Starting phenix.real_space_refine on Mon Mar 18 05:49:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv7_20487/03_2024/6pv7_20487.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv7_20487/03_2024/6pv7_20487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv7_20487/03_2024/6pv7_20487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv7_20487/03_2024/6pv7_20487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv7_20487/03_2024/6pv7_20487.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pv7_20487/03_2024/6pv7_20487.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 127 5.16 5 Na 1 4.78 5 C 13106 2.51 5 N 3094 2.21 5 O 3720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "D ARG 10": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D ARG 327": "NH1" <-> "NH2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 314": "NH1" <-> "NH2" Residue "E ARG 328": "NH1" <-> "NH2" Residue "E ARG 400": "NH1" <-> "NH2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "H ARG 57": "NH1" <-> "NH2" Residue "I ARG 84": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20048 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3167 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367} Chain breaks: 1 Chain: "B" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3149 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Chain: "C" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3126 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 363} Chain breaks: 1 Chain: "D" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3167 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 367} Chain breaks: 1 Chain: "E" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3149 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Chain: "F" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 911 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "G" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 911 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "I" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 99} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 69 Unusual residues: {' NA': 1, 'NCT': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 2, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 93 Unusual residues: {'DD9': 1, 'NAG': 2, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {'NCT': 1, 'Y01': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 2, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-2': 2, 'Y01:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 10.90, per 1000 atoms: 0.54 Number of scatterers: 20048 At special positions: 0 Unit cell: (151.94, 167.99, 157.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 127 16.00 Na 1 11.00 O 3720 8.00 N 3094 7.00 C 13106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.05 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 146 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 146 " distance=2.04 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.05 Simple disulfide: pdb=" SG CYS E 132 " - pdb=" SG CYS E 146 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS G 45 " - pdb=" SG CYS G 109 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS I 45 " - pdb=" SG CYS I 109 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA K 3 " - " MAN K 5 " " BMA M 3 " - " MAN M 5 " " BMA O 3 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " NAG-ASN " NAG B 701 " - " ASN B 15 " " NAG B 702 " - " ASN B 72 " " NAG C 701 " - " ASN C 15 " " NAG C 702 " - " ASN C 72 " " NAG E 701 " - " ASN E 15 " " NAG E 702 " - " ASN E 72 " " NAG J 1 " - " ASN A 24 " " NAG K 1 " - " ASN A 141 " " NAG L 1 " - " ASN B 117 " " NAG M 1 " - " ASN B 145 " " NAG N 1 " - " ASN C 117 " " NAG O 1 " - " ASN C 145 " " NAG P 1 " - " ASN D 24 " " NAG Q 1 " - " ASN D 141 " " NAG R 1 " - " ASN E 117 " " NAG S 1 " - " ASN E 145 " Time building additional restraints: 8.60 Conformation dependent library (CDL) restraints added in 3.8 seconds 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4570 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 31 sheets defined 33.2% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.759A pdb=" N PHE A 12 " --> pdb=" O PHE A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 227 through 228 No H-bonds generated for 'chain 'A' and resid 227 through 228' Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.727A pdb=" N PHE A 232 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A 233 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 263 removed outlier: 3.657A pdb=" N LEU A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 299 removed outlier: 3.948A pdb=" N PHE A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.899A pdb=" N THR A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.794A pdb=" N VAL A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 463 removed outlier: 3.651A pdb=" N ALA A 441 " --> pdb=" O TRP A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 14 removed outlier: 3.584A pdb=" N LYS B 8 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 14 " --> pdb=" O MET B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 228 removed outlier: 5.575A pdb=" N ILE B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 241 through 264 removed outlier: 3.885A pdb=" N LEU B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 298 removed outlier: 3.675A pdb=" N VAL B 298 " --> pdb=" O CYS B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 401 through 457 removed outlier: 4.102A pdb=" N GLU B 405 " --> pdb=" O GLN B 401 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 406 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 14 Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.964A pdb=" N ARG C 75 " --> pdb=" O ASN C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.538A pdb=" N ILE C 89 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 removed outlier: 3.588A pdb=" N ILE C 219 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 225 Processing helix chain 'C' and resid 241 