Starting phenix.real_space_refine on Sat Mar 16 16:00:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlv_23911/03_2024/7mlv_23911.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlv_23911/03_2024/7mlv_23911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlv_23911/03_2024/7mlv_23911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlv_23911/03_2024/7mlv_23911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlv_23911/03_2024/7mlv_23911.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlv_23911/03_2024/7mlv_23911.pdb" } resolution = 4.1 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= 0.003 sd= 0.022 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 94 5.16 5 C 9653 2.51 5 N 2448 2.21 5 O 2860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 31": "NH1" <-> "NH2" Residue "K TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 31": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 72": "NH1" <-> "NH2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 119": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C ARG 399": "NH1" <-> "NH2" 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: 15055 Number of models: 1 Model: "" Number of chains: 16 Chain: "J" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 881 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 782 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 878 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 777 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 884 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 777 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 875 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 111} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1299 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 9, 'TRANS': 160} Chain breaks: 4 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 2456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2456 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 14, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2292 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 14, 'TRANS': 281} Chain breaks: 4 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 5, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 2125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2125 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 5 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 8.26, per 1000 atoms: 0.55 Number of scatterers: 15055 At special positions: 0 Unit cell: (154.462, 131.334, 118.944, 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 94 16.00 O 2860 8.00 N 2448 7.00 C 9653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " 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 Atom "HETATM14862 O5 NAG O 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 501 " - " MAN D 502 " " MAN P 5 " - " MAN P 6 " ALPHA1-3 " MAN D 501 " - " BMA D 503 " ~> Even though BMA is a beta isomer, an alpha linkage is required... " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA D 503 " - " MAN D 507 " " MAN D 504 " - " MAN D 507 " " BMA N 3 " - " MAN N 5 " " BMA P 3 " - " MAN P 4 " " MAN P 4 " - " MAN P 5 " BETA1-4 " BMA D 503 " - " NAG D 506 " " NAG D 505 " - " NAG D 506 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG N 1 " - " ASN A 38 " " NAG O 1 " - " ASN B 38 " " NAG P 1 " - " ASN C 38 " Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.8 seconds 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3558 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 38 sheets defined 14.3% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.956A pdb=" N LYS F 65 " --> pdb=" O GLU F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.813A pdb=" N ASP L 90 " --> pdb=" O THR L 87 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER L 91 " --> pdb=" O SER L 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 87 through 91' Processing helix chain 'D' and resid 10 through 16 removed outlier: 4.333A pdb=" N PHE D 13 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU D 14 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP D 15 " --> pdb=" O ASP D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.521A pdb=" N ALA D 74 " --> pdb=" O PRO D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 4.047A pdb=" N SER D 92 " --> pdb=" O MET D 89 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 93' Processing helix chain 'D' and resid 162 through 166 removed outlier: 4.001A pdb=" N ASP D 165 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.516A pdb=" N MET A 89 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 90' Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.830A pdb=" N VAL A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.602A pdb=" N LEU A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.850A pdb=" N SER A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 298 removed outlier: 4.375A pdb=" N ALA A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N CYS A 290 " --> pdb=" O TRP A 286 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 297 " --> pdb=" O PHE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 302 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 402 through 405 Processing helix chain 'A' and resid 406 through 417 removed outlier: 4.071A pdb=" N PHE A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TRP A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 18 removed outlier: 3.838A