O PHE E 71 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.466A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 114 through 118 removed outlier: 6.099A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 144 through 148 Processing sheet with id=AG6, first strand: chain 'G' and resid 3 through 4 removed outlier: 3.862A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 57 through 60 removed outlier: 5.177A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL G 110 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 57 through 60 removed outlier: 5.177A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA G 92 " --> pdb=" O VAL G 117 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR G 94 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 68 through 73 Processing sheet with id=AH1, first strand: chain 'G' and resid 128 through 130 removed outlier: 3.533A pdb=" N LYS G 151 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU G 149 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER G 188 " --> pdb=" O LEU G 149 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS G 151 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU G 186 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 144 through 146 removed outlier: 3.651A pdb=" N VAL G 177 " --> pdb=" O SER G 185 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 158 through 162 removed outlier: 3.662A pdb=" N THR G 159 " --> pdb=" O ASN G 207 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.505A pdb=" N SER H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS H 23 " --> pdb=" O PHE H 71 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.683A pdb=" N ARG H 45 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.875A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 145 through 148 removed outlier: 3.530A pdb=" N LYS H 145 " --> pdb=" O THR H 197 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.804A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL J 20 " --> pdb=" O MET J 81 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA J 79 " --> pdb=" O CYS J 22 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.640A pdb=" N GLU J 10 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR J 118 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS J 12 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA J 92 " --> pdb=" O VAL J 117 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL J 93 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.640A pdb=" N GLU J 10 " --> pdb=" O THR J 116 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR J 118 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS J 12 " --> pdb=" O THR J 118 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA J 92 " --> pdb=" O VAL J 117 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL J 110 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 128 through 130 removed outlier: 6.240A pdb=" N TYR J 184 " --> pdb=" O ASP J 152 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AI4, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AI5, first strand: chain 'K' and resid 18 through 22 removed outlier: 3.551A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 45 through 48 removed outlier: 5.521A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR K 102 " --> pdb=" O TYR K 86 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'K' and resid 114 through 118 removed outlier: 3.509A pdb=" N SER K 114 " --> pdb=" O ASN K 137 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL K 133 " --> pdb=" O PHE K 118 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER K 177 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 153 through 155 removed outlier: 3.813A pdb=" N TRP K 148 " --> pdb=" O GLN K 155 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS K 145 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS K 207 " --> pdb=" O CYS K 194 " (cutoff:3.500A) 1204 hydrogen bonds defined for protein. 3228 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: 17.83 Time building geometry restraints manager: 15.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10926 1.34 - 1.47: 8730 1.47 - 1.59: 15112 1.59 - 1.71: 0 1.71 - 1.83: 183 Bond restraints: 34951 Sorted by residual: bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" C ALA G 102 " pdb=" N PHE G 103 " ideal model delta sigma weight residual 1.332 1.293 0.039 1.40e-02 5.10e+03 7.79e+00 bond pdb=" C1 NAG A1404 " pdb=" O5 NAG A1404 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb=" C1 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.33e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.98e+00 ... (remaining 34946 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.13: 650 105.13 - 112.35: 18145 112.35 - 119.57: 10797 119.57 - 126.79: 17571 126.79 - 134.01: 367 Bond angle restraints: 47530 Sorted by residual: angle pdb=" C ASN A 125 " pdb=" CA ASN A 125 " pdb=" CB ASN A 125 " ideal model delta sigma weight residual 116.54 110.56 5.98 1.15e+00 7.56e-01 2.70e+01 angle pdb=" CA PHE J 130 " pdb=" C PHE J 130 " pdb=" N PRO J 131 " ideal model delta sigma weight residual 119.06 114.33 4.73 1.05e+00 9.07e-01 2.03e+01 angle pdb=" CA ASN A 125 " pdb=" C ASN A 125 " pdb=" N VAL A 126 " ideal model delta sigma weight residual 119.52 116.30 3.22 7.90e-01 1.60e+00 1.66e+01 angle pdb=" N ASP C 389 " pdb=" CA ASP C 389 " pdb=" C ASP C 389 " ideal model delta sigma weight residual 