through 261 removed outlier: 3.905A pdb=" N LEU C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 298 removed outlier: 3.858A pdb=" N CYS C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 401 through 457 removed outlier: 4.266A pdb=" N GLU C 405 " --> pdb=" O GLN C 401 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA C 406 " --> pdb=" O ASP C 402 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 407 " --> pdb=" O VAL C 403 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE C 447 " --> pdb=" O TRP C 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.750A pdb=" N PHE D 12 " --> pdb=" O PHE D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 72 removed outlier: 3.593A pdb=" N ASP D 71 " --> pdb=" O ASN D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 230 through 234 removed outlier: 3.765A pdb=" N TYR D 233 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 263 removed outlier: 4.019A pdb=" N LEU D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 299 Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.849A pdb=" N THR D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 323 removed outlier: 3.646A pdb=" N ARG D 321 " --> pdb=" O ASN D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 464 removed outlier: 3.673A pdb=" N ALA D 441 " --> pdb=" O TRP D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 469 removed outlier: 3.574A pdb=" N LEU D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 14 removed outlier: 3.595A pdb=" N LYS E 8 " --> pdb=" O ASN E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.692A pdb=" N ILE E 89 " --> pdb=" O ALA E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 218 removed outlier: 3.568A pdb=" N ILE E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 230 removed outlier: 4.084A pdb=" N ILE E 230 " --> pdb=" O THR E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 264 removed outlier: 3.984A pdb=" N LEU E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N CYS E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS E 262 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 264 " --> pdb=" O ILE E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 298 removed outlier: 3.958A pdb=" N VAL E 298 " --> pdb=" O CYS E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 316 removed outlier: 3.728A pdb=" N PHE E 316 " --> pdb=" O VAL E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 324 removed outlier: 3.729A pdb=" N THR E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 457 removed outlier: 3.889A pdb=" N GLU E 405 " --> pdb=" O GLN E 401 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA E 406 " --> pdb=" O ASP E 402 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 407 " --> pdb=" O VAL E 403 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 110 removed outlier: 3.611A pdb=" N ASP F 109 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER F 110 " --> pdb=" O SER F 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 110' Processing helix chain 'H' and resid 81 through 84 removed outlier: 4.103A pdb=" N LYS H 84 " --> pdb=" O GLN H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.557A pdb=" N ASP H 109 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 110' Processing helix chain 'I' and resid 100 through 104 removed outlier: 4.142A pdb=" N ALA I 104 " --> pdb=" O ALA I 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 3.885A pdb=" N GLU A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 3.885A pdb=" N GLU A 115 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 42 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASN A 53 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU A 40 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N TRP A 55 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N SER A 38 " --> pdb=" O TRP A 55 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LYS A 57 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N SER A 36 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE A 59 " --> pdb=" O GLU A 34 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N GLU A 34 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N ASN A 61 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N HIS A 32 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 146 removed outlier: 6.993A pdb=" N TYR A 205 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 139 through 146 Processing sheet with id=AA5, first strand: chain 'B' and resid 81 through 85 removed outlier: 4.469A pdb=" N SER B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 126 " --> pdb=" O VAL B 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 81 through 85 removed outlier: 4.469A pdb=" N SER B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 46 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASN B 57 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU B 44 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N TRP B 59 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ALA B 42 " --> pdb=" O TRP B 59 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LYS B 61 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER B 40 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLU B 63 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N GLN B 38 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N THR B 65 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N LYS B 36 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 96 removed outlier: 7.608A pdb=" N ILE B 206 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 183 " --> pdb=" O ILE B 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AA9, first strand: chain 'C' and resid 113 through 114 removed outlier: 5.090A pdb=" N THR C 65 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N SER C 34 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE C 33 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL C 163 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE C 35 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 