Starting phenix.real_space_refine on Sun Mar 24 03:42:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ur4_26704/03_2024/7ur4_26704_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ur4_26704/03_2024/7ur4_26704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ur4_26704/03_2024/7ur4_26704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ur4_26704/03_2024/7ur4_26704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ur4_26704/03_2024/7ur4_26704_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ur4_26704/03_2024/7ur4_26704_trim.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9544 atoms to isotropic. 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 111 5.16 5 C 9534 2.51 5 N 2643 2.21 5 O 2994 1.98 5 H 14784 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30066 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 6543 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 416} Chain breaks: 1 Chain: "B" Number of atoms: 6543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 6543 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 416} Chain breaks: 1 Chain: "C" Number of atoms: 6538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 6538 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 416} Chain breaks: 1 Chain: "F" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1852 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1565 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1853 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "I" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1841 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1565 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "L" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1565 Classifications: {'peptide': 106} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" 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: "C" 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 Time building chain proxies: 12.67, per 1000 atoms: 0.42 Number of scatterers: 30066 At special positions: 0 Unit cell: (145.935, 139.59, 107.865, 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 111 16.00 O 2994 8.00 N 2643 7.00 C 9534 6.00 H 14784 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS C 249 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 322 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 153 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS B 84 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 463 " distance=2.02 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 322 " distance=2.03 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 153 " distance=2.04 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS C 84 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 463 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 182 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 322 " distance=2.03 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 153 " distance=2.04 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 463 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 390 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A 601 " - " ASN A 353 " " NAG A 602 " - " ASN A 57 " " NAG B 601 " - " ASN B 353 " " NAG B 602 " - " ASN B 57 " " NAG C 601 " - " ASN C 353 " " NAG C 602 " - " ASN C 57 " " NAG D 1 " - " ASN A 172 " " NAG E 1 " - " ASN B 172 " " NAG K 1 " - " ASN C 172 " Time building additional restraints: 21.85 Conformation dependent library (CDL) restraints added in 3.2 seconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3618 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 32 sheets defined 25.7% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 65 through 81 Processing helix chain 'A' and resid 104 through 129 removed outlier: 3.588A pdb=" N CYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 186 through 209 removed outlier: 4.480A pdb=" N ALA A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 237 through 247 removed outlier: 3.568A pdb=" N ILE A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 441 through 445 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 65 through 81 removed outlier: 3.522A pdb=" N ARG B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 104 through 129 removed outlier: 3.536A pdb=" N ILE B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 163 through 172 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 186 through 209 removed outlier: 4.237A pdb=" N ALA B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N PHE B 200 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 237 through 246 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 441 through 445 Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 65 through 83 removed outlier: 4.021A pdb=" N ARG C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 129 removed outlier: 4.179A pdb=" N CYS C 110 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 111 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 186 through 210 removed outlier: 4.490A pdb=" N ALA C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ARG C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE C 200 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 237 through 246 Processing helix chain 'C' and resid 247 through 255 removed outlier: 3.634A pdb=" N VAL C 251 " --> pdb=" O ASN C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 344 through 352 removed outlier: 3.550A pdb=" N LYS C 348 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.553A pdb=" N THR F 87 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.638A