114.75 109.86 4.89 1.26e+00 6.30e-01 1.51e+01 angle pdb=" N TYR A 380 " pdb=" CA TYR A 380 " pdb=" C TYR A 380 " ideal model delta sigma weight residual 114.75 109.86 4.89 1.26e+00 6.30e-01 1.51e+01 ... (remaining 47525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 19490 17.97 - 35.93: 1645 35.93 - 53.90: 309 53.90 - 71.87: 99 71.87 - 89.83: 40 Dihedral angle restraints: 21583 sinusoidal: 9051 harmonic: 12532 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -175.21 89.21 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 4.38 88.62 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -5.11 -80.89 1 1.00e+01 1.00e-02 8.08e+01 ... (remaining 21580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 5399 0.112 - 0.223: 153 0.223 - 0.334: 6 0.334 - 0.446: 2 0.446 - 0.557: 1 Chirality restraints: 5561 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" C1 NAG B1401 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1401 " pdb=" O5 NAG B1401 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" C1 NAG B1402 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1402 " pdb=" O5 NAG B1402 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 5558 not shown) Planarity restraints: 6109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 138 " 0.065 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO B 139 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO B 139 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO B 139 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " -0.004 2.00e-02 2.50e+03 3.01e-02 1.13e+01 pdb=" CG ASN A 616 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " -0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " 0.029 2.00e-02 2.50e+03 pdb=" C1 NAG A1404 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 64 " -0.022 2.00e-02 2.50e+03 1.85e-02 8.54e+00 pdb=" CG TRP B 64 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 64 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 64 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 64 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 64 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 64 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 64 " -0.000 2.00e-02 2.50e+03 ... (remaining 6106 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 13 2.22 - 2.89: 14198 2.89 - 3.56: 46062 3.56 - 4.23: 76011 4.23 - 4.90: 130954 Nonbonded interactions: 267238 Sorted by model distance: nonbonded pdb=" CE LYS A 129 " pdb=" CB CYS A 131 " model vdw 1.554 3.840 nonbonded pdb=" CE2 TYR A 660 " pdb=" OE1 GLN A 675 " model vdw 1.889 3.340 nonbonded pdb=" OH TYR B 38 " pdb=" OG1 THR B 284 " model vdw 2.046 2.440 nonbonded pdb=" OD1 ASP C 568 " pdb=" OG1 THR C 572 " model vdw 2.103 2.440 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.124 2.440 ... (remaining 267233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 620 or resid 641 through 939 or resid 944 throu \ gh 1146 or resid 1401 through 1405)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1405)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1146 or resid 1401 thr \ ough 1405)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' 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' } 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: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.530 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 95.880 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.580 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:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3516 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 34951 Z= 0.370 Angle : 0.713 10.150 47530 Z= 0.376 Chirality : 0.049 0.557 5561 Planarity : 0.005 0.100 6072 Dihedral : 14.145 89.832 13376 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.07 % Favored : 90.83 % Rotamer: Outliers : 0.93 % Allowed : 0.93 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.13), residues: 4265 helix: 1.23 (0.21), residues: 662 sheet: -1.16 (0.15), residues: 1268 loop : -2.10 (0.12), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 64 HIS 0.007 0.001 HIS C1048 PHE 0.037 0.002 PHE C 906 TYR 0.034 0.002 TYR A 508 ARG 0.009 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 910 time to evaluate : 3.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 7 residues processed: 935 average time/residue: 1.1020 time to fit residues: 1296.4564 Evaluate side-chains 546 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 539 time to evaluate : 3.572 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 4 average time/residue: 0.6663 time to fit residues: 8.8158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 3.9990 chunk 325 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 219 optimal weight: 4.9990 chunk 173 optimal weight: 0.5980 chunk 336 optimal weight: 0.7980 chunk 130 optimal weight: 0.0040 chunk 204 optimal weight: 6.9990 chunk 250 optimal weight: 0.1980 chunk 389 optimal weight: 4.