Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 10:13:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ply_20380/07_2023/6ply_20380_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ply_20380/07_2023/6ply_20380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ply_20380/07_2023/6ply_20380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ply_20380/07_2023/6ply_20380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ply_20380/07_2023/6ply_20380_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ply_20380/07_2023/6ply_20380_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.060 sd= 3.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9230 2.51 5 N 2275 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 407": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 14165 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" 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 chiralities: 3 Chain: "G" 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 chiralities: 3 Chain: "H" 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 chiralities: 3 Chain: "I" 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 chiralities: 3 Chain: "J" 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 chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 14 Unusual residues: {'ABU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.04, per 1000 atoms: 0.50 Number of scatterers: 14165 At special positions: 0 Unit cell: (107.813, 104.521, 135.795, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2560 8.00 N 2275 7.00 C 9230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.04 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.04 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.04 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 6.03 Conformation dependent library (CDL) restraints added in 2.1 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 25 sheets defined 31.2% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.537A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.685A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 239 through 242 No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.950A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 287 removed outlier: 3.531A pdb=" N THR A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 303 No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.858A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 removed outlier: 3.815A pdb=" N ARG A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 427 removed outlier: 4.064A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 removed outlier: 3.511A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.702A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 108 " --> pdb=" O MET B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 239 through 242 No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 249 through 258 removed outlier: 4.262A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N PHE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 287 removed outlier: 3.770A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 303 No H-bonds generated for 'chain 'B' and resid 300 through 303' Processing helix chain 'B' and resid 306 through 323 removed outlier: 3.625A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.845A pdb=" N ARG B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 427 removed outlier: 4.089A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.545A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.721A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER C 108 " --> pdb=" O MET C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 239 through 242 No H-bonds generated for 'chain 'C' and resid 239 through 242' Processing helix chain 'C' and resid 245 through 254 removed outlier: 4.056A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 258 No H-bonds generated for 'chain 'C' and resid 256 through 258' Processing helix chain 'C' and resid 268 through 287 removed outlier: 3.854A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 303 No H-bonds generated for 'chain 'C' and resid 300 through 303' Processing helix chain 'C' and resid 308 through 323 removed outlier: 3.990A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 404 removed outlier: 3.528A pdb=" N ARG C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 427 removed outlier: 4.016A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.568A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.680A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER D 108 " --> pdb=" O MET D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 239 through 242 No H-bonds generated for 'chain 'D' and resid 239 through 242' Processing helix chain 'D' and resid 245 through 254 removed outlier: 3.975A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 268 through 287 removed outlier: 3.785A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 303 No H-bonds generated for 'chain 'D' and resid 300 through 303' Processing helix chain 'D' and resid 308 through 323 removed outlier: 3.840A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 No H-bonds generated for 'chain 'D' and resid 393 through 396' Processing helix chain 'D' and resid 401 through 404 No H-bonds generated for 'chain 'D' and resid 401 through 404' Processing helix chain 'D' and resid 410 through 427 removed outlier: 4.052A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 34 removed outlier: 3.600A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.716A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER E 108 " --> pdb=" O MET E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 239 through 242 No H-bonds generated for 'chain 'E' and resid 239 through 242' Processing helix chain 'E' and