pdb=" N GLU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.623A pdb=" N THR I 87 " --> pdb=" O VAL I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 30 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.664A pdb=" N GLU J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.506A pdb=" N ARG L 29 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 329 removed outlier: 3.506A pdb=" N HIS A 332 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL A 333 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 36 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N CYS A 335 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 38 " --> pdb=" O CYS A 335 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER A 29 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA A 288 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 31 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 286 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU A 33 " --> pdb=" O TRP A 284 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TRP A 284 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR A 35 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER A 37 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 278 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP A 309 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR A 317 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329 removed outlier: 3.506A pdb=" N HIS A 332 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL A 333 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 36 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N CYS A 335 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 38 " --> pdb=" O CYS A 335 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLU A 21 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE A 437 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR A 23 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 6.633A pdb=" N THR A 45 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N THR A 160 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL A 47 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL A 162 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR A 49 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET A 270 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU A 259 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLN A 272 " --> pdb=" O GLY A 257 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLY A 257 " --> pdb=" O GLN A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 removed outlier: 3.756A pdb=" N ASN A 298 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N CYS A 365 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N PHE A 456 " --> pdb=" O CYS A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 376 Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.599A pdb=" N LYS A 401 " --> pdb=" O ILE A 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 316 through 320 removed outlier: 3.946A pdb=" N TRP B 309 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE B 279 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU B 39 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR B 281 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 35 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 285 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLU B 33 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LYS B 287 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE B 31 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL B 333 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 36 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N CYS B 335 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL B 38 " --> pdb=" O CYS B 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 316 through 320 removed outlier: 3.946A pdb=" N TRP B 309 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE B 279 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU B 39 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR B 281 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 35 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 285 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLU B 33 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LYS B 287 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE B 31 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLU B 21 " --> pdb=" O HIS B 435 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 437 " --> pdb=" O GLU B 21 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR B 23 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 150 removed outlier: 5.678A pdb=" N THR B 45 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL B 262 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE B 268 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 293 through 295 removed outlier: 3.747A pdb=" N GLY B 366 " --> pdb=" O CYS B 301 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N CYS B 365 " --> pdb=" O PHE B 456 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE B 456 " --> pdb=" O CYS B 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 372 through 376 Processing sheet with id=AB3, first strand: chain 'B' and resid 399 through 402 removed outlier: 6.919A pdb=" N ILE B 392 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLN B 402 " --> pdb=" O CYS B 390 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N CYS B 390 " --> pdb=" O GLN B 402 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 326 through 329 removed