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 542 ASN A 690 GLN A 787 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1125 ASN C 66 HIS C 188 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 901 GLN C 907 ASN C 955 ASN D 39 GLN E 158 ASN ** E 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4227 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34951 Z= 0.237 Angle : 0.779 15.276 47530 Z= 0.386 Chirality : 0.051 0.740 5561 Planarity : 0.005 0.073 6072 Dihedral : 7.489 59.943 5759 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.80 % Favored : 93.15 % Rotamer: Outliers : 3.90 % Allowed : 14.91 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.13), residues: 4265 helix: 1.21 (0.20), residues: 676 sheet: -0.98 (0.15), residues: 1256 loop : -2.05 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 148 HIS 0.006 0.001 HIS C1058 PHE 0.027 0.002 PHE K 209 TYR 0.022 0.002 TYR B1067 ARG 0.014 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 657 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 146 outliers final: 52 residues processed: 732 average time/residue: 1.0596 time to fit residues: 991.2781 Evaluate side-chains 568 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 516 time to evaluate : 3.703 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 30 residues processed: 23 average time/residue: 0.4007 time to fit residues: 20.9690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 324 optimal weight: 6.9990 chunk 265 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 390 optimal weight: 0.2980 chunk 421 optimal weight: 9.9990 chunk 347 optimal weight: 2.9990 chunk 387 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 313 optimal weight: 0.0000 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN A 536 ASN A 542 ASN A 751 ASN A 787 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN A1108 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B 450 ASN ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 613 GLN C 710 ASN C 764 ASN C1023 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN H 38 GLN ** H 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN ** K 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.7249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 34951 Z= 0.415 Angle : 1.035 24.669 47530 Z= 0.512 Chirality : 0.058 0.593 5561 Planarity : 0.008 0.170 6072 Dihedral : 7.429 59.055 5759 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.23 % Favored : 91.70 % Rotamer: Outliers : 7.44 % Allowed : 18.33 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.12), residues: 4265 helix: -0.01 (0.19), residues: 672 sheet: -0.89 (0.15), residues: 1186 loop : -2.11 (0.12), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP J 111 HIS 0.011 0.002 HIS A1048 PHE 0.049 0.003 PHE B 377 TYR 0.038 0.003 TYR A1067 ARG 0.017 0.001 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 818 time to evaluate : 3.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 279 outliers final: 87 residues processed: 996 average time/residue: 1.0149 time to fit residues: 1309.3134 Evaluate side-chains 688 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 601 time to evaluate : 3.627 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 62 residues processed: 32 average time/residue: 0.4934 time to fit residues: 30.1096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 262 optimal weight: 0.0970 chunk 391 optimal weight: 0.7980 chunk 414 optimal weight: 7.9990 chunk 204 optimal weight: 0.0030 chunk 371 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 644 GLN A 784 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS B 207 HIS B 245 HIS B 540 ASN B 804 GLN B 872 GLN B 935 GLN B1142 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 804 GLN C1058 HIS C1113 GLN E 160 GLN G 31 ASN J 163 ASN ** J 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.8231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 34951 Z= 0.236 Angle : 0.782 15.738 47530 Z= 0.381 Chirality : 0.048 0.388 5561 Planarity : 0.005 0.071 6072 Dihedral : 6.686 57.501 5759 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.28 % Favored : 93.69 % Rotamer: Outliers : 5.36 % Allowed : 24.97 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.12), residues: 4265 helix: 0.69 (0.20), residues: 662 sheet: -0.91 (0.14), residues: 1244 loop : -1.98 (0.12), residues: 2359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 886 HIS 0.012 0.001 HIS B 207 PHE 0.036 0.002 PHE D 29 TYR 0.028 0.002 TYR C 265 ARG 0.011 0.001 ARG C1014 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 647 time to evaluate : 3.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 201 outliers final: 108 residues processed: 779 average time/residue: 0.9467 time to fit residues: 969.9753 Evaluate side-chains 650 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 542 time to evaluate : 3.834 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 79 residues processed: 35 average time/residue: 0.4789 time to fit residues: 31.9331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 0.6980 chunk 235 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 308 optimal weight: 2.9990 chunk 171 optimal weight: 0.3980 chunk 353 optimal weight: 1.9990 chunk 286 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 372 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 450 ASN B 540 ASN B 762 GLN B1010 GLN B1119 ASN C 422 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN E 166 GLN G 31 ASN ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.9736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 34951 Z= 0.249 Angle : 0.787 21.138 47530 Z= 0.382 Chirality : 0.050 0.396 5561 Planarity : 0.006 0.113 6072 Dihedral : 6.371 56.724 5759 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.15 % Favored : 92.80 % Rotamer: Outliers : 6.48 % Allowed : 25.27 