48 removed outlier: 6.277A pdb=" N LEU C 44 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ASN C 57 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 46 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 94 through 96 removed outlier: 7.172A pdb=" N ILE C 206 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 96 Processing sheet with id=AB4, first strand: chain 'D' and resid 109 through 110 Processing sheet with id=AB5, first strand: chain 'D' and resid 109 through 110 removed outlier: 3.605A pdb=" N LYS D 42 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASN D 53 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU D 40 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N TRP D 55 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N SER D 38 " --> pdb=" O TRP D 55 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LYS D 57 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N SER D 36 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE D 59 " --> pdb=" O GLU D 34 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N GLU D 34 " --> pdb=" O ILE D 59 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 139 through 147 removed outlier: 7.183A pdb=" N TYR D 205 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 139 through 147 Processing sheet with id=AB8, first strand: chain 'E' and resid 82 through 84 Processing sheet with id=AB9, first strand: chain 'E' and resid 82 through 84 removed outlier: 3.649A pdb=" N SER E 46 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASN E 57 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU E 44 " --> pdb=" O ASN E 57 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N TRP E 59 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA E 42 " --> pdb=" O TRP E 59 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS E 61 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER E 40 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLU E 63 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLN E 38 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N THR E 65 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N LYS E 36 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE E 33 " --> pdb=" O ASP E 161 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL E 163 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE E 35 " --> pdb=" O VAL E 163 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 94 through 96 removed outlier: 5.478A pdb=" N SER E 152 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL E 199 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE E 206 " --> pdb=" O VAL E 183 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 94 through 96 removed outlier: 5.478A pdb=" N SER E 152 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL E 199 " --> pdb=" O SER E 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 22 through 25 Processing sheet with id=AC4, first strand: chain 'F' and resid 29 through 30 removed outlier: 3.613A pdb=" N THR F 136 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU F 53 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL F 69 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP F 55 " --> pdb=" O ILE F 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 29 through 30 removed outlier: 3.613A pdb=" N THR F 136 " --> pdb=" O GLU F 29 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 27 through 29 removed outlier: 6.323A pdb=" N THR G 90 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N SER G 49 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 9.737A pdb=" N SER G 88 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 11.965A pdb=" N MET G 51 " --> pdb=" O SER G 86 " (cutoff:3.500A) removed outlier: 11.790A pdb=" N SER G 86 " --> pdb=" O MET G 51 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 32 through 34 removed outlier: 3.543A pdb=" N MET G 33 " --> pdb=" O LYS G 124 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU G 126 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLN G 58 " --> pdb=" O ARG G 67 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ARG G 67 " --> pdb=" O GLN G 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AC9, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.601A pdb=" N LEU H 53 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL H 69 " --> pdb=" O LEU H 53 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP H 55 " --> pdb=" O ILE H 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 29 through 30 Processing sheet with id=AD2, first strand: chain 'I' and resid 27 through 29 removed outlier: 12.121A pdb=" N CYS I 45 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 11.115A pdb=" N THR I 95 " --> pdb=" O CYS I 45 " (cutoff:3.500A) removed outlier: 12.211A pdb=" N ALA I 47 " --> pdb=" O SER I 93 " (cutoff:3.500A) removed outlier: 11.797A pdb=" N SER I 93 " --> pdb=" O ALA I 47 " (cutoff:3.500A) removed outlier: 11.335A pdb=" N SER I 49 " --> pdb=" O SER I 91 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER I 91 " --> pdb=" O SER I 49 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 32 through 34 removed outlier: 6.127A pdb=" N GLN I 58 " --> pdb=" O ARG I 67 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ARG I 67 " --> pdb=" O GLN I 58 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 32 through 34 removed outlier: 3.543A pdb=" N THR I 118 " --> pdb=" O GLN I 111 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2625 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: 6.64 Time building geometry restraints manager: 9.