Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 00:35:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8saw_40282/05_2023/8saw_40282_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8saw_40282/05_2023/8saw_40282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8saw_40282/05_2023/8saw_40282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8saw_40282/05_2023/8saw_40282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8saw_40282/05_2023/8saw_40282_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8saw_40282/05_2023/8saw_40282_trim.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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: 5 Type Number sf(0) Gaussians S 135 5.16 5 C 12327 2.51 5 N 3324 2.21 5 O 3957 1.98 5 H 18589 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 38332 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 7144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7144 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "B" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1925 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain: "C" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1941 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1568 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 7144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7144 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "F" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1925 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain: "H" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1941 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1565 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 7145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7145 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "L" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1925 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain: "M" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1941 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "N" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1568 Classifications: {'peptide': 110} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 17.44, per 1000 atoms: 0.45 Number of scatterers: 38332 At special positions: 0 Unit cell: (158.834, 157.768, 139.646, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 O 3957 8.00 N 3324 7.00 C 12327 6.00 H 18589 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 121 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 43 " distance=2.03 Simple disulfide: pdb=" SG CYS K 88 " - pdb=" SG CYS K 166 " distance=2.03 Simple disulfide: pdb=" SG CYS K 95 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 100 " - pdb=" SG CYS K 116 " distance=2.03 Simple disulfide: pdb=" SG CYS K 162 " - pdb=" SG CYS K 390 " distance=2.03 Simple disulfide: pdb=" SG CYS K 179 " - pdb=" SG CYS K 208 " distance=2.03 Simple disulfide: pdb=" SG CYS K 189 " - pdb=" SG CYS K 200 " distance=2.03 Simple disulfide: pdb=" SG CYS K 257 " - pdb=" SG CYS K 291 " distance=2.03 Simple disulfide: pdb=" SG CYS K 337 " - pdb=" SG CYS K 402 " distance=2.03 Simple disulfide: pdb=" SG CYS K 344 " - pdb=" SG CYS K 375 " distance=2.03 Simple disulfide: pdb=" SG CYS K 458 " - pdb=" SG CYS L 73 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 72 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " 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 ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 8 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 9 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 9 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 9 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG G 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN E 301 " " NAG R 1 " - " ASN E 332 " " NAG S 1 " - " ASN E 156 " " NAG T 1 " - " ASN E 442 " " NAG U 1 " - " ASN K 262 " " NAG V 1 " - " ASN K 292 " " NAG W 1 " - " ASN K 115 " " NAG X 1 " - " ASN K 399 " Time building additional restraints: 33.27 Conformation dependent library (CDL) restraints added in 3.3 seconds 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 48 sheets defined 17.1% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.358A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.514A pdb=" N THR A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 4.048A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.533A pdb=" N VAL B 539 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG B 542 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 595 removed outlier: 4.280A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG B 579 " --> pdb=" O GLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.701A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.103A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.625A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.370A pdb=" N ASP E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.513A pdb=" N THR E 373 " --> pdb=" O MET E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 481 removed outlier: 4.047A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.529A pdb=" N VAL F 539 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG F 542 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 595 removed outlier: 4.285A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 664 removed outlier: 3.703A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.108A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 116 removed outlier: 3.625A pdb=" N GLU I 116 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 85 removed outlier: 4.372A pdb=" N ASP K 71 " --> pdb=" O ASN K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 310 Processing helix chain 'K' and resid 327 through 332 removed outlier: 3.515A pdb=" N THR K 332 " --> pdb=" O MET K 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 