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.12), residues: 4265 helix: 0.64 (0.20), residues: 678 sheet: -0.78 (0.14), residues: 1272 loop : -2.00 (0.12), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 36 HIS 0.015 0.002 HIS E 189 PHE 0.028 0.002 PHE B 92 TYR 0.030 0.002 TYR G 184 ARG 0.019 0.001 ARG A 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 657 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 243 outliers final: 123 residues processed: 830 average time/residue: 1.0294 time to fit residues: 1099.6730 Evaluate side-chains 665 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 542 time to evaluate : 3.656 Switching outliers to nearest non-outliers outliers start: 123 outliers final: 101 residues processed: 30 average time/residue: 0.4945 time to fit residues: 28.4140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 7.9990 chunk 373 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 243 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 415 optimal weight: 3.9990 chunk 344 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 81 ASN B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1036 GLN B1048 HIS ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1113 GLN D 6 GLN D 59 ASN G 31 ASN ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN J 172 HIS ** J 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 1.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.126 34951 Z= 0.583 Angle : 1.015 14.800 47530 Z= 0.513 Chirality : 0.058 0.397 5561 Planarity : 0.007 0.077 6072 Dihedral : 7.482 59.698 5759 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.79 % Favored : 91.16 % Rotamer: Outliers : 7.31 % Allowed : 26.97 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.12), residues: 4265 helix: -0.22 (0.19), residues: 688 sheet: -1.15 (0.14), residues: 1274 loop : -2.23 (0.12), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP J 162 HIS 0.016 0.002 HIS A1048 PHE 0.040 0.003 PHE G 103 TYR 0.039 0.003 TYR E 49 ARG 0.018 0.002 ARG A1091 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 616 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 274 outliers final: 110 residues processed: 827 average time/residue: 1.1770 time to fit residues: 1218.8629 Evaluate side-chains 559 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 449 time to evaluate : 3.802 Switching outliers to nearest non-outliers outliers start: 110 outliers final: 95 residues processed: 20 average time/residue: 0.3841 time to fit residues: 18.7288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 chunk 303 optimal weight: 0.8980 chunk 234 optimal weight: 0.9990 chunk 349 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 413 optimal weight: 0.0030 chunk 258 optimal weight: 0.5980 chunk 252 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 992 GLN B 49 HIS B 245 HIS B 540 ASN B 949 GLN B 954 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1023 ASN C1036 GLN C1113 GLN D 6 GLN D 59 ASN E 147 GLN E 158 ASN ** E 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN G 31 ASN ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 ASN J 163 ASN ** J 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 1.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34951 Z= 0.250 Angle : 0.842 12.384 47530 Z= 0.410 Chirality : 0.051 0.740 5561 Planarity : 0.005 0.074 6072 Dihedral : 7.088 59.334 5759 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.73 % Favored : 93.25 % Rotamer: Outliers : 5.18 % Allowed : 30.87 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.12), residues: 4265 helix: 0.36 (0.20), residues: 686 sheet: -0.91 (0.14), residues: 1283 loop : -2.10 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 162 HIS 0.010 0.001 HIS D 172 PHE 0.027 0.002 PHE B 562 TYR 0.039 0.002 TYR H 140 ARG 0.013 0.001 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 513 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 194 outliers final: 114 residues processed: 663 average time/residue: 1.0935 time to fit residues: 921.1648 Evaluate side-chains 543 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 429 time to evaluate : 3.818 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 114 outliers final: 98 residues processed: 22 average time/residue: 0.4855 time to fit residues: 22.1714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 281 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 chunk 325 optimal weight: 2.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 613 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 207 HIS B 245 HIS B 540 ASN B 954 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1142 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN D 6 GLN D 59 ASN D 172 HIS ** E 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN H 53 ASN ** J 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 1.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 34951 Z= 0.241 Angle : 0.818 15.094 47530 Z= 0.399 Chirality : 0.051 0.519 5561 Planarity : 0.005 0.074 6072 Dihedral : 6.975 59.561 5759 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.29 % Favored : 92.68 % Rotamer: Outliers : 4.46 % Allowed : 31.78 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.12), residues: 4265 helix: 0.62 (0.20), residues: 673 sheet: -0.86 (0.14), residues: 1317 loop : -2.02 (0.12), residues: 2275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 47 HIS 0.011 0.001 HIS B 207 PHE 0.040 0.002 PHE A 562 TYR 0.033 0.002 TYR H 140 ARG 0.013 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 463 time to evaluate : 3.