Starting phenix.real_space_refine on Fri Mar 15 16:48:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7up9_26658/03_2024/7up9_26658_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7up9_26658/03_2024/7up9_26658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7up9_26658/03_2024/7up9_26658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7up9_26658/03_2024/7up9_26658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7up9_26658/03_2024/7up9_26658_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7up9_26658/03_2024/7up9_26658_neut.pdb" } resolution = 2.9 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= 0.001 sd= 0.195 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 7698 2.51 5 N 1981 2.21 5 O 2416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 307": "OE1" <-> "OE2" Residue "G TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 361": "OE1" <-> "OE2" Residue "L GLU 34": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12168 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3404 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain breaks: 1 Chain: "D" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3404 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain breaks: 1 Chain: "G" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3404 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain breaks: 1 Chain: "H" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 894 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 866 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 105} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 6.67, per 1000 atoms: 0.55 Number of scatterers: 12168 At special positions: 0 Unit cell: (100.32, 102.96, 142.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 2416 8.00 N 1981 7.00 C 7698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.04 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.04 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 114 " distance=2.04 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 392 " distance=2.03 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS G 192 " distance=2.04 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS G 355 " - pdb=" SG CYS G 363 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 392 " distance=2.03 Simple disulfide: pdb=" SG CYS G 394 " - pdb=" SG CYS G 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG A 502 " - " ASN A 99 " " NAG A 503 " - " ASN A 414 " " NAG A 504 " - " ASN A 464 " " NAG B 1 " - " ASN G 67 " " NAG D 501 " - " ASN D 67 " " NAG D 502 " - " ASN D 99 " " NAG D 503 " - " ASN D 414 " " NAG D 504 " - " ASN D 464 " " NAG G 501 " - " ASN G 99 " " NAG G 502 " - " ASN G 414 " " NAG G 503 " - " ASN G 464 " Time building additional restraints: 4.63 Conformation dependent library (CDL) restraints added in 2.4 seconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2922 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 21 sheets defined 36.5% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.954A pdb=" N LYS A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 5.727A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.750A pdb=" N ASN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 3.804A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.544A pdb=" N ALA A 133 " --> pdb=" O THR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.890A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.664A pdb=" N ASP A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.794A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.934A pdb=" N ASP A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 removed outlier: 3.572A pdb=" N THR A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 363 removed outlier: 5.372A pdb=" N GLU A 361 " --> pdb=" O GLY A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.587A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 475 removed outlier: 3.940A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 65 through 72 removed outlier: 3.560A pdb=" N SER D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN D 70 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS D 71 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 100 removed outlier: 3.709A pdb=" N ASN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) Proline residue: D 89 - end of helix removed outlier: 3.923A pdb=" N ILE D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 125 through 145 removed outlier: 3.556A pdb=" N MET D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASN D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 175 through 183 removed outlier: 3.653A pdb=" N ILE D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 215 removed outlier: 3.765A pdb=" N THR D 195 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.781A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 removed outlier: 4.223A pdb=" N ASP D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP D 255 " --> pdb=" O GLU D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 357 Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.533A pdb=" N LYS D 362 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 441 removed outlier: 3.627A pdb=" N GLU D 441 " --> pdb=" O TYR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 475 removed outlier: 3.704A pdb=" N SER D 457 " --> pdb=" O LYS D 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 36 removed outlier: 3.825A pdb=" N LYS G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 72 removed outlier: 6.267A pdb=" N GLN G 70 " --> pdb=" O ASN G 67 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS G 71 " --> pdb=" O MET G 68 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR G 72 " --> pdb=" O SER G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 100 removed outlier: 3.658A pdb=" N ASN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Proline residue: G 89 - end