438 removed outlier: 4.046A pdb=" N TRP K 436 " --> pdb=" O MET K 432 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER K 438 " --> pdb=" O ASP K 434 " (cutoff:3.500A) Processing helix chain 'L' and resid 18 through 23 Processing helix chain 'L' and resid 25 through 31 removed outlier: 3.533A pdb=" N VAL L 28 " --> pdb=" O THR L 25 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG L 31 " --> pdb=" O VAL L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 63 removed outlier: 4.294A pdb=" N LEU L 44 " --> pdb=" O GLY L 40 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG L 47 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 90 Processing helix chain 'L' and resid 95 through 104 Processing helix chain 'L' and resid 106 through 132 removed outlier: 3.703A pdb=" N ILE L 110 " --> pdb=" O TYR L 106 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP L 132 " --> pdb=" O LEU L 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 30 No H-bonds generated for 'chain 'M' and resid 28 through 30' Processing helix chain 'M' and resid 87 through 91 removed outlier: 4.101A pdb=" N THR M 91 " --> pdb=" O SER M 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.624A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.424A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.834A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 67 removed outlier: 7.129A pdb=" N HIS A 66 " --> pdb=" O THR A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.823A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.634A pdb=" N ASN A 156 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.941A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.576A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.056A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.392A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.392A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.056A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 302 through 304 removed outlier: 6.721A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB4, first strand: chain 'C' and resid 9 through 11 removed outlier: 5.201A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TRP C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.729A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLN D 39 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LEU D 48 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.729A pdb=" N VAL D 10 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N THR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.436A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL E 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.830A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC2, first strand: chain 'E' and resid 66 through 67 removed outlier: 7.126A pdb=" N HIS E 66 " --> pdb=" O THR E 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.824A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.634A pdb=" N ASN E 156 " --> pdb=" O SER E 132 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.953A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.575A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.061A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.398A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.398A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.061A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 302 through 304 removed outlier: 6.738A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 307 through 308 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AD2, first strand: chain 'H' and resid 9 through 11 removed outlier: 5.136A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 41 through 43 removed outlier: 6.725A pdb=" N VAL I 41 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLN I 70 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N LEU I 79 " --> pdb=" O GLN I 70 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 41 through 43 removed outlier: 6.725A pdb=" N VAL I 41 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N THR I 129 " --> pdb=" O ALA I 125 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 49 through 54 Processing sheet with id=AD6, first strand: chain 'K' and resid 452 through 456 removed outlier: 5.423A pdb=" N VAL K 5 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR L 74 " --> pdb=" O VAL K 5 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL K 7 " --> pdb=" O CYS L 72 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 14 through 16 removed outlier: 3.831A pdb=" N ILE K 186 " --> pdb=" O VAL K 206 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL K 203 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 44 through 45 Processing sheet with id=AD9, first strand: chain 'K' and resid 35 through 36 removed outlier: 7.124A pdb=" N HIS K 35 " --> pdb=" O THR K 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'K' and resid 60 through 61 removed outlier: 3.822A pdb=" N GLU K 60 " --> pdb=" O CYS K 200 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 128 through 136 removed outlier: 3.637A pdb=" N ASN K 115 " --> pdb=" O SER K 101 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 163 through 164 removed outlier: 6.937A pdb=" N THR K 163 " --> pdb=" O TYR K 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 220 through 222 removed outlier: 6.573A pdb=" N LEU K 221 " --> pdb=" O THR K 407 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE K 400 " --> pdb=" O ARG K 259 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY K 408 " --> pdb=" O THR K 251 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N THR K 251 " --> pdb=" O GLY K 408 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N LEU K 410 " --> pdb=" O LEU K 249 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N LEU K 249 " --> pdb=" O LEU