pdb=" N ASP B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B 17 " --> pdb=" O PHE B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.862A pdb=" N MET B 89 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.966A pdb=" N ILE B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.714A pdb=" N ILE B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 Processing helix chain 'B' and resid 281 through 282 No H-bonds generated for 'chain 'B' and resid 281 through 282' Processing helix chain 'B' and resid 284 through 284 No H-bonds generated for 'chain 'B' and resid 284 through 284' Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.633A pdb=" N PHE B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 403 through 417 removed outlier: 3.621A pdb=" N LEU B 407 " --> pdb=" O PRO B 403 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TYR B 417 " --> pdb=" O TYR B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.651A pdb=" N LEU C 73 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA C 74 " --> pdb=" O PRO C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 74' Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.943A pdb=" N SER C 92 " --> pdb=" O MET C 89 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 93' Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.760A pdb=" N SER C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.895A pdb=" N GLY C 269 " --> pdb=" O THR C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 297 removed outlier: 3.680A pdb=" N LEU C 291 " --> pdb=" O MET C 287 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 406 Proline residue: C 403 - end of helix Processing helix chain 'C' and resid 406 through 417 removed outlier: 4.057A pdb=" N MET C 411 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C 412 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.715A pdb=" N THR J 5 " --> pdb=" O LYS J 24 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS J 23 " --> pdb=" O TYR J 71 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.504A pdb=" N THR J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN J 37 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR J 36 " --> pdb=" O TYR J 87 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 62 through 63 removed outlier: 4.266A pdb=" N THR J 63 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR J 74 " --> pdb=" O THR J 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'G' and resid 19 through 21 removed outlier: 3.823A pdb=" N ILE G 20 " --> pdb=" O MET G 81 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET G 81 " --> pdb=" O ILE G 20 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR G 78 " --> pdb=" O GLU G 73 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU G 73 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 58 through 60 removed outlier: 3.858A pdb=" N ASN G 59 " --> pdb=" O GLU G 50 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU G 50 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TRP G 47 " --> pdb=" O LYS G 38 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA G 92 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU G 114 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 36 through 37 Processing sheet with id=AA8, first strand: chain 'K' and resid 65 through 67 Processing sheet with id=AA9, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.782A pdb=" N GLU F 10 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN F 39 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR F 95 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU F 37 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE F 34 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE F 51 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TRP F 36 " --> pdb=" O GLY F 49 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU F 50 " --> pdb=" O ASN F 59 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN F 59 " --> pdb=" O GLU F 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.950A pdb=" N ILE F 20 " --> pdb=" O MET F 81 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET F 81 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR F 78 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.987A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR M 49 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR M 87 " --> pdb=" O TYR M 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 62 through 67 removed outlier: 3.715A pdb=" N THR M 72 " --> pdb=" O SER M 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'L' and resid 46 through 51 removed outlier: 6.201A pdb=" N TRP L 47 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TRP L 36 " --> pdb=" O GLY L 49 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE L 51 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE L 34 " --> pdb=" O ILE L 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 68 through 73 removed outlier: 4.037A pdb=" N THR L 71 " --> pdb=" O TYR L 80 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU L 73 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR L 78 " --> pdb=" O GLU L 73 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 45 through 46 removed outlier: 3.640A pdb=" N GLN I 37 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU I 85 " --> pdb=" O GLN I 38 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR I 102 " --> pdb=" O TYR I 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 48 