of helix removed outlier: 3.883A pdb=" N ILE G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN G 100 " --> pdb=" O ILE G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 Processing helix chain 'G' and resid 125 through 145 removed outlier: 4.091A pdb=" N LYS G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASN G 140 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN G 143 " --> pdb=" O LYS G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 153 Processing helix chain 'G' and resid 175 through 183 Processing helix chain 'G' and resid 191 through 215 removed outlier: 3.739A pdb=" N THR G 195 " --> pdb=" O PRO G 191 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N PHE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.711A pdb=" N LEU G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 328 through 331 Processing helix chain 'G' and resid 349 through 357 Processing helix chain 'G' and resid 359 through 363 removed outlier: 3.549A pdb=" N CYS G 363 " --> pdb=" O THR G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 441 removed outlier: 3.569A pdb=" N GLU G 441 " --> pdb=" O TYR G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 475 removed outlier: 3.675A pdb=" N SER G 457 " --> pdb=" O LYS G 453 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.848A pdb=" N LYS H 64 " --> pdb=" O SER H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.522A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 162 removed outlier: 11.035A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N LYS A 47 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLN A 289 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N LYS A 49 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N GLU A 287 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASN A 51 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 285 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 53 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LYS A 55 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYR A 281 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE A 57 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG A 279 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE A 59 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE A 277 " --> pdb=" O ILE A 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.108A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE A 277 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE A 59 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG A 279 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE A 57 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYR A 281 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LYS A 55 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 53 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 285 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N ASN A 51 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N GLU A 287 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N LYS A 49 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N GLN A 289 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N LYS A 47 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 323 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.527A pdb=" N GLN G 393 " --> pdb=" O VAL G 421 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N CYS G 392 " --> pdb=" O ILE G 401 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 400 through 401 removed outlier: 4.476A pdb=" N CYS A 392 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN A 393 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A 426 " --> pdb=" O MET D 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 160 removed outlier: 4.701A pdb=" N TYR D 170 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLU D 295 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR D 43 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 293 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS D 45 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ALA D 291 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N LYS D 47 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N GLN D 289 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N LYS D 49 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLU D 287 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N ASN D 51 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU D 285 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU D 53 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS D 55 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N TYR D 281 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE D 57 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ARG D 279 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE D 59 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE D 277 " --> pdb=" O ILE D 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 275 through 298 current: chain 'D' and resid 332 through 333 Processing sheet with id=AA9, first strand: chain 'D' and resid 226 through 227 removed outlier: 4.180A pdb=" N MET D 226 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR D 263 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE D 277 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N VAL D 269 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR D 275 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE D 277 " --> pdb=" O ILE D 59 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE D 59 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ARG D 279 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE D 57 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N TYR D 281 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS D 55 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU D 53 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU D 285 