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5789 1.34 - 1.47: 5288 1.47 - 1.59: 9282 1.59 - 1.72: 0 1.72 - 1.84: 206 Bond restraints: 20565 Sorted by residual: bond pdb=" C LYS D 241 " pdb=" N VAL D 242 " ideal model delta sigma weight residual 1.335 1.473 -0.138 1.20e-02 6.94e+03 1.33e+02 bond pdb=" C LEU D 234 " pdb=" N PRO D 235 " ideal model delta sigma weight residual 1.329 1.415 -0.085 1.25e-02 6.40e+03 4.67e+01 bond pdb=" C TRP B 153 " pdb=" N THR B 154 " ideal model delta sigma weight residual 1.334 1.380 -0.046 1.30e-02 5.92e+03 1.25e+01 bond pdb=" C TRP C 153 " pdb=" N THR C 154 " ideal model delta sigma weight residual 1.334 1.381 -0.047 1.33e-02 5.65e+03 1.25e+01 bond pdb=" N ILE C 23 " pdb=" CA ILE C 23 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.20e-02 6.94e+03 1.01e+01 ... (remaining 20560 not shown) Histogram of bond angle deviations from ideal: 96.96 - 104.65: 456 104.65 - 112.33: 10820 112.33 - 120.02: 7962 120.02 - 127.71: 8581 127.71 - 135.40: 247 Bond angle restraints: 28066 Sorted by residual: angle pdb=" O LEU A 234 " pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 121.31 113.11 8.20 8.50e-01 1.38e+00 9.31e+01 angle pdb=" C LEU A 234 " pdb=" N PRO A 235 " pdb=" CA PRO A 235 " ideal model delta sigma weight residual 119.78 128.66 -8.88 1.03e+00 9.43e-01 7.44e+01 angle pdb=" CA LEU A 234 " pdb=" C LEU A 234 " pdb=" N PRO A 235 " ideal model delta sigma weight residual 119.19 126.76 -7.57 9.50e-01 1.11e+00 6.35e+01 angle pdb=" C LYS D 241 " pdb=" N VAL D 242 " pdb=" CA VAL D 242 " ideal model delta sigma weight residual 120.30 132.14 -11.84 1.64e+00 3.72e-01 5.21e+01 angle pdb=" O LYS D 241 " pdb=" C LYS D 241 " pdb=" N VAL D 242 " ideal model delta sigma weight residual 122.28 113.76 8.52 1.47e+00 4.63e-01 3.36e+01 ... (remaining 28061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.54: 12735 22.54 - 45.08: 388 45.08 - 67.61: 77 67.61 - 90.15: 49 90.15 - 112.69: 32 Dihedral angle restraints: 13281 sinusoidal: 6227 harmonic: 7054 Sorted by residual: dihedral pdb=" CA CYS A 192 " pdb=" C CYS A 192 " pdb=" N CYS A 193 " pdb=" CA CYS A 193 " ideal model delta harmonic sigma weight residual -180.00 -150.68 -29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual -180.00 -151.37 -28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CB CYS D 128 " pdb=" SG CYS D 128 " pdb=" SG CYS D 142 " pdb=" CB CYS D 142 " ideal model delta sinusoidal sigma weight residual 93.00 48.14 44.86 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 13278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3217 0.134 - 0.269: 143 0.269 - 0.403: 25 0.403 - 0.537: 5 0.537 - 0.672: 1 Chirality restraints: 3391 Sorted by residual: chirality pdb=" C1 MAN M 5 " pdb=" O6 BMA M 3 " pdb=" C2 MAN M 5 " pdb=" O5 MAN M 5 " both_signs ideal model delta sigma weight residual False 2.40 2.08 0.32 2.00e-02 2.50e+03 2.61e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.54e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.02e+01 ... (remaining 3388 not shown) Planarity restraints: 3335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.118 2.00e-02 2.50e+03 9.73e-02 1.18e+02 pdb=" C7 NAG N 1 " -0.033 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.089 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.155 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.042 2.00e-02 2.50e+03 3.44e-02 1.48e+01 pdb=" C7 NAG N 2 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.054 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 152 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.34e+00 pdb=" C SER E 152 " -0.053 2.00e-02 2.50e+03 pdb=" O SER E 152 " 0.020 2.00e-02 2.50e+03 pdb=" N TRP E 153 " 0.018 2.00e-02 2.50e+03 ... (remaining 3332 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 62 2.54 - 3.13: 14032 3.13 - 3.72: 28641 3.72 - 4.31: 39984 4.31 - 4.90: 67428 Nonbonded interactions: 150147 Sorted by model distance: nonbonded pdb=" O GLY A 239 " pdb=" OE2 GLU B 241 " model vdw 1.952 3.040 nonbonded pdb=" O GLY D 239 " pdb=" OE2 GLU E 241 " model vdw 2.100 3.040 nonbonded pdb=" NH1 ARG E 188 " pdb=" OD2 ASP E 204 " model vdw 2.265 2.520 nonbonded pdb=" OD1 ASP C 181 " pdb=" NZ LYS C 210 " model vdw 2.297 2.520 nonbonded pdb=" O VAL A 22 " pdb=" ND2 ASN B 4 " model vdw 2.344 2.520 ... (remaining 150142 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 1 through 469 or resid 701 through 710)) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 4 through 459 or resid 701 through 712)) selection = (chain 'C' and (resid 4 through 459 or resid 701 through 712)) selection = (chain 'E' and (resid 4 through 459 or resid 701 through 712)) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'P' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.710 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 53.430 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 : 0.007 0.138 20565 Z= 0.458 Angle : 1.119 13.833 28066 Z= 0.555 Chirality : 0.071 0.672 3391 Planarity : 0.008 0.097 3319 Dihedral : 13.859 112.691 8678 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.64 % Allowed : 3.54 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % 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: -2.91 (0.15), residues: 2351 helix: -1.56 (0.15), residues: 715 sheet: -0.90 (0.20), residues: 588 loop : -2.79 (0.16), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP E 122 HIS 0.006 0.002 HIS B 416 PHE 0.037 0.003 PHE D 146 TYR 0.034 0.003 TYR B 97 ARG 0.018 0.001 ARG A 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 633 time to evaluate : 2.271 Fit side-chains revert: symmetry clash REVERT: C 227 LEU cc_start: 0.8584 (tt) cc_final: 0.8067 (mt) REVERT: C 323 PHE cc_start: 0.8111 (t80) cc_final: 0.7860 (t80) REVERT: C 404 GLN cc_start: 0.7062 (tt0) cc_final: 0.6798 (mt0) REVERT: C 411 SER cc_start: 0.8287 (t) cc_final: 0.8082 (p) REVERT: D 92 LEU cc_start: 0.8056 (pt) cc_final: 0.7738 (tt) REVERT: D 172 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7294 (mm-30) REVERT: D 454 LEU cc_start: 0.7663 (tt) cc_final: 0.7164 (mt) REVERT: D 458 LEU cc_start: 0.7742 (tp) cc_final: 0.7467 (mm) REVERT: H 32 ARG cc_start: 0.7302 (mtt180) cc_final: 0.6934 (mmp-170) REVERT: H 112 ILE cc_start: 0.8786 (mm) cc_final: 0.8553 (mt) REVERT: H 120 ASP cc_start: 0.7385 (p0) cc_final: 0.7076 (p0) outliers start: 14 outliers final: 3 residues processed: 644 average time/residue: 0.3234 time to fit residues: 314.8822 Evaluate side-chains 357 