through 49 Processing sheet with id=AC2, first strand: chain 'I' and resid 63 through 66 Processing sheet with id=AC3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.822A pdb=" N GLN H 3 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.983A pdb=" N ILE H 20 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR H 78 " --> pdb=" O GLU H 73 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.611A pdb=" N ASN H 59 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE H 51 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR H 95 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU H 114 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR H 94 " --> pdb=" O THR H 112 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 39 through 41 removed outlier: 5.872A pdb=" N VAL D 39 " --> pdb=" O GLU D 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 61 through 68 removed outlier: 3.616A pdb=" N ILE D 132 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 64 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D 120 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 83 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 195 through 196 removed outlier: 3.881A pdb=" N ARG D 196 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU D 211 " --> pdb=" O ARG D 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 37 through 38 removed outlier: 5.912A pdb=" N VAL A 37 " --> pdb=" O ILE A 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 60 through 69 removed outlier: 3.527A pdb=" N TRP A 68 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.944A pdb=" N THR A 208 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.732A pdb=" N CYS A 152 " --> pdb=" O PHE A 214 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 214 " --> pdb=" O CYS A 152 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.722A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 125 through 137 removed outlier: 3.721A pdb=" N ILE B 130 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 62 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 134 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 60 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B 177 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE B 45 " --> pdb=" O GLN B 177 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.076A pdb=" N LEU B 83 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 118 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 150 through 155 removed outlier: 3.636A pdb=" N CYS B 152 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET B 154 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 212 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU B 217 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 131 through 132 removed outlier: 7.226A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 46 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 169 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.877A pdb=" N PHE C 99 " --> pdb=" O GLU C 157 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU C 157 " --> pdb=" O PHE C 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 149 through 152 removed outlier: 3.513A pdb=" N CYS C 152 " --> pdb=" O PHE C 214 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 200 through 201 258 hydrogen bonds defined for protein. 648 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: 3.89 Time building geometry restraints manager: 6.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2428 1.32 - 1.45: 4559 1.45 - 1.58: 8276 1.58 - 1.71: 1 1.71 - 1.84: 150 Bond restraints: 15414 Sorted by residual: bond pdb=" CA LEU D 64 " pdb=" C LEU D 64 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.25e-02 6.40e+03 4.60e+01 bond pdb=" CA ILE D 62 " pdb=" C ILE D 62 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.27e-02 6.20e+03 2.89e+01 bond pdb=" CA PHE D 63 " pdb=" C PHE D 63 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.34e-02 5.57e+03 2.21e+01 bond pdb=" C5 MAN D 507 " pdb=" O5 MAN D 507 " ideal model delta sigma weight residual 1.418 1.489 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C ILE C 28 " pdb=" N ARG C 29 " ideal model delta sigma weight residual 1.331 1.403 -0.072 2.07e-02 2.33e+03 1.21e+01 ... (remaining 15409 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.74: 508 106.74 - 113.56: 8260 113.56 - 120.38: 5434 120.38 - 127.20: 6556 127.20 - 134.02: 183 Bond angle restraints: 20941 Sorted by residual: angle pdb=" N LEU D 64 " pdb=" CA LEU D 64 " pdb=" C LEU D 64 " ideal model delta sigma weight residual 110.17 99.91 10.26 1.61e+00 3.86e-01 4.06e+01 angle pdb=" C TYR C 228 " pdb=" N ILE C 229 " pdb=" CA ILE C 229 " ideal model delta sigma weight residual 120.33 124.86 -4.53 8.00e-01 1.56e+00 3.21e+01 angle pdb=" N VAL A 253 " pdb=" CA VAL A 253 " pdb=" C VAL A 253 " ideal model delta sigma weight residual 112.90 108.16 4.74 9.60e-01 1.09e+00 2.44e+01 angle pdb=" C PRO C 185 " pdb=" N GLN C 186 " pdb=" CA GLN C 186 " ideal model delta sigma weight residual 121.54 130.92 -9.38 1.91e+00 2.74e-01 2.41e+01 angle pdb=" C VAL K 29 " pdb=" N SER K 30 " pdb=" CA SER K 30 " ideal model delta sigma weight residual 121.19 128.90 -7.71 1.59e+00 3.96e-01 2.35e+01 ... (remaining 20936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.49: 8891 23.49 - 46.99: 312 46.99 - 70.48: 33 70.48 - 93.97: 47 93.97 - 117.47: 34 Dihedral angle restraints: 9317 sinusoidal: 3769 harmonic: 5548 