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N ASN D 51 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N GLU D 287 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N LYS D 49 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N GLN D 289 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N LYS D 47 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ALA D 291 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LYS D 45 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE D 293 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR D 43 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLU D 295 " --> pdb=" O GLY D 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 38 through 60 current: chain 'D' and resid 323 through 326 Processing sheet with id=AB1, first strand: chain 'D' and resid 301 through 303 removed outlier: 6.313A pdb=" N ARG D 365 " --> pdb=" O VAL D 449 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB3, first strand: chain 'D' and resid 400 through 401 removed outlier: 4.556A pdb=" N CYS D 392 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN D 393 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE D 426 " --> pdb=" O MET G 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 158 through 162 removed outlier: 11.165A pdb=" N THR G 168 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASP G 56 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TYR G 170 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU G 295 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N THR G 43 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE G 293 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS G 45 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ALA G 291 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N LYS G 47 " --> pdb=" O GLN G 289 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N GLN G 289 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N LYS G 49 " --> pdb=" O GLU G 287 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLU G 287 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ASN G 51 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU G 285 " --> pdb=" O ASN G 51 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU G 53 " --> pdb=" O PRO G 283 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS G 55 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TYR G 281 " --> pdb=" O LYS G 55 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE G 57 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ARG G 279 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE G 59 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE G 277 " --> pdb=" O ILE G 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 275 through 298 current: chain 'G' and resid 332 through 334 Processing sheet with id=AB5, first strand: chain 'G' and resid 226 through 227 removed outlier: 4.119A pdb=" N MET G 226 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR G 263 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE G 277 " --> pdb=" O ILE G 267 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL G 269 " --> pdb=" O TYR G 275 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR G 275 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE G 277 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE G 59 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ARG G 279 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE G 57 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TYR G 281 " --> pdb=" O LYS G 55 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS G 55 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU G 53 " --> pdb=" O PRO G 283 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU G 285 " --> pdb=" O ASN G 51 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ASN G 51 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N GLU G 287 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N LYS G 49 " --> pdb=" O GLU G 287 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N GLN G 289 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N LYS G 47 " --> pdb=" O GLN G 289 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ALA G 291 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LYS G 45 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE G 293 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N THR G 43 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N GLU G 295 " --> pdb=" O GLY G 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 38 through 60 current: chain 'G' and resid 322 through 326 Processing sheet with id=AB6, first strand: chain 'G' and resid 301 through 302 Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.871A pdb=" N LEU H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.118A pdb=" N TYR H 102 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.746A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.755A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1356 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: 4.00 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3874 1.34 - 1.46: 2706 1.46 - 1.59: 5672 1.59 - 1.71: 0 1.71 - 1.83: 106 Bond restraints: 12358 Sorted by residual: bond pdb=" C ILE A 190 " pdb=" N PRO A 191 " ideal model delta sigma weight residual 1.331 1.371 -0.040 1.27e-02 6.20e+03 1.01e+01 bond pdb=" N ILE G 36 " pdb=" CA ILE G 36 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.88e+00 bond pdb=" N GLN A 393 " pdb=" CA GLN A 393 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.25e-02 6.40e+03 8.69e+00 bond pdb=" N LYS A 362 " pdb=" CA LYS A 362 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.16e-02 7.43e+03 7.96e+00 bond pdb=" N CYS A 363 " pdb=" CA CYS A 363 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 7.74e+00 ... (remaining 12353 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.24: 326 107.24 - 113.92: 7318 