resid 245 through 258 removed outlier: 4.001A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 287 removed outlier: 3.826A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 303 No H-bonds generated for 'chain 'E' and resid 300 through 303' Processing helix chain 'E' and resid 306 through 323 removed outlier: 3.574A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 404 removed outlier: 3.540A pdb=" N ARG E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 427 removed outlier: 4.127A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 186 removed outlier: 6.250A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 59 through 61 Processing sheet with id= C, first strand: chain 'A' and resid 98 through 100 Processing sheet with id= D, first strand: chain 'A' and resid 114 through 116 removed outlier: 3.506A pdb=" N ILE A 226 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 211 through 213 Processing sheet with id= F, first strand: chain 'B' and resid 182 through 186 removed outlier: 6.230A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 59 through 61 Processing sheet with id= H, first strand: chain 'B' and resid 98 through 100 Processing sheet with id= I, first strand: chain 'B' and resid 114 through 116 Processing sheet with id= J, first strand: chain 'B' and resid 211 through 213 Processing sheet with id= K, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.217A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 59 through 61 Processing sheet with id= M, first strand: chain 'C' and resid 98 through 100 Processing sheet with id= N, first strand: chain 'C' and resid 114 through 116 Processing sheet with id= O, first strand: chain 'C' and resid 211 through 213 Processing sheet with id= P, first strand: chain 'D' and resid 182 through 186 removed outlier: 6.246A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 59 through 61 Processing sheet with id= R, first strand: chain 'D' and resid 98 through 100 Processing sheet with id= S, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= T, first strand: chain 'D' and resid 211 through 213 Processing sheet with id= U, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.265A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= W, first strand: chain 'E' and resid 98 through 100 Processing sheet with id= X, first strand: chain 'E' and resid 114 through 116 Processing sheet with id= Y, first strand: chain 'E' and resid 211 through 213 433 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4280 1.34 - 1.46: 3608 1.46 - 1.58: 6452 1.58 - 1.71: 0 1.71 - 1.83: 170 Bond restraints: 14510 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.552 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.552 -0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 ... (remaining 14505 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.04: 389 106.04 - 113.05: 7717 113.05 - 120.06: 5274 120.06 - 127.06: 6111 127.06 - 134.07: 189 Bond angle restraints: 19680 Sorted by residual: angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 132.58 -11.04 1.91e+00 2.74e-01 3.34e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 132.56 -11.02 1.91e+00 2.74e-01 3.33e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 132.31 -10.77 1.91e+00 2.74e-01 3.18e+01 angle pdb=" N VAL E 37 " pdb=" CA VAL E 37 " pdb=" C VAL E 37 " ideal model delta sigma weight residual 113.71 108.92 4.79 9.50e-01 1.11e+00 2.54e+01 ... (remaining 19675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 8060 14.99 - 29.97: 431 29.97 - 44.96: 69 44.96 - 59.95: 5 59.95 - 74.93: 5 Dihedral angle restraints: 8570 sinusoidal: 3455 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASN A 160 " pdb=" C ASN A 160 " pdb=" N PHE A 161 " pdb=" CA PHE A 161 " ideal model delta harmonic sigma weight residual -180.00 -153.29 -26.71 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA ASN C 160 " pdb=" C ASN C 160 " pdb=" N PHE C 161 " pdb=" CA PHE C 161 " ideal model delta harmonic sigma weight residual -180.00 -153.40 -26.60 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 48.59 44.41 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 8567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1509 0.052 - 0.104: 588 0.104 - 0.156: 122 0.156 - 0.208: 29 0.208 - 0.260: 12 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.50e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2257 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 410 " -0.049 5.00e-02 4.00e+02 7.31e-02 8.56e+00 pdb=" N PRO E 411 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 411 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 411 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 410 " 0.047 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO B 411 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO A 411 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " -0.039 5.00e-02 4.00e+02 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4578 2.84 - 3.36: 12208 3.36 - 3.87: 22583 3.87 - 4.39: 26969 4.39 - 4.90: 45362 Nonbonded interactions: 111700 Sorted by model distance: nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.330 2.440 nonbonded pdb=" OE2 GLU A 69 " pdb=" NH2 ARG A 234 " model vdw 2.335 2.520 nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.341 2.440 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.342 2.440 nonbonded pdb=" OE2 GLU D 69 " pdb=" NH2 ARG D 234 " model vdw 2.343 2.520 ... (remaining 111695 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 23 through 428) selection = (chain 'B' and resid 23 through 428) selection = (chain 'C' and resid 23 through 428) selection = (chain 'D' and resid 23 through 428) selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.880 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: 7.930 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 37.730 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.100 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:13.