Sorted by residual: dihedral pdb=" CB CYS K 23 " pdb=" SG CYS K 23 " pdb=" SG CYS K 88 " pdb=" CB CYS K 88 " ideal model delta sinusoidal sigma weight residual 93.00 16.97 76.03 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 88 " pdb=" CB CYS J 88 " ideal model delta sinusoidal sigma weight residual 93.00 155.05 -62.05 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CA CYS C 198 " pdb=" C CYS C 198 " pdb=" N THR C 199 " pdb=" CA THR C 199 " ideal model delta harmonic sigma weight residual -180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 9314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 2388 0.164 - 0.328: 21 0.328 - 0.492: 1 0.492 - 0.657: 0 0.657 - 0.821: 1 Chirality restraints: 2411 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 38 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.68e+01 chirality pdb=" C1 MAN P 4 " pdb=" O6 BMA P 3 " pdb=" C2 MAN P 4 " pdb=" O5 MAN P 4 " both_signs ideal model delta sigma weight residual False 2.40 2.46 -0.06 2.00e-02 2.50e+03 9.99e+00 chirality pdb=" C1 BMA D 503 " pdb=" C2 BMA D 503 " pdb=" O5 BMA D 503 " pdb=" O4 NAG D 506 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 9.39e+00 ... (remaining 2408 not shown) Planarity restraints: 2589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 38 " -0.124 2.00e-02 2.50e+03 2.45e-01 7.49e+02 pdb=" CG ASN C 38 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN C 38 " 0.249 2.00e-02 2.50e+03 pdb=" ND2 ASN C 38 " -0.364 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.295 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 38 " 0.050 2.00e-02 2.50e+03 6.46e-02 5.22e+01 pdb=" CG ASN B 38 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 38 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B 38 " -0.109 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 61 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.58e+00 pdb=" C ASN D 61 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN D 61 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE D 62 " 0.017 2.00e-02 2.50e+03 ... (remaining 2586 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 645 2.71 - 3.26: 13255 3.26 - 3.81: 23360 3.81 - 4.35: 28119 4.35 - 4.90: 45532 Nonbonded interactions: 110911 Sorted by model distance: nonbonded pdb=" OG SER A 40 " pdb=" O7 NAG N 1 " model vdw 2.168 2.440 nonbonded pdb=" OD1 ASN D 38 " pdb=" C1 NAG D 505 " model vdw 2.194 3.470 nonbonded pdb=" OG SER J 14 " pdb=" OD2 ASP J 17 " model vdw 2.299 2.440 nonbonded pdb=" OG SER I 14 " pdb=" OD2 ASP I 17 " model vdw 2.303 2.440 nonbonded pdb=" OD1 ASN B 38 " pdb=" C8 NAG O 1 " model vdw 2.304 3.460 ... (remaining 110906 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 10 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 through 24 or (resid 25 through 28 and (na \ me N or name CA or name C or name O or name CB )) or resid 29 through 32 or (res \ id 33 and (name N or name CA or name C or name O or name CB )) or resid 34 throu \ gh 41 or (resid 42 through 43 and (name N or name CA or name C or name O or name \ CB )) or resid 44 through 49 or (resid 50 and (name N or name CA or name C or n \ ame O or name CB )) or resid 58 or (resid 59 through 60 and (name N or name CA o \ r name C or name O or name CB )) or resid 61 through 64 or (resid 65 and (name N \ or name CA or name C or name O or name CB )) or resid 66 through 75 or (resid 7 \ 6 through 77 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 8 through 83 or (resid 84 and (name N or name CA or name C or name O or name CB \ )) or resid 85 or (resid 86 and (name N or name CA or name C or name O or name C \ B )) or resid 87 or (resid 88 and (name N or name CA or name C or name O or name \ CB )) or resid 89 through 90 or (resid 91 and (name N or name CA or name C or n \ ame O or name CB )) or resid 92 through 94 or (resid 95 and (name N or name CA o \ r name C or name O or name CB )) or resid 96 through 103 or resid 115 through 12 \ 1 or (resid 122 through 123 and (name N or name CA or name C or name O or name C \ B )) or resid 124 through 131 or (resid 132 and (name N or name CA or name C or \ name O or name CB )) or resid 133 through 140 or (resid 141 and (name N or name \ CA or name C or name O or name CB )) or resid 142 through 144 or (resid 145 and \ (name N or name CA or name C or name O or name CB )) or resid 146 or (resid 147 \ through 149 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 0 through 155 or (resid 156 through 157 and (name N or name CA or name C or name \ O or name CB )) or resid 158 through 171 or (resid 172 through 173 and (name N \ or name CA or name C or name O or name CB )) or resid 174 through 185 or (resid \ 186 and (name N or name CA or name C or name O or name CB )) or resid 187 throug \ h 189 or (resid 190 through 192 and (name N or name CA or name C or name O or na \ me CB )) or resid 193 through 203 or (resid 204 and (name N or name CA or name C \ or name O or name CB )) or resid 205 through 210 or (resid 211 through 213 and \ (name N or name CA or name C or name O or name CB )) or resid 214 or (resid 215 \ and (name N or name CA or name C or name O or name CB )) or resid 216 or (resid \ 217 through 220 and (name N or name CA or name C or name O or name CB )) or resi \ d 221 through 223 or (resid 224 through 225 and (name N or name CA or name C or \ name O or name CB )) or resid 226 through 239 or resid 255 through 273 or resid \ 282 or resid 284 through 299 or