113.92 - 120.61: 4563 120.61 - 127.29: 4505 127.29 - 133.97: 67 Bond angle restraints: 16779 Sorted by residual: angle pdb=" N THR A 415 " pdb=" CA THR A 415 " pdb=" C THR A 415 " ideal model delta sigma weight residual 112.89 105.88 7.01 1.24e+00 6.50e-01 3.19e+01 angle pdb=" N THR A 416 " pdb=" CA THR A 416 " pdb=" C THR A 416 " ideal model delta sigma weight residual 113.12 108.09 5.03 1.25e+00 6.40e-01 1.62e+01 angle pdb=" N ILE A 36 " pdb=" CA ILE A 36 " pdb=" C ILE A 36 " ideal model delta sigma weight residual 113.07 107.75 5.32 1.37e+00 5.33e-01 1.51e+01 angle pdb=" CA GLN A 342 " pdb=" C GLN A 342 " pdb=" O GLN A 342 " ideal model delta sigma weight residual 121.40 117.42 3.98 1.13e+00 7.83e-01 1.24e+01 angle pdb=" C PRO A 191 " pdb=" CA PRO A 191 " pdb=" CB PRO A 191 " ideal model delta sigma weight residual 111.56 107.09 4.47 1.27e+00 6.20e-01 1.24e+01 ... (remaining 16774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 7167 17.58 - 35.15: 440 35.15 - 52.73: 102 52.73 - 70.31: 32 70.31 - 87.88: 10 Dihedral angle restraints: 7751 sinusoidal: 3212 harmonic: 4539 Sorted by residual: dihedral pdb=" CB CYS A 394 " pdb=" SG CYS A 394 " pdb=" SG CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sinusoidal sigma weight residual 93.00 160.52 -67.52 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CB CYS D 71 " pdb=" SG CYS D 71 " pdb=" SG CYS D 192 " pdb=" CB CYS D 192 " ideal model delta sinusoidal sigma weight residual -86.00 -151.19 65.19 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CB CYS A 355 " pdb=" SG CYS A 355 " pdb=" SG CYS A 363 " pdb=" CB CYS A 363 " ideal model delta sinusoidal sigma weight residual -86.00 -136.51 50.51 1 1.00e+01 1.00e-02 3.50e+01 ... (remaining 7748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1695 0.059 - 0.118: 323 0.118 - 0.178: 32 0.178 - 0.237: 5 0.237 - 0.296: 1 Chirality restraints: 2056 Sorted by residual: chirality pdb=" CA ILE A 339 " pdb=" N ILE A 339 " pdb=" C ILE A 339 " pdb=" CB ILE A 339 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA GLN A 342 " pdb=" N GLN A 342 " pdb=" C GLN A 342 " pdb=" CB GLN A 342 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA CYS A 392 " pdb=" N CYS A 392 " pdb=" C CYS A 392 " pdb=" CB CYS A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2053 not shown) Planarity restraints: 2116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 390 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C VAL A 390 " 0.037 2.00e-02 2.50e+03 pdb=" O VAL A 390 " -0.014 2.00e-02 2.50e+03 pdb=" N THR A 391 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 179 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C ILE G 179 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE G 179 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN G 180 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY G 446 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO G 447 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO G 447 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 447 " -0.019 5.00e-02 4.00e+02 ... (remaining 2113 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 539 2.73 - 3.28: 11648 3.28 - 3.82: 18613 3.82 - 4.36: 23633 4.36 - 4.90: 40814 Nonbonded interactions: 95247 Sorted by model distance: nonbonded pdb=" O SER H 98 " pdb=" OG1 THR H 99 " model vdw 2.192 2.440 nonbonded pdb=" OG SER G 359 " pdb=" OE2 GLU G 361 " model vdw 2.215 2.440 nonbonded pdb=" OE2 GLU D 152 " pdb=" OG SER D 273 " model vdw 2.240 2.440 nonbonded pdb=" OD1 ASP G 103 " pdb=" OH TYR G 135 " model vdw 2.261 2.440 nonbonded pdb=" NZ LYS A 148 " pdb=" OG SER A 273 " model vdw 2.272 2.520 ... (remaining 95242 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 475 or resid 501 through 503)) selection = (chain 'D' and (resid 27 through 475 or resid 501 through 503)) selection = chain 'G' } 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: 7.270 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: 0.010 Extract box with map and model: 33.870 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 34.900 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.003 0.040 12358 Z= 0.222 Angle : 0.607 7.007 16779 Z= 0.357 Chirality : 0.047 0.296 2056 Planarity : 0.004 0.034 2104 Dihedral : 12.629 87.883 4769 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.51 % Allowed : 0.58 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.12 (0.21), residues: 1540 helix: 0.90 (0.25), residues: 423 sheet: 0.58 (0.26), residues: 400 loop : -0.66 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 47 HIS 0.002 0.001 HIS G 102 PHE 0.008 0.001 PHE D 301 TYR 0.008 0.001 TYR L 49 ARG 0.004 0.000 ARG G 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 160 average time/residue: 1.4101 time to fit residues: 243.0338 Evaluate side-chains 116 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 4.9990 chunk 116 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 372 HIS H 16 GLN H 73 ASN L 6 GLN L 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12358 Z= 0.195 Angle : 0.533 8.436 16779 Z= 0.281 Chirality : 0.046 0.232 2056 Planarity : 0.004 0.036 2104 Dihedral : 5.780 53.894 1949 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.38 % Allowed : 7.54 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.35 (0.21), residues: 1540 helix: 1.46 (0.26), residues: 441 sheet: 0.60 (0.26), residues: 397 loop : -0.76 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.010 0.001 HIS G 372 PHE 0.014 0.001 PHE A 330 TYR 0.020 0.001 TYR L 49 ARG 0.007 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.403 Fit side-chains REVERT: G 290 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7422 (mp-120) outliers start: 19 outliers final: 8 residues processed: 137 average time/residue: 1.4205 time to fit residues: 210.0221 Evaluate side-chains 115 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 290 