K 410 " (cutoff:3.500A) removed outlier: 11.059A pdb=" N THR K 412 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N VAL K 247 " --> pdb=" O THR K 412 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLU K 254 " --> pdb=" O SER K 294 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER K 294 " --> pdb=" O GLU K 254 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE K 341 " --> pdb=" O LYS K 378 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 232 through 234 removed outlier: 11.395A pdb=" N VAL K 247 " --> pdb=" O THR K 412 " (cutoff:3.500A) removed outlier: 11.059A pdb=" N THR K 412 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N LEU K 249 " --> pdb=" O LEU K 410 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N LEU K 410 " --> pdb=" O LEU K 249 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N THR K 251 " --> pdb=" O GLY K 408 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY K 408 " --> pdb=" O THR K 251 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE K 400 " --> pdb=" O ARG K 259 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS K 319 " --> pdb=" O PHE K 425 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 263 through 265 removed outlier: 6.716A pdb=" N THR K 264 " --> pdb=" O GLY K 280 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 268 through 269 Processing sheet with id=AE8, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AE9, first strand: chain 'M' and resid 9 through 11 removed outlier: 5.168A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N MET M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TRP M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.725A pdb=" N VAL N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLN N 39 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU N 48 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.725A pdb=" N VAL N 10 " --> pdb=" O THR N 108 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N THR N 98 " --> pdb=" O ALA N 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 18 through 23 672 hydrogen bonds defined for protein. 1746 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: 15.52 Time building geometry restraints manager: 34.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 18586 1.04 - 1.23: 368 1.23 - 1.43: 8122 1.43 - 1.62: 11487 1.62 - 1.82: 183 Bond restraints: 38746 Sorted by residual: bond pdb=" C THR K 92 " pdb=" N PRO K 93 " ideal model delta sigma weight residual 1.334 1.349 -0.015 8.40e-03 1.42e+04 3.34e+00 bond pdb=" C THR A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.334 1.348 -0.015 8.40e-03 1.42e+04 3.06e+00 bond pdb=" C1 MAN R 4 " pdb=" C2 MAN R 4 " ideal model delta sigma weight residual 1.526 1.561 -0.035 2.00e-02 2.50e+03 3.04e+00 bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.97e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.97e+00 ... (remaining 38741 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.14: 1252 107.14 - 113.87: 45634 113.87 - 120.60: 11621 120.60 - 127.32: 10752 127.32 - 134.05: 261 Bond angle restraints: 69520 Sorted by residual: angle pdb=" C LEU K 91 " pdb=" N THR K 92 " pdb=" CA THR K 92 " ideal model delta sigma weight residual 121.80 129.83 -8.03 2.44e+00 1.68e-01 1.08e+01 angle pdb=" C LEU E 122 " pdb=" N THR E 123 " pdb=" CA THR E 123 " ideal model delta sigma weight residual 121.80 129.78 -7.98 2.44e+00 1.68e-01 1.07e+01 angle pdb=" C LEU A 122 " pdb=" N THR A 123 " pdb=" CA THR A 123 " ideal model delta sigma weight residual 121.80 129.75 -7.95 2.44e+00 1.68e-01 1.06e+01 angle pdb=" C GLU I 83 " pdb=" N VAL I 84 " pdb=" CA VAL I 84 " ideal model delta sigma weight residual 121.97 126.84 -4.87 1.80e+00 3.09e-01 7.31e+00 angle pdb=" CA VAL N 53 " pdb=" CB VAL N 53 " pdb=" CG2 VAL N 53 " ideal model delta sigma weight residual 110.40 114.98 -4.58 1.70e+00 3.46e-01 7.27e+00 ... (remaining 69515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.14: 13736 11.14 - 22.27: 1242 22.27 - 33.41: 352 33.41 - 44.54: 69 44.54 - 55.68: 33 Dihedral angle restraints: 15432 sinusoidal: 7134 harmonic: 8298 Sorted by residual: dihedral pdb=" CA THR E 123 " pdb=" C THR E 123 " pdb=" N PRO E 124 " pdb=" CA PRO E 124 " ideal model delta harmonic sigma weight residual -180.00 -157.90 -22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA THR A 123 " pdb=" C THR A 123 " pdb=" N PRO A 124 " pdb=" CA PRO A 124 " ideal model delta harmonic sigma weight residual -180.00 -158.31 -21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA THR K 92 " pdb=" C THR K 92 " pdb=" N PRO K 93 " pdb=" CA PRO K 93 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 15429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2696 0.055 - 0.111: 343 0.111 - 0.166: 159 0.166 - 0.221: 0 0.221 - 0.277: 6 Chirality restraints: 3204 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3201 not shown) Planarity restraints: 5799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 123 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO E 124 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 124 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 124 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR K 92 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO K 93 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO K 93 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO K 93 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 123 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO A 124 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.030 5.00e-02 4.00e+02 ... (remaining 5796 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 4298 2.26 - 2.84: 82821 2.84 - 3.43: 88618 3.43 - 4.01: 127124 4.01 - 4.60: 191942 Nonbonded interactions: 494803 Sorted by model distance: nonbonded pdb=" O GLU D 52 " pdb=" H SER D 54 " model vdw 1.675 1.850 