resid 399 through 419)) selection = (chain 'B' and (resid 10 through 15 or (resid 16 and (name N or name CA or name \ C or name O or name CB )) or resid 17 through 19 or (resid 20 and (name N or nam \ e CA or name C or name O or name CB )) or resid 21 through 24 or (resid 25 throu \ gh 28 and (name N or name CA or name C or name O or name CB )) or resid 29 throu \ gh 31 or (resid 32 through 33 and (name N or name CA or name C or name O or name \ CB )) or resid 34 through 42 or (resid 43 and (name N or name CA or name C or n \ ame O or name CB )) or resid 44 through 49 or (resid 50 and (name N or name CA o \ r name C or name O or name CB )) or resid 58 or (resid 59 through 60 and (name N \ or name CA or name C or name O or name CB )) or resid 61 through 68 or (resid 6 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 70 through 7 \ 1 or (resid 72 and (name N or name CA or name C or name O or name CB )) or resid \ 73 through 115 or (resid 116 and (name N or name CA or name C or name O or name \ CB )) or resid 117 through 144 or (resid 145 and (name N or name CA or name C o \ r name O or name CB )) or resid 146 through 155 or (resid 156 through 157 and (n \ ame N or name CA or name C or name O or name CB )) or resid 158 through 171 or ( \ resid 172 through 173 and (name N or name CA or name C or name O or name CB )) o \ r resid 174 through 182 or (resid 183 and (name N or name CA or name C or name O \ or name CB )) or resid 184 through 188 or (resid 189 through 192 and (name N or \ name CA or name C or name O or name CB )) or resid 193 through 203 or (resid 20 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 205 through \ 210 or (resid 211 through 213 and (name N or name CA or name C or name O or name \ CB )) or resid 214 through 239 or resid 255 through 273 or resid 282 through 29 \ 9 or resid 399 through 419)) selection = (chain 'C' and (resid 10 through 31 or (resid 32 through 33 and (name N or name \ CA or name C or name O or name CB )) or resid 34 through 41 or (resid 42 through \ 43 and (name N or name CA or name C or name O or name CB )) or resid 44 through \ 59 or (resid 60 and (name N or name CA or name C or name O or name CB )) or res \ id 61 through 64 or (resid 65 and (name N or name CA or name C or name O or name \ CB )) or resid 66 through 68 or (resid 69 and (name N or name CA or name C or n \ ame O or name CB )) or resid 70 through 75 or (resid 76 through 77 and (name N o \ r name CA or name C or name O or name CB )) or resid 78 through 83 or (resid 84 \ and (name N or name CA or name C or name O or name CB )) or resid 85 or (resid 8 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 87 or (resid \ 88 and (name N or name CA or name C or name O or name CB )) or resid 89 through \ 90 or (resid 91 and (name N or name CA or name C or name O or name CB )) or res \ id 92 through 103 or resid 115 or (resid 116 and (name N or name CA or name C or \ name O or name CB )) or resid 117 through 121 or (resid 122 through 123 and (na \ me N or name CA or name C or name O or name CB )) or resid 124 through 131 or (r \ esid 132 and (name N or name CA or name C or name O or name CB )) or resid 133 t \ hrough 140 or (resid 141 and (name N or name CA or name C or name O or name CB ) \ ) or resid 142 through 147 or (resid 148 through 149 and (name N or name CA or n \ ame C or name O or name CB )) or resid 150 through 156 or (resid 157 and (name N \ or name CA or name C or name O or name CB )) or resid 158 through 182 or (resid \ 183 and (name N or name CA or name C or name O or name CB )) or resid 184 throu \ gh 188 or (resid 189 through 192 and (name N or name CA or name C or name O or n \ ame CB )) or resid 193 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 or (resid 215 and (name N or name CA or n \ ame C or name O or name CB )) or resid 216 through 218 or (resid 219 through 220 \ and (name N or name CA or name C or name O or name CB )) or resid 221 through 2 \ 23 or (resid 224 through 225 and (name N or name CA or name C or name O or name \ CB )) or resid 226 through 282 or resid 284 through 299 or resid 399 through 419 \ )) } ncs_group { reference = (chain 'F' and (resid 2 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 116)) selection = (chain 'G' and (resid 2 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 30 or (resid 31 and (name N or name \ CA or name C or name O or name CB )) or resid 32 through 116)) selection = (chain 'H' and (resid 2 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 116)) selection = (chain 'L' and (resid 2 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 116)) } ncs_group { reference = (chain 'I' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 60 or (resid 61 and (name N or name CA \ or name C or name O or name CB )) or resid 62 through 102)) selection = (chain 'J' and (resid 2 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 60 or (resid 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 102)) selection = (chain 'K' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 17 or (resid 18 and (name N or name CA \ or name C or name O or name CB )) or resid 19 through 60 or (resid 61 and (name \ N or name CA or name C or name O or name CB )) or resid 62 through 91 or (resid \ 92 and (name N or name CA or name C or name O or name CB )) or resid 93 through \ 102)) selection = (chain 'M' and (resid 2 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 17 or (resid 18 and (name N or