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 140 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 393 GLN H 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12358 Z= 0.263 Angle : 0.558 8.897 16779 Z= 0.292 Chirality : 0.048 0.250 2056 Planarity : 0.004 0.035 2104 Dihedral : 5.552 53.889 1949 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.17 % Allowed : 10.07 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.33 (0.21), residues: 1540 helix: 1.43 (0.25), residues: 459 sheet: 0.49 (0.26), residues: 400 loop : -0.76 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.003 0.001 HIS D 29 PHE 0.016 0.001 PHE A 330 TYR 0.025 0.001 TYR L 49 ARG 0.004 0.000 ARG H 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 1.449 Fit side-chains REVERT: A 61 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8587 (mtp) REVERT: D 61 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8418 (mtp) REVERT: D 197 LEU cc_start: 0.8313 (tp) cc_final: 0.7822 (mt) REVERT: G 290 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7431 (mp-120) REVERT: H 75 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7911 (mmtp) outliers start: 30 outliers final: 14 residues processed: 134 average time/residue: 1.3618 time to fit residues: 197.1021 Evaluate side-chains 128 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 290 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.0970 chunk 105 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 148 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 16 GLN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12358 Z= 0.133 Angle : 0.479 8.378 16779 Z= 0.251 Chirality : 0.045 0.220 2056 Planarity : 0.004 0.032 2104 Dihedral : 5.105 54.050 1949 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.45 % Allowed : 12.32 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.55 (0.21), residues: 1540 helix: 1.98 (0.27), residues: 426 sheet: 0.54 (0.26), residues: 400 loop : -0.73 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.002 0.000 HIS G 102 PHE 0.011 0.001 PHE A 330 TYR 0.022 0.001 TYR L 49 ARG 0.003 0.000 ARG D 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.417 Fit side-chains REVERT: D 197 LEU cc_start: 0.8166 (tp) cc_final: 0.7927 (mt) REVERT: G 290 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7408 (mp-120) outliers start: 20 outliers final: 9 residues processed: 141 average time/residue: 1.4443 time to fit residues: 219.3499 Evaluate side-chains 125 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 290 GLN Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 0.0770 chunk 127 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN H 3 GLN H 16 GLN L 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12358 Z= 0.242 Angle : 0.536 8.071 16779 Z= 0.278 Chirality : 0.047 0.255 2056 Planarity : 0.004 0.033 2104 Dihedral : 5.158 53.728 1949 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.46 % Allowed : 12.39 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.49 (0.21), residues: 1540 helix: 1.80 (0.26), residues: 444 sheet: 0.52 (0.26), residues: 400 loop : -0.75 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS D 102 PHE 0.016 0.001 PHE A 330 TYR 0.025 0.001 TYR L 49 ARG 0.005 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 1.447 Fit side-chains REVERT: A 61 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8560 (mtp) REVERT: D 197 LEU cc_start: 0.8336 (tp) cc_final: 0.8001 (mt) REVERT: G 290 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7424 (mp-120) REVERT: H 75 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7902 (mmtp) outliers start: 34 outliers final: 17 residues processed: 139 average time/residue: 1.3823 time to fit residues: 207.7735 Evaluate side-chains 132 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain G residue 290 GLN Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 60 ASN Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 149 optimal weight: 0.0470 chunk 123 optimal weight: 0.9990 chunk 68 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12358 Z= 0.117 Angle : 0.456 7.153 16779 Z= 0.239 Chirality : 0.044 0.215 2056 Planarity : 0.003 0.031 2104 Dihedral : 4.732 54.136 1949 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.67 % Allowed : 13.77 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.67 (0.22), residues: 1540 helix: 2.20 (0.26), residues: 426 sheet: 0.56 (0.25), residues: 445 loop : -0.78 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS D 102 PHE 0.010 0.001 PHE A 330 TYR 0.022 0.001 TYR L 49 ARG 0.005 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.473 Fit side-chains REVERT: A 61 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8394 (mtt) REVERT: D 197 LEU cc_start: 0.8240 (tp) cc_final: 0.7844 (mt) REVERT: G 181 THR cc_start: 0.8662 (m) cc_final: 0.8407 (m) REVERT: G 290 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7406 (mp-120) outliers start: 23 outliers final: 13 residues processed: 137 average time/residue: 1.3148 time to fit residues: 195.1620 Evaluate side-chains 130 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 290 GLN Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12358 Z= 0.321 Angle : 0.571 8.847 16779 Z= 0.295 Chirality : 0.048 0.248 2056 Planarity : 0.004 0.033 2104 Dihedral : 5.119 53.794 1949 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.17 % Allowed : 13.41 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.47 (0.21), residues: 1540 helix: 1.84 (0.26), residues: 444 sheet: 0.54 (0.26), residues: 385 loop : -0.79 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS G 372 PHE 0.015 0.001 PHE A 330 TYR 0.026 0.002 TYR L 49 ARG 0.003 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 1.417 Fit side-chains REVERT: A 61 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8569 (mtp) REVERT: D 197 LEU cc_start: 0.8377 (tp) cc_final: 0.8016 (mt) REVERT: G 290 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7409 (mp-120) REVERT: H 16 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6742 (mt0) REVERT: H 75 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7943 (mmtp) outliers start: 30 outliers final: 14 residues processed: 128 average time/residue: 1.3495 time to fit residues: 186.7435 Evaluate side-chains 125 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain G residue 290 GLN Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 445 ILE Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.0370 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 116 optimal weight: 0.0980 chunk 135 optimal weight: 6.