nonbonded pdb=" O GLU N 52 " pdb=" H SER N 54 " model vdw 1.676 1.850 nonbonded pdb=" O GLU I 83 " pdb=" H SER I 85 " model vdw 1.676 1.850 nonbonded pdb=" O VAL A 496 " pdb=" HE1 TRP B 631 " model vdw 1.679 1.850 nonbonded pdb=" O VAL E 496 " pdb=" HE1 TRP F 631 " model vdw 1.681 1.850 ... (remaining 494798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = (chain 'K' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 2 through 462)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = (chain 'D' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 2 through 110)) selection = chain 'I' selection = (chain 'N' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 2 through 110)) } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'R' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' } 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: 1.460 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: 0.310 Extract box with map and model: 5.680 Check model and map are aligned: 0.600 Set scattering table: 0.340 Process input model: 119.180 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.330 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 20157 Z= 0.253 Angle : 0.649 8.028 27396 Z= 0.311 Chirality : 0.047 0.277 3204 Planarity : 0.003 0.054 3435 Dihedral : 9.000 55.677 7071 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.76 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2439 helix: 2.04 (0.30), residues: 330 sheet: 0.31 (0.20), residues: 658 loop : -1.03 (0.15), residues: 1451 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 476 time to evaluate : 3.113 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 500 average time/residue: 0.6810 time to fit residues: 515.7418 Evaluate side-chains 275 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 263 time to evaluate : 3.473 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4025 time to fit residues: 13.4254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 190 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 220 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 630 GLN B 653 GLN F 630 GLN K 156 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 20157 Z= 0.386 Angle : 0.611 5.669 27396 Z= 0.319 Chirality : 0.045 0.166 3204 Planarity : 0.005 0.057 3435 Dihedral : 4.058 23.240 2655 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.81 % Favored : 95.94 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.17), residues: 2439 helix: 1.52 (0.30), residues: 345 sheet: 0.07 (0.20), residues: 670 loop : -1.07 (0.16), residues: 1424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 258 time to evaluate : 2.986 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: 38 outliers final: 34 residues processed: 288 average time/residue: 0.7384 time to fit residues: 326.9255 Evaluate side-chains 261 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 227 time to evaluate : 3.152 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.4556 time to fit residues: 31.5915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 221 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 219 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN D 33 ASN F 652 GLN K 156 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.101 20157 Z= 0.209 Angle : 0.517 14.680 27396 Z= 0.268 Chirality : 0.042 0.144 3204 Planarity : 0.004 0.057 3435 Dihedral : 3.946 22.538 2655 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.28 % Favored : 96.47 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.17), residues: 2439 helix: 1.74 (0.30), residues: 347 sheet: -0.07 (0.20), residues: 711 loop : -1.07 (0.16), residues: 1381 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 235 time to evaluate : 3.420 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: 10 outliers final: 6 residues processed: 243 average time/residue: 0.7275 time to fit residues: 268.5611 Evaluate side-chains 219 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 213 time to evaluate : 3.510 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4052 time to fit residues: 8.6989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 221 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.097 20157 Z= 0.360 Angle : 0.610 13.514 27396 Z= 0.317 Chirality : 0.045 0.172 3204 Planarity : 0.005 0.059 3435 Dihedral : 4.355 24.757 2655 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.13 % Favored : 94.63 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.17), residues: 2439 helix: 1.16 (0.29), residues: 346 sheet: -0.30 (0.19), residues: 724 loop : -1.31 (0.16), residues: 1369 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 243 time to evaluate : 3.488 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: 23 outliers final: 12 residues processed: 258 average time/residue: 0.6918 time to fit residues: 273.3756 Evaluate side-chains 240 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 228 time to evaluate : 3.476 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4117 time to fit residues: 13.6086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 3 optimal weight: 0.0670 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 20157 Z= 0.178 Angle : 0.507 11.694 27396 Z= 0.262 Chirality : 0.042 0.139 3204 Planarity : 0.004 0.057 3435 Dihedral : 4.102 22.945 2655 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.28 % Favored : 96.47 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2439 helix: 1.54 (0.30), residues: 349 sheet: -0.17 (0.20), residues: 722 loop : -1.26 (0.16), residues: 1368 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 242 time to evaluate : 3.101 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 outliers start: 9 outliers final: 5 residues processed: 247 average time/residue: 0.7330 time to fit residues: 276.8391 Evaluate side-chains 233 