name CA \ or name C or name O or name CB )) or resid 19 through 102)) } 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 group one per residue 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: 4.690 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: 13.620 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 39.690 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.080 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4164 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 : 0.005 0.085 15414 Z= 0.310 Angle : 1.025 11.407 20941 Z= 0.526 Chirality : 0.058 0.821 2411 Planarity : 0.007 0.068 2586 Dihedral : 15.502 117.467 5714 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.14 (0.14), residues: 1865 helix: -4.75 (0.12), residues: 227 sheet: -2.77 (0.21), residues: 494 loop : -3.60 (0.13), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 50 HIS 0.004 0.001 HIS L 27 PHE 0.022 0.002 PHE H 105 TYR 0.018 0.002 TYR C 58 ARG 0.009 0.001 ARG C 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 55 HIS cc_start: 0.5158 (t-90) cc_final: 0.4623 (t70) REVERT: F 98 MET cc_start: 0.2150 (ttp) cc_final: 0.0941 (mtp) REVERT: I 4 MET cc_start: 0.3514 (tmm) cc_final: 0.2581 (tpt) REVERT: B 257 ILE cc_start: 0.7469 (mt) cc_final: 0.7174 (mm) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.3279 time to fit residues: 112.7698 Evaluate side-chains 145 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 89 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN K 89 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 HIS ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN A 125 ASN B 115 ASN B 150 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5098 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 15414 Z= 0.382 Angle : 0.886 13.255 20941 Z= 0.441 Chirality : 0.052 0.304 2411 Planarity : 0.006 0.086 2586 Dihedral : 13.396 110.275 2486 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.64 % Allowed : 5.59 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.16), residues: 1865 helix: -3.05 (0.25), residues: 239 sheet: -2.74 (0.20), residues: 533 loop : -2.88 (0.16), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 94 HIS 0.011 0.002 HIS C 215 PHE 0.032 0.003 PHE G 70 TYR 0.030 0.003 TYR H 80 ARG 0.024 0.001 ARG M 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 101 ARG cc_start: 0.4662 (tpt170) cc_final: 0.4251 (tpt170) REVERT: K 4 MET cc_start: 0.3529 (mmm) cc_final: 0.2930 (mmm) REVERT: I 4 MET cc_start: 0.3795 (tmm) cc_final: 0.2707 (tpt) REVERT: I 11 MET cc_start: 0.3248 (mpp) cc_final: 0.2658 (mmt) REVERT: I 53 THR cc_start: 0.7439 (m) cc_final: 0.7162 (m) outliers start: 10 outliers final: 0 residues processed: 180 average time/residue: 0.3281 time to fit residues: 84.5780 Evaluate side-chains 131 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5557 moved from start: 0.6219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 15414 Z= 0.354 Angle : 0.837 14.548 20941 Z= 0.418 Chirality : 0.050 0.372 2411 Planarity : 0.006 0.096 2586 Dihedral : 12.976 113.657 2486 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 25.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 0.39 % Allowed : 5.98 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.17), residues: 1865 helix: -2.28 (0.31), residues: 228 sheet: -2.73 (0.21), residues: 509 loop : -2.70 (0.16), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP B 239 HIS 0.008 0.002 HIS B 201 PHE 0.027 0.003 PHE B 242 TYR 0.023 0.002 TYR A 228 ARG 0.010 0.001 ARG M 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 1.747 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: K 4 MET cc_start: 0.3985 (mmm) cc_final: 0.2839 (mmm) REVERT: K 55 HIS cc_start: 0.8397 (t-90) cc_final: 0.8158 (t70) REVERT: I 4 MET cc_start: 0.4405 (tmm) cc_final: 0.3379 (tpt) REVERT: H 114 LEU cc_start: 0.8003 (mm) cc_final: 0.7730 (mm) REVERT: D 18 MET cc_start: 0.2677 (ttm) cc_final: 0.2407 (ttm) REVERT: A 81 ASP cc_start: 0.6733 (t0) cc_final: 0.6413 (t0) REVERT: A 411 MET cc_start: 0.7697 (ppp) cc_final: 0.7483 (ppp) outliers start: 6 outliers final: 3 residues processed: 161 average time/residue: 0.3016 time to fit residues: 69.6011 Evaluate side-chains 129 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.0980 chunk 128 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 171 optimal weight: 8.9990 chunk 181 optimal weight: 40.0000 chunk 89 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 90 GLN ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 HIS ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5724 moved from start: 0.7309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15414 Z= 0.342 Angle : 0.768 11.746 20941 Z= 0.381 Chirality : 0.048 0.304 2411 Planarity : 0.005 0.081 2586 Dihedral : 11.551 111.821 2486 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 26.