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 354 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain D residue 43 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 118 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN B 416 HIS D 48 GLN D 191 ASN D 428 ASN F 58 GLN F 76 ASN F 81 GLN G 59 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20565 Z= 0.207 Angle : 0.667 9.654 28066 Z= 0.321 Chirality : 0.045 0.393 3391 Planarity : 0.005 0.042 3319 Dihedral : 12.396 85.665 4147 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.91 % Allowed : 10.90 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.17), residues: 2351 helix: 0.65 (0.19), residues: 738 sheet: -0.36 (0.21), residues: 602 loop : -2.28 (0.17), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 118 HIS 0.004 0.001 HIS A 298 PHE 0.027 0.001 PHE E 323 TYR 0.024 0.001 TYR H 122 ARG 0.007 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 370 time to evaluate : 2.447 Fit side-chains revert: symmetry clash REVERT: A 321 ARG cc_start: 0.7136 (ttp80) cc_final: 0.6903 (ttm110) REVERT: B 43 GLN cc_start: 0.8680 (tt0) cc_final: 0.8479 (tt0) REVERT: B 79 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8513 (m) REVERT: B 230 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.7949 (mm) REVERT: B 231 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8932 (tp) REVERT: B 295 VAL cc_start: 0.8445 (p) cc_final: 0.8158 (m) REVERT: B 428 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6818 (mm-30) REVERT: B 438 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: C 227 LEU cc_start: 0.8651 (tt) cc_final: 0.8079 (mt) REVERT: C 323 PHE cc_start: 0.8140 (t80) cc_final: 0.7774 (t80) REVERT: C 435 MET cc_start: 0.8154 (ttm) cc_final: 0.7873 (ttm) REVERT: C 438 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7133 (m-30) REVERT: D 92 LEU cc_start: 0.8091 (pt) cc_final: 0.7445 (tt) REVERT: D 144 MET cc_start: 0.8136 (mtt) cc_final: 0.7915 (mtt) REVERT: D 323 MET cc_start: 0.8163 (mtm) cc_final: 0.7584 (mtm) REVERT: D 454 LEU cc_start: 0.7815 (tt) cc_final: 0.7221 (mt) REVERT: D 458 LEU cc_start: 0.7753 (tp) cc_final: 0.7318 (mm) REVERT: E 38 GLN cc_start: 0.8241 (tp40) cc_final: 0.7950 (tp40) REVERT: E 231 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8618 (tp) REVERT: E 241 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7497 (mp0) REVERT: F 83 PHE cc_start: 0.8820 (m-10) cc_final: 0.8428 (m-10) REVERT: F 89 MET cc_start: 0.8411 (mtp) cc_final: 0.8193 (mtp) REVERT: H 32 ARG cc_start: 0.7274 (mtt180) cc_final: 0.6820 (mmp-170) outliers start: 85 outliers final: 48 residues processed: 423 average time/residue: 0.2841 time to fit residues: 189.1489 Evaluate side-chains 374 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 319 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 153 TRP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 216 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 418 LYS Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 175 optimal weight: 0.1980 chunk 143 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 211 optimal weight: 0.6980 chunk 228 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 chunk 71 optimal weight: 0.0770 chunk 169 optimal weight: 1.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 HIS D 48 GLN E 419 ASN F 58 GLN G 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20565 Z= 0.150 Angle : 0.596 9.711 28066 Z= 0.284 Chirality : 0.043 0.377 3391 Planarity : 0.004 0.050 3319 Dihedral : 10.485 76.261 4140 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.27 % Allowed : 13.52 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.18), residues: 2351 helix: 1.68 (0.20), residues: 733 sheet: -0.05 (0.22), residues: 602 loop : -1.90 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 118 HIS 0.001 0.000 HIS D 32 PHE 0.027 0.001 PHE E 323 TYR 0.019 0.001 TYR H 122 ARG 0.007 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 356 time to evaluate : 2.219 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7330 (tt0) cc_final: 0.7107 (tt0) REVERT: A 321 ARG cc_start: 0.7252 (ttp80) cc_final: 0.7043 (ttm110) REVERT: A 445 ASP cc_start: 0.8287 (t0) cc_final: 0.8017 (m-30) REVERT: B 79 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8592 (m) REVERT: B 230 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7984 (mm) REVERT: B 231 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8943 (tp) REVERT: B 295 VAL cc_start: 0.8483 (p) cc_final: 0.8243 (m) REVERT: B 428 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6843 (mm-30) REVERT: B 438 ASP cc_start: 0.7971 (t0) cc_final: 0.7620 (m-30) REVERT: C 208 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7572 (mtpp) REVERT: C 227 LEU cc_start: 0.8753 (tt) cc_final: 0.8129 (mt) REVERT: C 422 GLU cc_start: 0.6916 (mp0) cc_final: 0.6502 (mp0) REVERT: D 92 LEU cc_start: 0.8026 (pt) cc_final: 0.7596 (tt) REVERT: D 323 MET cc_start: 0.8175 (mtm) cc_final: 0.7607 (mtm) REVERT: D 428 ASN cc_start: 0.7801 (t0) cc_final: 0.7594 (m-40) REVERT: D 454 LEU cc_start: 0.7911 (tt) cc_final: 0.7256 (mt) REVERT: E 231 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8645 (tp) REVERT: E 241 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7522 (mp0) REVERT: G 74 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8292 (mm-40) REVERT: G 99 MET cc_start: 0.8069 (tpp) cc_final: 0.7401 (tpp) REVERT: H 32 ARG cc_start: 0.7238 (mtt180) cc_final: 0.6754 (mmp-170) outliers start: 71 outliers final: 44 residues processed: 397 average time/residue: 0.2835 time to fit residues: 176.1829 Evaluate side-chains 374 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 324 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 418 LYS Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 125 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 141 optimal weight: 0.2980 chunk 211 optimal weight: 0.8980 chunk 224 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20565 Z= 0.226 Angle : 0.619 9.460 28066 Z= 0.295 Chirality : 0.045 0.392 3391 Planarity : 0.004 0.048 3319 Dihedral : 9.531 67.997 4140 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.91 % Allowed : 15.41 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2351 helix: 1.98 (0.20), residues: 739 sheet: 0.12 (0.22), residues: 598 loop : -1.78 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 153 HIS 0.004 0.001 HIS A 5 PHE 0.029 0.002 PHE E 323 TYR 0.016 0.001 TYR E 97 ARG 0.007 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 328 time to evaluate : 2.203 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7954 (tt) REVERT: A 445 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: B 79 VAL cc_start: 0.8803 (OUTLIER) cc_final: 0.8510 (m) REVERT: B 207 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8526 (mt) REVERT: B 230 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8019 (mm) REVERT: B 231 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8980 (tp) REVERT: B 428 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6857 (mm-30) REVERT: B 438 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7737 (m-30) REVERT: C 227 LEU cc_start: 0.8760 (tt) cc_final: 0.8138 (mt) REVERT: D 92 LEU cc_start: 0.8156 (pt) cc_final: 0.7863 (tt) REVERT: D 323 MET cc_start: 0.8178 (mtm) cc_final: 0.7602 (mtm) REVERT: D 454 LEU cc_start: 0.7867 (tt) cc_final: 0.7249 (mt) REVERT: E 231 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8695 (tp) REVERT: E 241 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7555 (mp0) REVERT: F 82 LYS cc_start: 0.9107 (mtpp) cc_final: 0.8733 (mtmt) REVERT: G 99 MET cc_start: 0.8241 (tpp) cc_final: 0.7897 (tpp) REVERT: H 32 ARG cc_start: 0.7210 (mtt180) cc_final: 0.6717 (mmp-170) outliers start: 85 outliers final: 58 residues processed: 383 average time/residue: 0.2814 time to fit residues: 171.5748 Evaluate side-chains 374 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 307 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 428 GLU Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 404 GLN Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 125 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 191 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 48 GLN ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 HIS E 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20565 Z= 0.275 Angle : 0.639 9.713 28066 Z= 0.305 Chirality : 0.045 0.389 3391 Planarity : 0.004 0.047 3319 Dihedral : 9.226 64.695 4140 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.55 % Allowed : 16.56 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.18), residues: 2351 helix: 2.07 (0.20), residues: 745 sheet: 0.18 (0.22), residues: 598 loop : -1.72 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 153 HIS 0.003 0.001 HIS A 5 PHE 0.031 0.002 PHE E 323 TYR 0.018 0.002 TYR H 122 ARG 0.006 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 307 time to evaluate : 2.436 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8011 (tt) REVERT: A 445 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8097 (m-30) REVERT: B 79 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8551 (m) REVERT: B 230 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.7977 (mm) REVERT: B 231 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9002 (tp) REVERT: B 438 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: C 227 LEU cc_start: 0.8767 (tt) cc_final: 0.8127 (mt) REVERT: C 231 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9122 (tp) REVERT: C 422 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: C 438 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7219 (m-30) REVERT: D 92 LEU cc_start: 0.8251 (pt) cc_final: 0.7962 (tt) REVERT: D 454 LEU cc_start: 0.7848 (tt) cc_final: 0.7243 (mt) REVERT: E 231 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8748 (tp) REVERT: E 241 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7133 (mp0) REVERT: G 74 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8432 (mm-40) REVERT: G 99 MET cc_start: 0.8390 (tpp) cc_final: 0.8086 (tpp) REVERT: H 32 ARG cc_start: 0.7248 (mtt180) cc_final: 0.6732 (mmp-170) REVERT: H 82 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8220 (mtpp) outliers start: 99 outliers final: 77 residues processed: 371 average time/residue: 0.2811 time to fit residues: 167.2878 Evaluate side-chains 385 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 298 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 418 LYS Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 125 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 131 optimal weight: 0.2980 chunk 55 optimal weight: 0.0370 chunk 224 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 419 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20565 Z= 0.213 Angle : 0.602 10.055 28066 Z= 0.287 Chirality : 0.044 0.376 3391 Planarity : 0.004 0.046 3319 Dihedral : 8.836 62.306 4140 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.51 % Allowed : 17.20 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2351 helix: 2.27 (0.20), residues: 745 sheet: 0.24 (0.22), residues: 598 loop : -1.65 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 153 HIS 0.003 0.001 HIS A 5 PHE 0.030 0.001 PHE E 323 TYR 0.017 0.001 TYR H 122 ARG 0.010 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 311 time to evaluate : 1.925 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7992 (tt) REVERT: A 105 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7519 (pttt) REVERT: A 168 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8050 (mtmt) REVERT: A 445 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: B 79 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8488 (m) REVERT: B 230 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8078 (mm) REVERT: B 231 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9016 (tp) REVERT: B 438 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7818 (m-30) REVERT: C 227 LEU cc_start: 0.8806 (tt) cc_final: 0.8125 (mt) REVERT: C 231 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9096 (tp) REVERT: C 