outlier: 3.549A pdb=" N HIS C 332 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL C 333 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU C 36 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N CYS C 335 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL C 38 " --> pdb=" O CYS C 335 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ILE C 31 " --> pdb=" O LYS C 287 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LYS C 287 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLU C 33 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE C 285 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 35 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR C 281 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU C 39 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE C 279 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TRP C 309 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR C 317 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 326 through 329 removed outlier: 3.549A pdb=" N HIS C 332 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL C 333 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU C 36 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N CYS C 335 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL C 38 " --> pdb=" O CYS C 335 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU C 21 " --> pdb=" O HIS C 435 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ILE C 437 " --> pdb=" O GLU C 21 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR C 23 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 146 through 150 removed outlier: 6.701A pdb=" N THR C 45 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N THR C 160 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL C 47 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL C 162 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR C 49 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER C 266 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N VAL C 262 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE C 268 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 293 through 295 removed outlier: 3.550A pdb=" N GLY C 366 " --> pdb=" O CYS C 301 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 372 through 376 Processing sheet with id=AB9, first strand: chain 'C' and resid 401 through 402 removed outlier: 3.518A pdb=" N LYS C 401 " --> pdb=" O ILE C 392 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.844A pdb=" N VAL F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N MET F 34 " --> pdb=" O GLY F 50 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLY F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AC4, first strand: chain 'G' and resid 9 through 13 removed outlier: 6.004A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 9 through 13 Processing sheet with id=AC6, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AC7, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.012A pdb=" N GLY H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.915A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY I 33 " --> pdb=" O ASP I 95 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AD2, first strand: chain 'J' and resid 9 through 14 removed outlier: 6.750A pdb=" N VAL J 11 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEU J 106A" --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL J 13 " --> pdb=" O LEU J 106A" (cutoff:3.500A) removed outlier: 6.055A pdb=" N CYS J 88 " --> pdb=" O GLY J 99 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY J 101 " --> pdb=" O TYR J 86 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N TYR J 86 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AD4, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.696A pdb=" N VAL L 11 " --> pdb=" O ARG L 103 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.696A pdb=" N VAL L 11 " --> pdb=" O ARG L 103 " (cutoff:3.500A) 709 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: 12.42 Time building geometry restraints manager: 22.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14782 1.03 - 1.23: 120 1.23 - 1.43: 6391 1.43 - 1.62: 8902 1.62 - 1.82: 138 Bond restraints: 30333 Sorted by residual: bond pdb=" N HIS C 368 " pdb=" H HIS C 368 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.72e+01 bond pdb=" CA HIS C 368 " pdb=" HA HIS C 368 " ideal model delta sigma weight residual 0.970 1.089 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.30e+00 bond pdb=" N HIS C 368 " pdb=" CA HIS C 368 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.47e-02 4.63e+03 4.86e+00 bond pdb=" C1 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.16e+00 ... (remaining 30328 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.91: 407 106.91 - 113.69: 36030 113.69 - 120.47: 9662 120.47 - 127.25: 8336 127.25 - 134.02: 136 Bond angle restraints: 54571 Sorted by residual: angle pdb=" CA CYS F 92 " pdb=" CB CYS F 92 " pdb=" SG CYS F 92 " ideal model delta sigma weight residual 114.40 120.61 -6.21 2.30e+00 1.89e-01 7.30e+00 angle pdb=" CA CYS H 92 " pdb=" CB CYS H 92 " pdb=" SG CYS H 92 " ideal model delta sigma weight residual 114.40 120.52 -6.12 2.30e+00 1.89e-01 7.08e+00 angle pdb=" N ASP H 31 " pdb=" CA ASP H 31 " pdb=" C ASP H 31 " ideal model delta sigma weight residual 110.80 116.24 -5.44 2.13e+00 2.20e-01 6.52e+00 angle pdb=" CA CYS I 92 " pdb=" CB CYS I 92 " pdb=" SG CYS I 92 " ideal model delta sigma weight residual 114.40 120.11 -5.71 2.30e+00 1.89e-01 6.17e+00 angle pdb=" N LEU F 108 " pdb=" CA LEU F 108 " pdb=" C LEU F 108 " ideal model delta sigma weight residual 107.73 111.66 -3.93 1.80e+00 3.09e-01 4.78e+00 ... (remaining 54566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.38: 13410 20.38 - 40.77: 661 40.77 - 61.15: 412 61.15 - 81.53: 116 81.53 - 101.92: 20 Dihedral angle restraints: 14619 sinusoidal: 8126 harmonic: 6493 Sorted by residual: dihedral pdb=" CB CYS A 384 " pdb=" SG CYS A 384 " pdb=" SG CYS A 390 " pdb=" CB CYS A 390 " ideal model delta sinusoidal sigma weight residual -86.00 -145.12 59.12 1 1.00e+01 1.00e-02 4.67e+01 dihedral pdb=" CA ASN B 178 " pdb=" C ASN B 178 " pdb=" N LYS B 179 " pdb=" CA LYS B 179 " ideal model delta harmonic sigma weight residual -180.00 -153.32 -26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA VAL A 162 " pdb=" C VAL A 162 " pdb=" N ARG A 163 " pdb=" CA ARG A 163 " ideal model delta harmonic sigma weight residual -180.00 -153.52 -26.48 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 14616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2177 0.078 - 0.155: 252 0.155 - 0.233: 4 0.233 - 0.310: 5 0.310 - 0.388: 1 Chirality restraints: 2439 Sorted by residual: chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 353 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 172 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 2436 not shown) Planarity restraints: 4611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 47 " 0.009 2.00e-02 2.50e+03 1.97e-02 1.56e+01 pdb=" CG TRP F 47 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP F 47 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP F 47 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 47 " -0.059 2.00e-02 2.50e+03 pdb=" CE2 TRP F 47 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 47 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 47 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 47 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP F 47 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP F 47 " 0.049 2.00e-02 2.50e+03 pdb=" HE3 TRP F 47 " -0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP F 47 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP F 47 " 0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP F 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 367 " 0.147 9.50e-02 1.11e+02 5.45e-02 1.53e+01 pdb=" NE ARG A 367 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 367 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 367 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG A 367 " -0.042 2.00e-02 2.50e+03 pdb="HH11 ARG A 367 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 367 " 0.015 2.00e-02 2.50e+03 pdb="HH21 ARG A 367 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 367 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 61 " -0.215 9.50e-02 1.11e+02 7.45e-02 1.48e+01 pdb=" NE ARG G 61 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG G 61 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG G 61 " 0.047 2.00e-02 2.50e+03 pdb=" NH2 ARG G 61 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG G 61 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG G 61 " -0.039 2.00e-02 2.50e+03 pdb="HH21 ARG G 61 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG G 61 " -0.001 2.00e-02 2.50e+03 ... (remaining 4608 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 732 2.11 - 2.73: 53231 2.73 - 3.36: 82211 3.36 - 3.98: 107251 3.98 - 4.60: 170006 Nonbonded interactions: 413431 Sorted by model distance: nonbonded pdb=" OE2 GLU C 25 " pdb=" H GLY C 439 " model vdw 1.489 1.850 nonbonded pdb=" OE2 GLU A 25 " pdb=" H GLY A 439 " model vdw 1.510 1.850 nonbonded pdb=" HG SER A 37 " pdb=" OG1 THR A 281 " model vdw 1.523 1.850 nonbonded pdb="HH22 ARG C 156 " pdb=" O ASP H 31 " model vdw 1.542 1.850 nonbonded pdb=" OD1 ASP L 92 " pdb=" HG SER L 94 " model vdw 1.544 1.850 ... (remaining 413426 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 19 through 367 or (resid 368 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA )) or resid 369 through 466 or resid 601 through 602)) selection = (chain 'B' and (resid 19 through 367 or (resid 368 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA )) or resid 369 through 466 or resid 601 through 602)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' } ncs_group { reference = (chain 'F' and (resid 4 through 63 or (resid 64 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or n \ ame HA )) or resid 65 through 113)) selection = (chain 'H' and (resid 4 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE \ 1)) or resid 36 through 63 or (resid 64 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name CE or name NZ or name H or name HA ) \ ) or resid 65 through 113)) selection = chain 'I' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'L' } 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.460 Extract box with map and model: 8.580 Check model and map are aligned: 0.490 Set scattering table: 0.280 Process input model: 88.660 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.210 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 0.050 15549 Z= 0.370 Angle : 0.632 6.328 21072 Z= 0.346 Chirality : 0.048 0.388 2439 Planarity : 0.008 0.106 2706 Dihedral : 14.498 101.917 5874 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.42 % Allowed : 2.89 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.89 (0.18), residues: 1950 helix: -1.30 (0.20), residues: 396 sheet: -0.09 (0.20), residues: 624 loop : -0.47 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP F 47 HIS 0.007 0.002 HIS F 35 PHE 0.018 0.002 PHE B 451 