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 0.06 % Allowed : 4.63 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.18), residues: 1865 helix: -1.70 (0.32), residues: 251 sheet: -2.67 (0.23), residues: 458 loop : -2.52 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP G 33 HIS 0.011 0.002 HIS J 91 PHE 0.026 0.002 PHE A 100 TYR 0.024 0.002 TYR A 417 ARG 0.021 0.001 ARG F 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 1.828 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: K 55 HIS cc_start: 0.8545 (t-90) cc_final: 0.8316 (t70) REVERT: I 4 MET cc_start: 0.4755 (tmm) cc_final: 0.3417 (tpt) REVERT: D 18 MET cc_start: 0.3300 (ttm) cc_final: 0.2942 (ttm) REVERT: D 64 LEU cc_start: 0.7640 (tp) cc_final: 0.7354 (tt) REVERT: D 163 MET cc_start: 0.6808 (mtm) cc_final: 0.5894 (mtm) REVERT: A 81 ASP cc_start: 0.6784 (t0) cc_final: 0.6485 (t0) REVERT: A 263 MET cc_start: 0.7911 (tmm) cc_final: 0.7637 (tmm) REVERT: A 411 MET cc_start: 0.7707 (ppp) cc_final: 0.7397 (ppp) REVERT: B 200 LYS cc_start: 0.7440 (mtmm) cc_final: 0.6577 (mttt) REVERT: C 89 MET cc_start: 0.6328 (mmm) cc_final: 0.6087 (mmt) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.2848 time to fit residues: 62.1557 Evaluate side-chains 120 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN B 226 GLN C 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5889 moved from start: 0.8448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15414 Z= 0.331 Angle : 0.798 12.741 20941 Z= 0.395 Chirality : 0.049 0.309 2411 Planarity : 0.005 0.077 2586 Dihedral : 11.106 114.037 2486 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 30.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.18), residues: 1865 helix: -1.36 (0.33), residues: 233 sheet: -2.87 (0.21), residues: 489 loop : -2.44 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 33 HIS 0.017 0.002 HIS J 91 PHE 0.021 0.002 PHE C 99 TYR 0.030 0.003 TYR D 197 ARG 0.010 0.001 ARG G 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.449 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: J 49 TYR cc_start: 0.7492 (p90) cc_final: 0.7178 (p90) REVERT: F 98 MET cc_start: 0.5217 (tmm) cc_final: 0.4995 (ttp) REVERT: I 4 MET cc_start: 0.4351 (tmm) cc_final: 0.2912 (tpt) REVERT: H 98 MET cc_start: 0.7120 (ttp) cc_final: 0.6848 (tmm) REVERT: D 64 LEU cc_start: 0.7685 (tp) cc_final: 0.7446 (tt) REVERT: A 411 MET cc_start: 0.7745 (ppp) cc_final: 0.7506 (ppp) REVERT: C 18 MET cc_start: 0.8362 (mmm) cc_final: 0.7837 (mpp) REVERT: C 89 MET cc_start: 0.6943 (mmm) cc_final: 0.6626 (mmt) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2784 time to fit residues: 54.3603 Evaluate side-chains 115 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 35 optimal weight: 30.0000 chunk 106 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 181 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.8709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15414 Z= 0.275 Angle : 0.730 13.164 20941 Z= 0.356 Chirality : 0.046 0.291 2411 Planarity : 0.004 0.053 2586 Dihedral : 10.485 108.849 2486 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 27.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.18), residues: 1865 helix: -1.14 (0.34), residues: 238 sheet: -2.89 (0.21), residues: 496 loop : -2.44 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 33 HIS 0.012 0.002 HIS J 91 PHE 0.019 0.002 PHE A 100 TYR 0.022 0.002 TYR J 49 ARG 0.010 0.001 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.426 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: I 4 MET cc_start: 0.4394 (tmm) cc_final: 0.2940 (tpt) REVERT: A 411 MET cc_start: 0.7768 (ppp) cc_final: 0.7492 (ppp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2709 time to fit residues: 49.9601 Evaluate side-chains 109 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 chunk 102 optimal weight: 20.0000 chunk 153 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 181 optimal weight: 0.0770 chunk 113 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 overall best weight: 1.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN L 6 GLN ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5763 moved from start: 0.8705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15414 Z= 0.171 Angle : 0.692 12.466 20941 Z= 0.328 Chirality : 0.045 0.288 2411 Planarity : 0.004 0.052 2586 Dihedral : 9.871 104.607 2486 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.18), residues: 1865 helix: -0.97 (0.35), residues: 236 sheet: -2.66 (0.21), residues: 506 loop : -2.27 (0.17), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 33 HIS 0.007 0.001 HIS J 91 PHE 0.017 0.001 PHE A 99 TYR 0.020 0.002 TYR J 49 ARG 0.011 0.001 ARG B 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.654 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: G 101 ARG cc_start: 0.6035 (tpt170) cc_final: 0.5547 (tpt170) REVERT: K 55 HIS cc_start: 0.8292 (t70) cc_final: 0.7988 (t70) REVERT: F 81 MET cc_start: 0.6483 (mmm) cc_final: 0.5671 (mmm) REVERT: I 4 MET cc_start: 0.2416 (tmm) cc_final: 0.1512 (tpt) REVERT: H 114 LEU cc_start: 0.8100 (mm) cc_final: 0.7358 (mm) REVERT: A 81 ASP cc_start: 0.7155 (t0) cc_final: 0.6875 (t0) REVERT: A 411 MET cc_start: 0.7778 (ppp) cc_final: 0.7473 (ppp) REVERT: C 18 MET cc_start: 0.8624 (mmm) cc_final: 0.8423 (mmm) REVERT: C 89 MET cc_start: 0.6796 (mmm) cc_final: 0.6543 (mmt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2703 time to fit residues: 52.4281 Evaluate side-chains 117 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 40.0000 chunk 115 optimal weight: 0.7980 chunk 123 optimal weight: 40.0000 chunk 89 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 142 optimal weight: 20.0000 chunk 164 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 moved from start: 0.8723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15414 Z= 0.157 Angle : 0.680 11.321 20941 Z= 0.321 Chirality : 0.045 0.283 2411 Planarity : 0.004 0.052 2586 Dihedral : 9.355 101.524 2486 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.06 % Allowed : 1.67 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.18), residues: 1865 helix: -0.88 (0.35), residues: 236 sheet: -2.58 (0.22), residues: 497 loop : -2.26 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 33 HIS 0.006 0.001 HIS J 91 PHE 0.019 0.001 PHE I 62 TYR 0.019 0.002 TYR D 128 ARG 0.006 0.001 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 132 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 MET cc_start: 0.3472 (pmm) cc_final: 0.2362 (pmm) REVERT: F 81 MET cc_start: 0.6662 (mmm) cc_final: 0.5937 (mmm) REVERT: I 4 MET cc_start: 0.2502 (tmm) cc_final: 0.1919 (tpp) REVERT: H 90 ASP cc_start: 0.7053 (t0) cc_final: 0.6844 (t0) REVERT: A 81 ASP cc_start: 0.7038 (t0) cc_final: 0.6752 (t0) REVERT: A 411 MET cc_start: 0.7762 (ppp) cc_final: 0.7436 (ppp) REVERT: C 89 MET cc_start: 0.6756 (mmm) cc_final: 0.6508 (mmt) REVERT: C 163 MET cc_start: 0.6166 (mmp) cc_final: 0.5594 (mmt) REVERT: C 404 MET cc_start: 0.8169 (ptt) cc_final: 0.7917 (ppp) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.2666 time to fit residues: 53.1651 Evaluate side-chains 115 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 168 optimal weight: 0.0370 chunk 101 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 51 optimal weight: 0.4980 chunk 152 optimal weight: 10.0000 chunk 159 optimal weight: 50.0000 chunk 110 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 overall best weight: 5.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 HIS ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 115 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 HIS A 67 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.9617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15414 Z= 0.328 Angle : 0.782 12.754 20941 Z= 0.383 Chirality : 0.048 0.293 2411 Planarity : 0.005 0.052 2586 Dihedral : 9.159 95.557 2486 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 31.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.64 % Favored : 88.36 % Rotamer: Outliers : 0.06 % Allowed : 1.41 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.18), residues: 1865 helix: -0.72 (0.35), residues: 236 sheet: -2.89 (0.20), residues: 543 loop : -2.34 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 33 HIS 0.015 0.002 HIS J 91 PHE 0.030 0.002 PHE A 145 TYR 0.026 0.003 TYR I 87 ARG 0.009 0.001 ARG F 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 55 HIS cc_start: 0.8495 (t-90) cc_final: 0.8155 (t70) REVERT: I 4 MET cc_start: 0.2760 (tmm) cc_final: 0.2506 (tpp) REVERT: A 411 MET cc_start: 0.7798 (ppp) cc_final: 0.7475 (ppp) REVERT: C 163 MET cc_start: 0.6448 (mmp) cc_final: 0.5861 (mmt) REVERT: C 404 MET cc_start: 0.8239 (ptt) cc_final: 0.7968 (ppp) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.2600 time to fit residues: 48.9603 Evaluate side-chains 106 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 30.0000 chunk 124 optimal weight: 0.1980 chunk 187 optimal weight: 30.0000 chunk 172 optimal weight: 5.9990 chunk 149 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.9629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15414 Z= 0.201 Angle : 0.721 12.563 20941 Z= 0.342 Chirality : 0.046 0.289 2411 Planarity : 0.004 0.051 2586 Dihedral : 8.842 92.478 2486 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.18), residues: 1865 helix: -0.72 (0.36), residues: 241 sheet: -2.73 (0.21), residues: 501 loop : -2.30 (0.17), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 33 HIS 0.010 0.001 HIS J 91 PHE 0.017 0.001 PHE A 99 TYR 0.017 0.002 TYR A 228 ARG 0.007 0.001 ARG J 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3730 Ramachandran restraints generated. 1865 Oldfield, 0 Emsley, 1865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 55 HIS cc_start: 0.8472 (t-90) cc_final: 0.8181 (t70) REVERT: F 81 MET cc_start: 0.6506 (mmm) cc_final: 0.6215 (mmm) REVERT: A 411 MET cc_start: 0.7780 (ppp) cc_final: 0.7453 (ppp) REVERT: C 163 MET cc_start: 0.6471 (mmp) cc_final: 0.6111 (mmt) REVERT: C 404 MET cc_start: 0.8209 (ptt) cc_final: 0.7985 (ppp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2597 time to fit residues: 49.6514 Evaluate side-chains 108 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 22 optimal weight: 40.0000 chunk 41 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 ASN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN B 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.046663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.038531 restraints weight = 214530.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.038774 restraints weight = 187680.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.038969 restraints weight = 147066.228| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 1.0339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15414 Z= 0.342 Angle : 0.797 13.092 20941 Z= 0.388 Chirality : 0.048 0.294 2411 Planarity : 0.005 0.052 2586 Dihedral : 8.734 85.762 2486 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 32.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.18), residues: 1865 helix: -0.76 (0.36), residues: 235 sheet: -3.03 (0.19), residues: 561 loop : -2.27 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP G 33 HIS 0.015 0.002 HIS J 91 PHE 0.022 0.002 PHE A 100 TYR 0.022 0.003 TYR I 87 ARG 0.007 0.001 ARG F 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2613.07 seconds wall clock time: 49 minutes 3.56 seconds (2943.56 seconds total)