270 ASP cc_start: 0.7595 (t0) cc_final: 0.7393 (t0) REVERT: C 422 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: D 83 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7407 (mp10) REVERT: D 92 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7958 (tt) REVERT: D 454 LEU cc_start: 0.7840 (tt) cc_final: 0.7242 (mt) REVERT: E 50 ARG cc_start: 0.8535 (ttt90) cc_final: 0.8299 (mmm160) REVERT: E 231 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8731 (tp) REVERT: E 241 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7498 (mp0) REVERT: G 99 MET cc_start: 0.8338 (tpp) cc_final: 0.8039 (tpp) REVERT: H 32 ARG cc_start: 0.7243 (mtt180) cc_final: 0.6734 (mmp-170) REVERT: H 82 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8257 (mtpp) outliers start: 98 outliers final: 70 residues processed: 372 average time/residue: 0.2878 time to fit residues: 170.2903 Evaluate side-chains 379 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 297 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 0.0970 chunk 25 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 419 ASN G 115 ASN I 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20565 Z= 0.177 Angle : 0.585 10.800 28066 Z= 0.279 Chirality : 0.043 0.368 3391 Planarity : 0.004 0.048 3319 Dihedral : 8.511 59.731 4140 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.46 % Allowed : 17.66 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.18), residues: 2351 helix: 2.42 (0.20), residues: 739 sheet: 0.23 (0.22), residues: 609 loop : -1.53 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 66 HIS 0.002 0.000 HIS A 5 PHE 0.028 0.001 PHE E 323 TYR 0.017 0.001 TYR D 419 ARG 0.010 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 302 time to evaluate : 2.165 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7974 (tt) REVERT: A 105 LYS cc_start: 0.7883 (mtmm) cc_final: 0.7516 (pttt) REVERT: A 168 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8026 (mtmt) REVERT: A 445 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.8034 (m-30) REVERT: B 79 VAL cc_start: 0.8762 (OUTLIER) cc_final: 0.8474 (m) REVERT: B 230 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8125 (mm) REVERT: B 231 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9010 (tp) REVERT: B 438 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: C 227 LEU cc_start: 0.8813 (tt) cc_final: 0.8129 (mt) REVERT: C 231 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9078 (tp) REVERT: C 422 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: D 83 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: D 454 LEU cc_start: 0.7836 (tt) cc_final: 0.7270 (mt) REVERT: E 79 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8446 (m) REVERT: E 231 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8691 (tp) REVERT: E 241 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7517 (mp0) REVERT: E 445 PHE cc_start: 0.6572 (m-10) cc_final: 0.6314 (m-80) REVERT: G 99 MET cc_start: 0.8318 (tpp) cc_final: 0.8019 (tpp) REVERT: H 32 ARG cc_start: 0.7271 (mtt180) cc_final: 0.6734 (mmp-170) REVERT: H 82 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8227 (mtpp) outliers start: 97 outliers final: 72 residues processed: 361 average time/residue: 0.2825 time to fit residues: 161.7514 Evaluate side-chains 378 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 294 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 125 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 142 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 203 optimal weight: 0.4980 chunk 214 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20565 Z= 0.264 Angle : 0.631 9.990 28066 Z= 0.302 Chirality : 0.045 0.377 3391 Planarity : 0.004 0.052 3319 Dihedral : 8.455 59.851 4140 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.55 % Allowed : 17.57 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.18), residues: 2351 helix: 2.37 (0.20), residues: 745 sheet: 0.20 (0.22), residues: 608 loop : -1.55 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 153 HIS 0.003 0.001 HIS A 5 PHE 0.031 0.002 PHE E 323 TYR 0.018 0.001 TYR D 419 ARG 0.013 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 303 time to evaluate : 2.321 Fit side-chains REVERT: A 92 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8037 (tt) REVERT: A 105 LYS cc_start: 0.7933 (mtmm) cc_final: 0.7600 (pttm) REVERT: A 168 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8069 (mtmt) REVERT: A 445 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: B 230 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8139 (mm) REVERT: B 231 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9025 (tp) REVERT: B 438 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7816 (m-30) REVERT: C 227 LEU cc_start: 0.8804 (tt) cc_final: 0.8126 (mt) REVERT: C 231 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9151 (tp) REVERT: C 422 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: D 83 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: D 454 LEU cc_start: 0.7807 (tt) cc_final: 0.7201 (mt) REVERT: E 231 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8732 (tp) REVERT: E 241 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7499 (mp0) REVERT: G 74 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8460 (mm-40) REVERT: G 99 MET cc_start: 0.8317 (tpp) cc_final: 0.8050 (tpp) REVERT: G 112 TRP cc_start: 0.6605 (t-100) cc_final: 0.6167 (t-100) REVERT: H 32 ARG cc_start: 0.7298 (mtt180) cc_final: 0.6751 (mmp-170) REVERT: H 82 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8258 (mtpp) outliers start: 99 outliers final: 79 residues processed: 368 average time/residue: 0.2851 time to fit residues: 167.4052 Evaluate side-chains 382 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 293 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 438 ASP Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain D residue 464 PHE Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 125 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.2980 