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 228 time to evaluate : 3.171 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4071 time to fit residues: 7.8634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.7980 chunk 211 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.101 20157 Z= 0.460 Angle : 0.659 12.092 27396 Z= 0.341 Chirality : 0.047 0.185 3204 Planarity : 0.005 0.060 3435 Dihedral : 4.660 26.515 2655 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.81 % Favored : 92.95 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.17), residues: 2439 helix: 0.74 (0.28), residues: 346 sheet: -0.44 (0.19), residues: 746 loop : -1.54 (0.16), residues: 1347 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 237 time to evaluate : 3.250 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: 27 outliers final: 19 residues processed: 255 average time/residue: 0.7731 time to fit residues: 297.0473 Evaluate side-chains 249 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 230 time to evaluate : 3.238 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4316 time to fit residues: 19.4621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 234 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 144 optimal weight: 0.3980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 20157 Z= 0.201 Angle : 0.531 12.380 27396 Z= 0.274 Chirality : 0.042 0.145 3204 Planarity : 0.004 0.059 3435 Dihedral : 4.353 24.360 2655 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.57 % Favored : 96.19 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2439 helix: 1.21 (0.29), residues: 346 sheet: -0.33 (0.19), residues: 753 loop : -1.37 (0.16), residues: 1340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 240 time to evaluate : 3.265 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: 6 outliers final: 3 residues processed: 245 average time/residue: 0.7326 time to fit residues: 272.5561 Evaluate side-chains 223 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 220 time to evaluate : 3.194 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4419 time to fit residues: 6.3913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 20157 Z= 0.248 Angle : 0.541 11.480 27396 Z= 0.279 Chirality : 0.042 0.145 3204 Planarity : 0.004 0.058 3435 Dihedral : 4.382 24.454 2655 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.04 % Favored : 94.71 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2439 helix: 1.26 (0.29), residues: 346 sheet: -0.34 (0.19), residues: 754 loop : -1.39 (0.16), residues: 1339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 224 time to evaluate : 3.263 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 outliers start: 7 outliers final: 5 residues processed: 230 average time/residue: 0.7575 time to fit residues: 263.1030 Evaluate side-chains 228 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 223 time to evaluate : 3.475 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4748 time to fit residues: 8.4893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 7.9990 chunk 204 optimal weight: 0.0970 chunk 218 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 171 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 20157 Z= 0.186 Angle : 0.513 10.578 27396 Z= 0.265 Chirality : 0.042 0.163 3204 Planarity : 0.004 0.056 3435 Dihedral : 4.260 23.654 2655 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.18 % Favored : 95.57 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2439 helix: 1.47 (0.29), residues: 346 sheet: -0.29 (0.19), residues: 754 loop : -1.32 (0.16), residues: 1339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 3.108 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 outliers start: 2 outliers final: 2 residues processed: 230 average time/residue: 0.7394 time to fit residues: 256.1252 Evaluate side-chains 226 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 3.158 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4100 time to fit residues: 5.4540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 3.9990 chunk 140 optimal weight: 0.0870 chunk 109 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 20157 Z= 0.235 Angle : 0.527 10.318 27396 Z= 0.271 Chirality : 0.042 0.145 3204 Planarity : 0.004 0.055 3435 Dihedral : 4.276 24.161 2655 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.29 % Favored : 94.46 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2439 helix: 1.42 (0.29), residues: 346 sheet: -0.30 (0.19), residues: 752 loop : -1.36 (0.16), residues: 1341 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 3.892 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: 1 outliers final: 0 residues processed: 231 average time/residue: 0.7659 time to fit residues: 267.9232 Evaluate side-chains 224 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 3.381 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.4157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 6.9990 chunk 59 optimal weight: 0.1980 chunk 177 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.173447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.143107 restraints weight = 68091.252| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.30 r_work: 0.3341 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 20157 Z= 0.182 Angle : 0.500 9.862 27396 Z= 0.258 Chirality : 0.042 0.141 3204 Planarity : 0.004 0.052 3435 Dihedral : 4.179 23.282 2655 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.77 % Favored : 95.98 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.17), residues: 2439 helix: 1.58 (0.30), residues: 346 sheet: -0.23 (0.19), residues: 752 loop : -1.30 (0.16), residues: 1341 =============================================================================== Job complete usr+sys time: 7840.83 seconds wall clock time: 140 minutes 39.21 seconds (8439.21 seconds total)