TYR 0.019 0.003 TYR I 52A ARG 0.016 0.002 ARG I 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 164 time to evaluate : 2.516 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: A 72 ASP cc_start: 0.8600 (t0) cc_final: 0.8207 (t0) REVERT: C 72 ASP cc_start: 0.8517 (t0) cc_final: 0.8294 (t0) REVERT: G 79 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7980 (mm110) REVERT: J 79 GLN cc_start: 0.8468 (mm-40) cc_final: 0.7756 (mm110) REVERT: L 79 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8264 (mp10) outliers start: 7 outliers final: 1 residues processed: 171 average time/residue: 0.8042 time to fit residues: 187.6897 Evaluate side-chains 84 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 89 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 152 optimal weight: 0.1980 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15549 Z= 0.252 Angle : 0.581 6.735 21072 Z= 0.319 Chirality : 0.044 0.336 2439 Planarity : 0.004 0.049 2706 Dihedral : 9.151 63.008 2450 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.66 % Allowed : 5.23 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.42 (0.18), residues: 1950 helix: -0.09 (0.24), residues: 429 sheet: -0.06 (0.19), residues: 620 loop : -0.38 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 284 HIS 0.003 0.001 HIS H 100F PHE 0.013 0.001 PHE I 29 TYR 0.011 0.001 TYR J 49 ARG 0.003 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 2.230 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: A 72 ASP cc_start: 0.8623 (t0) cc_final: 0.8261 (t0) outliers start: 11 outliers final: 7 residues processed: 102 average time/residue: 0.6683 time to fit residues: 100.1839 Evaluate side-chains 92 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain L residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN I 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 15549 Z= 0.437 Angle : 0.599 9.621 21072 Z= 0.326 Chirality : 0.044 0.259 2439 Planarity : 0.004 0.048 2706 Dihedral : 7.084 59.923 2450 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.14 % Allowed : 6.26 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.50 (0.19), residues: 1950 helix: 0.31 (0.25), residues: 435 sheet: -0.27 (0.19), residues: 635 loop : -0.56 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 284 HIS 0.005 0.001 HIS J 95B PHE 0.011 0.001 PHE J 32 TYR 0.014 0.002 TYR J 49 ARG 0.006 0.001 ARG C 396 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 2.145 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: A 72 ASP cc_start: 0.8666 (t0) cc_final: 0.8358 (t0) outliers start: 19 outliers final: 17 residues processed: 102 average time/residue: 0.6481 time to fit residues: 97.8975 Evaluate side-chains 95 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain B residue 147 CYS Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15549 Z= 0.242 Angle : 0.501 4.902 21072 Z= 0.274 Chirality : 0.043 0.279 2439 Planarity : 0.003 0.029 2706 Dihedral : 6.302 58.509 2450 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.14 % Allowed : 6.56 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.22 (0.19), residues: 1950 helix: 0.89 (0.26), residues: 438 sheet: -0.28 (0.20), residues: 620 loop : -0.45 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 284 HIS 0.003 0.001 HIS J 95B PHE 0.009 0.001 PHE G 98 TYR 0.008 0.001 TYR C 269 ARG 0.003 0.000 ARG C 396 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 2.591 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: A 72 ASP cc_start: 0.8610 (t0) cc_final: 0.8327 (t0) REVERT: F 34 MET cc_start: 0.8721 (mmm) cc_final: 0.8487 (mmm) outliers start: 19 outliers final: 15 residues processed: 97 average time/residue: 0.6342 time to fit residues: 91.1078 Evaluate side-chains 92 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15549 Z= 0.359 Angle : 0.528 6.249 21072 Z= 0.288 Chirality : 0.043 0.255 2439 Planarity : 0.003 0.034 2706 Dihedral : 6.114 59.843 2450 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.50 % Allowed : 6.50 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.34 (0.19), residues: 1950 helix: 0.95 (0.26), residues: 438 sheet: -0.37 (0.20), residues: 619 loop : -0.60 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 284 HIS 0.004 0.001 HIS J 95B PHE 0.010 0.001 PHE I 29 TYR 0.010 0.001 TYR L 49 ARG 0.004 0.000 ARG C 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 2.596 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: A 72 ASP cc_start: 0.8638 (t0) cc_final: 0.8379 (t0) REVERT: I 34 MET cc_start: 0.8948 (mmm) cc_final: 0.8721 (mmt) outliers start: 25 outliers final: 20 residues processed: 100 average time/residue: 0.6238 time to fit residues: 94.4419 Evaluate side-chains 94 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 188 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15549 Z= 0.209 Angle : 0.481 7.531 21072 Z= 0.261 Chirality : 0.042 0.264 2439 Planarity : 0.003 0.034 2706 Dihedral : 5.838 59.398 2450 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.32 % Allowed : 6.44 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.15 (0.19), residues: 1950 helix: 1.24 (0.26), residues: 438 sheet: -0.31 (0.20), residues: 619 loop : -0.51 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 284 HIS 0.002 0.001 HIS J 95B PHE 0.009 0.001 PHE I 29 TYR 0.008 0.001 TYR C 269 ARG 0.003 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 2.333 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: A 72 ASP cc_start: 0.8595 (t0) cc_final: 0.8344 (t0) REVERT: A 236 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8711 (m) outliers start: 22 outliers final: 19 residues processed: 96 average time/residue: 0.6133 time to fit residues: 89.6606 Evaluate side-chains 96 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 76 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15549 Z= 0.210 Angle : 0.469 6.190 21072 Z= 0.254 Chirality : 0.042 0.251 2439 Planarity : 0.003 0.035 2706 Dihedral : 5.630 57.453 2450 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.32 % Allowed : 6.98 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.05 (0.19), residues: 1950 helix: 1.40 (0.26), residues: 438 sheet: -0.25 (0.20), residues: 619 loop : -0.50 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 284 HIS 0.002 0.001 HIS J 95B PHE 0.010 0.001 PHE I 29 TYR 0.008 0.001 TYR B 385 ARG 0.002 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 2.391 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: A 72 ASP cc_start: 0.8620 (t0) cc_final: 0.8381 (t0) REVERT: A 236 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8706 (m) outliers start: 22 outliers final: 19 residues processed: 100 average time/residue: 0.5819 time to fit residues: 88.6616 Evaluate side-chains 97 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 15549 Z= 0.365 Angle : 0.522 5.836 21072 Z= 0.283 Chirality : 0.042 0.247 2439 Planarity : 0.003 0.036 2706 Dihedral : 5.697 53.465 2450 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.26 % Allowed : 7.22 % Favored : 91.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.26 (0.19), residues: 1950 helix: 1.38 (0.27), residues: 423 sheet: -0.37 (0.20), residues: 619 loop : -0.69 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 47 HIS 0.004 0.001 HIS J 95B PHE 0.011 0.001 PHE I 29 TYR 0.011 0.001 TYR L 49 ARG 0.003 0.000 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 76 time to evaluate : 2.551 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: A 72 ASP cc_start: 0.8621 (t0) cc_final: 0.8390 (t0) REVERT: A 236 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8692 (m) outliers start: 21 outliers final: 20 residues processed: 95 average time/residue: 0.6328 time to fit residues: 89.8368 Evaluate side-chains 95 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.0030 chunk 164 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15549 Z= 0.209 Angle : 0.470 6.024 21072 Z= 0.254 Chirality : 0.042 0.252 2439 Planarity : 0.003 0.033 2706 Dihedral : 5.450 51.520 2450 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.26 % Allowed : 7.34 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.06 (0.19), residues: 1950 helix: 1.47 (0.27), residues: 438 sheet: -0.27 (0.20), residues: 619 loop : -0.55 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 284 HIS 0.003 0.001 HIS J 95B PHE 0.010 0.001 PHE I 29 TYR 0.008 0.001 TYR B 385 ARG 0.008 0.000 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 2.450 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: A 72 ASP cc_start: 0.8617 (t0) cc_final: 0.8383 (t0) REVERT: A 236 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8688 (m) REVERT: F 34 MET cc_start: 0.8746 (mmm) cc_final: 0.8503 (mmm) outliers start: 21 outliers final: 19 residues processed: 96 average time/residue: 0.6390 time to fit residues: 92.2605 Evaluate side-chains 94 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 74 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain L residue 45 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 chunk 87 optimal weight: 0.6980 chunk 128 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15549 Z= 0.149 Angle : 0.450 6.841 21072 Z= 0.241 Chirality : 0.042 0.246 2439 Planarity : 0.003 0.033 2706 Dihedral : 5.184 49.235 2450 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.84 % Allowed : 7.76 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.21 (0.20), residues: 1950 helix: 1.71 (0.27), residues: 438 sheet: -0.06 (0.21), residues: 612 loop : -0.42 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 284 HIS 0.002 0.001 HIS J 95B PHE 0.010 0.001 PHE I 29 TYR 0.018 0.001 TYR F 79 ARG 0.009 0.000 ARG A 396 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 64 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8592 (t0) cc_final: 0.8360 (t0) REVERT: A 236 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8710 (m) REVERT: F 34 MET cc_start: 0.8756 (mmm) cc_final: 0.8521 (mmm) outliers start: 14 outliers final: 13 residues processed: 90 average time/residue: 0.6448 time to fit residues: 85.6295 Evaluate side-chains 89 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain C residue 147 CYS Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain I residue 101 ASP Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.053506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.042252 restraints weight = 138499.516| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 3.62 r_work: 0.2502 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15549 Z= 0.253 Angle : 0.472 6.188 21072 Z= 0.253 Chirality : 0.042 0.240 2439 Planarity : 0.003 0.035 2706 Dihedral : 5.200 48.290 2450 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.96 % Allowed : 7.82 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.08 (0.20), residues: 1950 helix: 1.63 (0.27), residues: 438 sheet: -0.15 (0.21), residues: 619 loop : -0.51 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 47 HIS 0.002 0.001 HIS J 95B PHE 0.011 0.001 PHE I 29 TYR 0.008 0.001 TYR L 49 ARG 0.004 0.000 ARG I 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4999.16 seconds wall clock time: 89 minutes 46.69 seconds (5386.69 seconds total)