chunk 208 optimal weight: 0.4980 chunk 214 optimal weight: 3.9990 chunk 125 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 419 ASN G 74 GLN G 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20565 Z= 0.152 Angle : 0.572 10.795 28066 Z= 0.274 Chirality : 0.043 0.359 3391 Planarity : 0.004 0.048 3319 Dihedral : 7.952 59.982 4140 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.77 % Allowed : 18.35 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2351 helix: 2.58 (0.20), residues: 745 sheet: 0.26 (0.22), residues: 603 loop : -1.46 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 60 HIS 0.001 0.000 HIS I 55 PHE 0.030 0.001 PHE E 323 TYR 0.019 0.001 TYR D 419 ARG 0.010 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 303 time to evaluate : 2.234 Fit side-chains revert: symmetry clash REVERT: A 92 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8043 (tt) REVERT: A 105 LYS cc_start: 0.7619 (mtmm) cc_final: 0.7359 (pttt) REVERT: A 445 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.8019 (m-30) REVERT: B 230 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8150 (mm) REVERT: B 231 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8999 (tp) REVERT: B 438 ASP cc_start: 0.8106 (t0) cc_final: 0.7806 (m-30) REVERT: C 227 LEU cc_start: 0.8811 (tt) cc_final: 0.8114 (mt) REVERT: C 231 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9070 (tp) REVERT: C 422 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: D 83 GLN cc_start: 0.7705 (mt0) cc_final: 0.7404 (mp10) REVERT: D 454 LEU cc_start: 0.7833 (tt) cc_final: 0.7264 (mt) REVERT: E 79 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8451 (m) REVERT: E 231 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8665 (tp) REVERT: F 82 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8325 (mtmt) REVERT: G 99 MET cc_start: 0.8253 (tpp) cc_final: 0.7989 (tpp) REVERT: G 112 TRP cc_start: 0.6266 (t-100) cc_final: 0.5909 (t-100) REVERT: H 32 ARG cc_start: 0.7251 (mtt180) cc_final: 0.6724 (mmp-170) REVERT: H 82 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8284 (mtpp) outliers start: 82 outliers final: 63 residues processed: 355 average time/residue: 0.2806 time to fit residues: 157.8291 Evaluate side-chains 365 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 294 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 122 TYR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 125 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 231 optimal weight: 0.6980 chunk 212 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN G 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20565 Z= 0.195 Angle : 0.589 10.301 28066 Z= 0.283 Chirality : 0.043 0.364 3391 Planarity : 0.004 0.057 3319 Dihedral : 7.800 59.985 4140 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.59 % Allowed : 18.63 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2351 helix: 2.59 (0.20), residues: 745 sheet: 0.29 (0.22), residues: 608 loop : -1.47 (0.20), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 66 HIS 0.003 0.001 HIS A 5 PHE 0.031 0.001 PHE B 447 TYR 0.018 0.001 TYR E 234 ARG 0.015 0.000 ARG B 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4702 Ramachandran restraints generated. 2351 Oldfield, 0 Emsley, 2351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 297 time to evaluate : 2.379 Fit side-chains REVERT: A 92 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8065 (tt) REVERT: A 105 LYS cc_start: 0.7677 (mtmm) cc_final: 0.7404 (pttt) REVERT: B 230 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8044 (mm) REVERT: B 231 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9001 (tp) REVERT: B 438 ASP cc_start: 0.8115 (t0) cc_final: 0.7816 (m-30) REVERT: C 227 LEU cc_start: 0.8832 (tt) cc_final: 0.8114 (mt) REVERT: C 231 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9086 (tp) REVERT: C 422 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: D 83 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7428 (mt0) REVERT: D 454 LEU cc_start: 0.7791 (tt) cc_final: 0.7228 (mt) REVERT: E 79 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8519 (m) REVERT: E 231 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8713 (tp) REVERT: F 82 LYS cc_start: 0.8768 (mtmt) cc_final: 0.8325 (mtmt) REVERT: G 74 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8446 (mm-40) REVERT: G 99 MET cc_start: 0.8238 (tpp) cc_final: 0.8004 (tpp) REVERT: G 112 TRP cc_start: 0.6379 (t-100) cc_final: 0.6127 (t-100) REVERT: H 32 ARG cc_start: 0.7263 (mtt180) cc_final: 0.6725 (mmp-170) outliers start: 78 outliers final: 65 residues processed: 348 average time/residue: 0.2942 time to fit residues: 164.4071 Evaluate side-chains 366 residues out of total 2174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 293 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain C residue 57 ASN Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 122 TYR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 47 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 112 TRP Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 125 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 23 optimal weight: 0.0370 chunk 33 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.098906 restraints weight = 28186.877| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.14 r_work: 0.2957 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20565 Z= 0.178 Angle : 0.579 10.360 28066 Z= 0.277 Chirality : 0.043 0.361 3391 Planarity : 0.004 0.058 3319 Dihedral : 7.682 59.919 4140 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.50 % Allowed : 18.77 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2351 helix: 2.64 (0.20), residues: 745 sheet: 0.32 (0.22), residues: 607 loop : -1.44 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 66 HIS 0.002 0.000 HIS A 5 PHE 0.029 0.001 PHE E 323 TYR 0.018 0.001 TYR E 234 ARG 0.013 0.000 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4657.05 seconds wall clock time: 84 minutes 26.20 seconds (5066.20 seconds total)