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 6 GLN H 16 GLN ** L 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12358 Z= 0.117 Angle : 0.460 6.840 16779 Z= 0.242 Chirality : 0.044 0.163 2056 Planarity : 0.004 0.033 2104 Dihedral : 4.772 54.383 1949 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.74 % Allowed : 14.35 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.70 (0.22), residues: 1540 helix: 2.18 (0.26), residues: 438 sheet: 0.55 (0.25), residues: 430 loop : -0.75 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.000 HIS H 96 PHE 0.007 0.001 PHE A 330 TYR 0.021 0.001 TYR L 49 ARG 0.005 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.406 Fit side-chains REVERT: A 61 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8431 (mtt) REVERT: D 197 LEU cc_start: 0.8252 (tp) cc_final: 0.7863 (mt) REVERT: G 181 THR cc_start: 0.8682 (m) cc_final: 0.8455 (m) REVERT: G 290 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7419 (mp-120) REVERT: L 75 ILE cc_start: 0.7261 (mt) cc_final: 0.6937 (mt) outliers start: 24 outliers final: 15 residues processed: 129 average time/residue: 1.3042 time to fit residues: 182.9424 Evaluate side-chains 128 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain G residue 290 GLN Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 16 GLN Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 16 GLN ** L 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12358 Z= 0.170 Angle : 0.487 6.988 16779 Z= 0.254 Chirality : 0.045 0.167 2056 Planarity : 0.004 0.031 2104 Dihedral : 4.761 53.986 1949 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.67 % Allowed : 14.42 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.71 (0.22), residues: 1540 helix: 2.23 (0.26), residues: 435 sheet: 0.56 (0.25), residues: 430 loop : -0.76 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.002 0.000 HIS G 102 PHE 0.010 0.001 PHE A 330 TYR 0.026 0.001 TYR L 49 ARG 0.004 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 1.437 Fit side-chains REVERT: A 61 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8442 (mtt) REVERT: D 197 LEU cc_start: 0.8296 (tp) cc_final: 0.7901 (mt) REVERT: G 181 THR cc_start: 0.8694 (m) cc_final: 0.8461 (m) REVERT: G 290 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7392 (mp-120) REVERT: L 75 ILE cc_start: 0.7239 (mt) cc_final: 0.6917 (mt) outliers start: 23 outliers final: 14 residues processed: 129 average time/residue: 1.3702 time to fit residues: 191.2833 Evaluate side-chains 126 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain G residue 290 GLN Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN ** L 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12358 Z= 0.173 Angle : 0.488 7.010 16779 Z= 0.254 Chirality : 0.045 0.164 2056 Planarity : 0.004 0.031 2104 Dihedral : 4.767 54.087 1949 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.38 % Allowed : 14.78 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.71 (0.22), residues: 1540 helix: 2.24 (0.26), residues: 435 sheet: 0.57 (0.25), residues: 430 loop : -0.78 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.002 0.001 HIS G 102 PHE 0.010 0.001 PHE A 330 TYR 0.023 0.001 TYR L 49 ARG 0.005 0.000 ARG A 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.361 Fit side-chains REVERT: A 61 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8447 (mtt) REVERT: D 197 LEU cc_start: 0.8318 (tp) cc_final: 0.7913 (mt) REVERT: G 181 THR cc_start: 0.8703 (m) cc_final: 0.8475 (m) REVERT: G 290 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7389 (mp-120) REVERT: L 75 ILE cc_start: 0.7238 (mt) cc_final: 0.6913 (mt) outliers start: 19 outliers final: 14 residues processed: 127 average time/residue: 1.3245 time to fit residues: 181.8786 Evaluate side-chains 127 residues out of total 1380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain G residue 290 GLN Chi-restraints excluded: chain G residue 350 ASN Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 474 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 60 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 3.9990 chunk 37 optimal weight: 0.0670 chunk 112 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 122 optimal weight: 0.1980 chunk 51 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.0070 chunk 107 optimal weight: 0.8980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 16 GLN ** L 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.090720 restraints weight = 17009.716| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.93 r_work: 0.3029 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12358 Z= 0.113 Angle : 0.452 6.787 16779 Z= 0.236 Chirality : 0.044 0.156 2056 Planarity : 0.003 0.031 2104 Dihedral : 4.596 54.112 1949 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.30 % Allowed : 14.93 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.82 (0.22), residues: 1540 helix: 2.37 (0.26), residues: 435 sheet: 0.60 (0.25), residues: 430 loop : -0.71 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.002 0.000 HIS G 102 PHE 0.006 0.001 PHE D 376 TYR 0.023 0.001 TYR L 49 ARG 0.005 0.000 ARG A 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4323.99 seconds wall clock time: 77 minutes 31.09 seconds (4651.09 seconds total)