Starting phenix.real_space_refine on Thu Nov 16 10:13:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlv_23911/11_2023/7mlv_23911.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlv_23911/11_2023/7mlv_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_23911/11_2023/7mlv_23911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlv_23911/11_2023/7mlv_23911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlv_23911/11_2023/7mlv_23911.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mlv_23911/11_2023/7mlv_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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 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 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 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 chiralities: 7 Time building chain proxies: 8.33, 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: 6.41 Conformation dependent library (CDL) restraints added in 2.7 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: 1.62 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: 3.80 Time building geometry restraints manager: 6.84 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 - 15.33: 8287 15.33 - 30.66: 451 30.66 - 45.99: 117 45.99 - 61.32: 13 61.32 - 76.65: 15 Dihedral angle restraints: 8883 sinusoidal: 3335 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 8880 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: 5.320 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: 0.020 Extract box with map and model: 13.880 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 40.580 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.060 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.060 ------------------------------------------------------------------------------- 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 : 10.905 76.646 5280 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 *********************** 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 : 1.782 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 outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.3291 time to fit residues: 112.9476 Evaluate side-chains 144 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.670 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1737 ------------------------------------------------------------------------------- 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 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 HIS ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5067 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 15414 Z= 0.384 Angle : 0.842 13.014 20941 Z= 0.425 Chirality : 0.050 0.393 2411 Planarity : 0.006 0.079 2586 Dihedral : 5.894 23.083 2052 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.45 % Allowed : 5.53 % Favored : 94.02 % 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: -4.30 (0.16), residues: 1865 helix: -3.17 (0.25), residues: 237 sheet: -2.71 (0.20), residues: 523 loop : -2.94 (0.15), residues: 1105 *********************** 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 178 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 171 time to evaluate : 1.830 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 outliers start: 7 outliers final: 0 residues processed: 177 average time/residue: 0.3237 time to fit residues: 81.3034 Evaluate side-chains 132 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.832 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3194 ------------------------------------------------------------------------------- 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: 5.9990 chunk 116 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 152 optimal weight: 0.5980 chunk 169 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** 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** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN ** 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** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5322 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 15414 Z= 0.265 Angle : 0.723 13.481 20941 Z= 0.359 Chirality : 0.046 0.356 2411 Planarity : 0.005 0.118 2586 Dihedral : 5.789 23.187 2052 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % 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: -2.44 (0.30), residues: 237 sheet: -2.62 (0.21), residues: 508 loop : -2.73 (0.16), residues: 1120 *********************** 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 166 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.3073 time to fit residues: 73.5802 Evaluate side-chains 129 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.679 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4184 ------------------------------------------------------------------------------- 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: 2.9990 chunk 128 optimal weight: 0.0030 chunk 88 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** 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 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** ** 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5494 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 15414 Z= 0.278 Angle : 0.696 14.085 20941 Z= 0.345 Chirality : 0.045 0.298 2411 Planarity : 0.004 0.053 2586 Dihedral : 5.678 27.379 2052 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % 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: -3.62 (0.18), residues: 1865 helix: -1.89 (0.31), residues: 248 sheet: -2.60 (0.21), residues: 533 loop : -2.46 (0.17), residues: 1084 *********************** 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 151 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2980 time to fit residues: 65.3296 Evaluate side-chains 120 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.715 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2464 ------------------------------------------------------------------------------- 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: 0.8980 chunk 103 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 163 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 HIS ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** 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 46 ASN ** 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 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN C 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.8228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 15414 Z= 0.407 Angle : 0.854 15.251 20941 Z= 0.428 Chirality : 0.050 0.338 2411 Planarity : 0.006 0.098 2586 Dihedral : 6.335 24.640 2052 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 33.