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 167 outliers final: 113 residues processed: 595 average time/residue: 1.0514 time to fit residues: 805.9978 Evaluate side-chains 536 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 423 time to evaluate : 4.006 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 98 residues processed: 19 average time/residue: 0.5595 time to fit residues: 21.3379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 3.9990 chunk 396 optimal weight: 3.9990 chunk 361 optimal weight: 0.6980 chunk 385 optimal weight: 0.8980 chunk 231 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 348 optimal weight: 2.9990 chunk 364 optimal weight: 3.9990 chunk 383 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 957 GLN A 992 GLN A1005 GLN B 207 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1113 GLN D 6 GLN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN E 147 GLN E 158 ASN E 199 GLN G 31 ASN H 53 ASN ** J 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 1.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 34951 Z= 0.429 Angle : 0.951 23.873 47530 Z= 0.467 Chirality : 0.059 1.506 5561 Planarity : 0.006 0.083 6072 Dihedral : 7.322 59.348 5759 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.05 % Favored : 90.90 % Rotamer: Outliers : 4.06 % Allowed : 32.18 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.12), residues: 4265 helix: 0.37 (0.20), residues: 675 sheet: -0.89 (0.14), residues: 1240 loop : -2.16 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP G 162 HIS 0.018 0.002 HIS H 189 PHE 0.030 0.002 PHE B 562 TYR 0.032 0.003 TYR B 508 ARG 0.015 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 452 time to evaluate : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 152 outliers final: 105 residues processed: 576 average time/residue: 1.0554 time to fit residues: 784.2772 Evaluate side-chains 499 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 394 time to evaluate : 3.624 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 97 residues processed: 13 average time/residue: 0.5143 time to fit residues: 15.3127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 2.9990 chunk 407 optimal weight: 20.0000 chunk 248 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 283 optimal weight: 0.2980 chunk 427 optimal weight: 0.8980 chunk 393 optimal weight: 0.7980 chunk 340 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 GLN B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B1002 GLN B1005 GLN B1142 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN C1113 GLN D 6 GLN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 1.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34951 Z= 0.252 Angle : 0.844 16.534 47530 Z= 0.412 Chirality : 0.052 0.729 5561 Planarity : 0.005 0.075 6072 Dihedral : 6.814 57.623 5759 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.39 % Favored : 92.57 % Rotamer: Outliers : 3.15 % Allowed : 33.22 % Favored : 63.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.12), residues: 4265 helix: 0.69 (0.20), residues: 672 sheet: -0.84 (0.15), residues: 1195 loop : -2.00 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 36 HIS 0.012 0.001 HIS B 207 PHE 0.050 0.002 PHE A 562 TYR 0.029 0.002 TYR A 473 ARG 0.017 0.001 ARG K 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 444 time to evaluate : 4.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 95 residues processed: 544 average time/residue: 1.1127 time to fit residues: 773.9719 Evaluate side-chains 491 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 396 time to evaluate : 3.807 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 89 residues processed: 9 average time/residue: 0.4210 time to fit residues: 11.8179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 3.9990 chunk 362 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 313 optimal weight: 0.0470 chunk 50 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 340 optimal weight: 9.9990 chunk 142 optimal weight: 0.8980 chunk 350 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN A 957 GLN A 992 GLN B 207 HIS B 245 HIS B 360 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 ASN ** J 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.112430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.086845 restraints weight = 88762.677| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.38 r_work: 0.3387 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 1.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 34951 Z= 0.235 Angle : 0.823 14.250 47530 Z= 0.401 Chirality : 0.050 0.599 5561 Planarity : 0.005 0.075 6072 Dihedral : 6.498 57.116 5759 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.69 % Favored : 92.26 % Rotamer: Outliers : 2.93 % Allowed : 33.48 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.13), residues: 4265 helix: 0.89 (0.20), residues: 671 sheet: -0.81 (0.14), residues: 1294 loop : -1.93 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 162 HIS 0.011 0.001 HIS B 207 PHE 0.034 0.001 PHE K 118 TYR 0.030 0.001 TYR A 473 ARG 0.013 0.001 ARG G 87 =============================================================================== Job complete usr+sys time: 15406.60 seconds wall clock time: 273 minutes 39.94 seconds (16419.94 seconds total)