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % 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: -3.61 (0.18), residues: 1865 helix: -1.40 (0.33), residues: 236 sheet: -2.94 (0.21), residues: 506 loop : -2.40 (0.17), residues: 1123 *********************** 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 134 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.3199 time to fit residues: 64.4503 Evaluate side-chains 110 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.749 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2527 ------------------------------------------------------------------------------- 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: 20.0000 chunk 163 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 95 optimal weight: 0.0570 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 ASN A 150 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5695 moved from start: 0.8047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15414 Z= 0.184 Angle : 0.692 11.749 20941 Z= 0.334 Chirality : 0.045 0.317 2411 Planarity : 0.004 0.049 2586 Dihedral : 5.793 24.736 2052 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.06 % Allowed : 2.32 % Favored : 97.62 % 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: -3.33 (0.18), residues: 1865 helix: -1.20 (0.34), residues: 234 sheet: -2.67 (0.22), residues: 483 loop : -2.29 (0.17), residues: 1148 *********************** 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 141 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.2889 time to fit residues: 60.5175 Evaluate side-chains 116 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.853 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4361 ------------------------------------------------------------------------------- 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: 10.0000 chunk 20 optimal weight: 4.9990 chunk 103 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 55 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 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.8682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15414 Z= 0.276 Angle : 0.713 12.162 20941 Z= 0.352 Chirality : 0.045 0.322 2411 Planarity : 0.005 0.059 2586 Dihedral : 5.828 23.680 2052 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 27.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: -3.31 (0.18), residues: 1865 helix: -0.92 (0.34), residues: 236 sheet: -2.77 (0.21), residues: 519 loop : -2.23 (0.18), residues: 1110 *********************** 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 127 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2852 time to fit residues: 54.4973 Evaluate side-chains 109 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.743 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2804 ------------------------------------------------------------------------------- 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: 5.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 123 optimal weight: 30.0000 chunk 89 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 142 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 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** I 6 GLN ** 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 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5821 moved from start: 0.8882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15414 Z= 0.211 Angle : 0.689 11.854 20941 Z= 0.333 Chirality : 0.045 0.317 2411 Planarity : 0.004 0.048 2586 Dihedral : 5.705 24.371 2052 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: -3.28 (0.18), residues: 1865 helix: -0.79 (0.35), residues: 235 sheet: -2.74 (0.21), residues: 511 loop : -2.25 (0.17), residues: 1119 *********************** 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 125 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2498 time to fit residues: 47.8115 Evaluate side-chains 109 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.627 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1321 ------------------------------------------------------------------------------- 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: 9.9990 chunk 158 optimal weight: 5.9990 chunk 168 optimal weight: 0.6980 chunk 101 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 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** ** 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** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.9411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15414 Z= 0.275 Angle : 0.725 11.967 20941 Z= 0.353 Chirality : 0.046 0.323 2411 Planarity : 0.004 0.050 2586 Dihedral : 5.810 23.307 2052 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 27.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: -3.33 (0.18), residues: 1865 helix: -0.68 (0.35), residues: 235 sheet: -2.83 (0.21), residues: 497 loop : -2.31 (0.17), residues: 1133 *********************** 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: 0 poor density : 124 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.2608 time to fit residues: 50.1538 Evaluate side-chains 104 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.778 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3136 ------------------------------------------------------------------------------- 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: 8.9990 chunk 84 optimal weight: 10.0000 chunk 124 optimal weight: 0.4980 chunk 187 optimal weight: 0.7980 chunk 172 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 chunk 15 optimal weight: 0.2980 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 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** ** 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 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN B 226 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5754 moved from start: 0.9291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15414 Z= 0.167 Angle : 0.689 10.940 20941 Z= 0.327 Chirality : 0.045 0.315 2411 Planarity : 0.004 0.043 2586 Dihedral : 5.497 25.039 2052 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.06 % Allowed : 0.06 % Favored : 99.87 % 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: -3.21 (0.18), residues: 1865 helix: -0.80 (0.35), residues: 245 sheet: -2.68 (0.21), residues: 523 loop : -2.20 (0.18), residues: 1097 ********************** 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 130 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.2840 time to fit residues: 55.7244 Evaluate side-chains 109 residues out of total 1673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.815 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2922 ------------------------------------------------------------------------------- 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: 8.9990 chunk 137 optimal weight: 10.0000 chunk 22 optimal weight: 30.0000 chunk 41 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 131 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 55 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** ** 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 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** ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.047229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.039146 restraints weight = 214497.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.039436 restraints weight = 174921.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.039640 restraints weight = 144546.869| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.9984 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= 0.310 Angle : 0.753 11.519 20941 Z= 0.368 Chirality : 0.046 0.329 2411 Planarity : 0.005 0.066 2586 Dihedral : 5.787 23.440 2052 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 29.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % 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: -3.33 (0.18), residues: 1865 helix: -0.72 (0.35), residues: 245 sheet: -2.80 (0.20), residues: 505 loop : -2.31 (0.17), residues: 1115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2695.24 seconds wall clock time: 50 minutes 56.69 seconds (3056.69 seconds total)