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 0.057 14510 Z= 0.461 Angle : 1.026 11.234 19680 Z= 0.525 Chirality : 0.058 0.260 2260 Planarity : 0.007 0.073 2435 Dihedral : 9.397 74.935 5220 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.14), residues: 1710 helix: -4.84 (0.08), residues: 560 sheet: -2.43 (0.22), residues: 390 loop : -2.73 (0.17), residues: 760 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 451 time to evaluate : 1.686 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 1.1489 time to fit residues: 570.1727 Evaluate side-chains 279 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.680 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.0570 chunk 68 optimal weight: 3.9990 chunk 133 optimal weight: 0.0470 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 231 HIS B 62 ASN B 180 ASN B 231 HIS C 62 ASN C 231 HIS D 62 ASN D 123 ASN D 231 HIS D 282 GLN E 62 ASN E 82 GLN E 180 ASN E 231 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 14510 Z= 0.205 Angle : 0.689 7.301 19680 Z= 0.349 Chirality : 0.046 0.145 2260 Planarity : 0.005 0.044 2435 Dihedral : 6.014 28.986 1890 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 4.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.16), residues: 1710 helix: -3.51 (0.14), residues: 565 sheet: -1.56 (0.26), residues: 345 loop : -2.55 (0.17), residues: 800 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 311 time to evaluate : 1.627 Fit side-chains outliers start: 69 outliers final: 19 residues processed: 349 average time/residue: 0.9689 time to fit residues: 378.5443 Evaluate side-chains 296 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 277 time to evaluate : 1.613 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 9 residues processed: 10 average time/residue: 0.6464 time to fit residues: 9.9017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 0.0060 chunk 154 optimal weight: 0.0010 chunk 167 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 153 optimal weight: 0.0370 chunk 52 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 82 GLN A 141 ASN A 180 ASN B 82 GLN B 141 ASN B 282 GLN C 82 GLN C 141 ASN C 180 ASN C 282 GLN D 82 GLN D 141 ASN E 62 ASN E 141 ASN E 282 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 14510 Z= 0.182 Angle : 0.635 8.795 19680 Z= 0.320 Chirality : 0.045 0.152 2260 Planarity : 0.004 0.039 2435 Dihedral : 5.486 25.282 1890 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.17), residues: 1710 helix: -2.66 (0.17), residues: 570 sheet: -1.04 (0.27), residues: 345 loop : -2.40 (0.18), residues: 795 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 282 time to evaluate : 1.673 Fit side-chains outliers start: 49 outliers final: 20 residues processed: 308 average time/residue: 1.0367 time to fit residues: 356.9367 Evaluate side-chains 276 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 256 time to evaluate : 1.620 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 10 residues processed: 11 average time/residue: 0.4388 time to fit residues: 8.2886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 103 optimal weight: 0.0470 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 14510 Z= 0.197 Angle : 0.622 9.047 19680 Z= 0.312 Chirality : 0.045 0.169 2260 Planarity : 0.003 0.037 2435 Dihedral : 5.303 22.293 1890 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 4.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.18), residues: 1710 helix: -1.92 (0.20), residues: 560 sheet: -0.68 (0.27), residues: 345 loop : -2.32 (0.19), residues: 805 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 263 time to evaluate : 1.640 Fit side-chains outliers start: 67 outliers final: 27 residues processed: 301 average time/residue: 0.9036 time to fit residues: 308.3029 Evaluate side-chains 275 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 248 time to evaluate : 1.731 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 13 residues processed: 16 average time/residue: 0.6917 time to fit residues: 15.2594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.0010 chunk 93 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 0.0770 chunk 113 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 282 GLN D 180 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 14510 Z= 0.194 Angle : 0.616 10.849 19680 Z= 0.306 Chirality : 0.045 0.178 2260 Planarity : 0.003 0.033 2435 Dihedral : 5.134 21.514 1890 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 4.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.19), residues: 1710 helix: -1.51 (0.22), residues: 555 sheet: -0.28 (0.28), residues: 320 loop : -2.12 (0.19), residues: 835 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 264 time to evaluate : 1.769 Fit side-chains outliers start: 62 outliers final: 30 residues processed: 302 average time/residue: 0.9575 time to fit residues: 326.9129 Evaluate side-chains 280 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 250 time to evaluate : 1.637 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 20 residues processed: 12 average time/residue: 0.2731 time to fit residues: 6.8824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 136 optimal weight: 0.0020 chunk 76 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN B 62 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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 0.065 14510 Z= 0.206 Angle : 0.628 10.589 19680 Z= 0.311 Chirality : 0.045 0.164 2260 Planarity : 0.003 0.033 2435 Dihedral : 5.155 41.479 1890 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.21 (0.19), residues: 1710 helix: -1.37 (0.22), residues: 555 sheet: -0.19 (0.28), residues: 320 loop : -2.05 (0.19), residues: 835 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 261 time to evaluate : 1.668 Fit side-chains outliers start: 59 outliers final: 33 residues processed: 298 average time/residue: 0.9367 time to fit residues: 314.8164 Evaluate side-chains 287 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 254 time to evaluate : 1.607 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 22 residues processed: 14 average time/residue: 0.4012 time to fit residues: 9.7526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 138 optimal weight: 0.0170 chunk 91 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN D 261 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 14510 Z= 0.211 Angle : 0.636 13.647 19680 Z= 0.314 Chirality : 0.045 0.174 2260 Planarity : 0.003 0.033 2435 Dihedral : 5.232 46.447 1890 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 3.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.12 (0.19), residues: 1710 helix: -1.27 (0.23), residues: 555 sheet: -0.10 (0.28), residues: 320 loop : -2.02 (0.19), residues: 835 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 269 time to evaluate : 1.684 Fit side-chains outliers start: 57 outliers final: 33 residues processed: 311 average time/residue: 0.9026 time to fit residues: 317.8613 Evaluate side-chains 298 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 265 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 27 residues processed: 9 average time/residue: 0.3362 time to fit residues: 6.4881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN C 261 ASN C 418 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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 : 0.005 0.078 14510 Z= 0.287 Angle : 0.684 14.101 19680 Z= 0.340 Chirality : 0.047 0.198 2260 Planarity : 0.003 0.034 2435 Dihedral : 5.560 46.487 1890 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.85 % Favored : 95.03 % Rotamer Outliers : 3.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.08 (0.19), residues: 1710 helix: -1.30 (0.22), residues: 555 sheet: 0.07 (0.29), residues: 320 loop : -2.03 (0.19), residues: 835 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 272 time to evaluate : 1.678 Fit side-chains outliers start: 60 outliers final: 42 residues processed: 315 average time/residue: 0.9967 time to fit residues: 352.2926 Evaluate side-chains 302 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 260 time to evaluate : 1.530 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 32 residues processed: 12 average time/residue: 0.4723 time to fit residues: 9.1233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN C 82 GLN D 82 GLN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 14510 Z= 0.311 Angle : 0.687 9.323 19680 Z= 0.345 Chirality : 0.047 0.181 2260 Planarity : 0.003 0.036 2435 Dihedral : 5.667 47.333 1890 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.15 % Favored : 94.74 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.98 (0.20), residues: 1710 helix: -1.29 (0.22), residues: 555 sheet: -0.21 (0.27), residues: 370 loop : -1.83 (0.20), residues: 785 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 263 time to evaluate : 1.736 Fit side-chains outliers start: 54 outliers final: 38 residues processed: 306 average time/residue: 0.9813 time to fit residues: 337.2276 Evaluate side-chains 288 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 250 time to evaluate : 1.606 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 33 residues processed: 7 average time/residue: 0.4537 time to fit residues: 6.1619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 0.0770 chunk 112 optimal weight: 0.1980 chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN C 62 ASN C 82 GLN D 82 GLN E 58 ASN E 62 ASN E 82 GLN E 282 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 14510 Z= 0.212 Angle : 0.655 10.137 19680 Z= 0.327 Chirality : 0.046 0.179 2260 Planarity : 0.003 0.032 2435 Dihedral : 5.445 47.946 1890 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.15 % Favored : 95.67 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.86 (0.20), residues: 1710 helix: -1.15 (0.23), residues: 555 sheet: -0.13 (0.27), residues: 365 loop : -1.77 (0.21), residues: 790 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 259 time to evaluate : 1.503 Fit side-chains outliers start: 43 outliers final: 33 residues processed: 299 average time/residue: 0.9460 time to fit residues: 318.0236 Evaluate side-chains 299 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 266 time to evaluate : 1.583 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 32 residues processed: 2 average time/residue: 0.2474 time to fit residues: 2.9148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 56 optimal weight: 0.0170 chunk 138 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.0270 chunk 118 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN B 82 GLN E 282 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.150622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113841 restraints weight = 16519.265| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.37 r_work: 0.3114 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 14510 Z= 0.201 Angle : 0.637 10.532 19680 Z= 0.319 Chirality : 0.045 0.207 2260 Planarity : 0.003 0.031 2435 Dihedral : 5.292 46.104 1890 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.74 % Favored : 95.20 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.78 (0.20), residues: 1710 helix: -1.07 (0.23), residues: 555 sheet: -0.09 (0.27), residues: 365 loop : -1.75 (0.21), residues: 790 =============================================================================== Job complete usr+sys time: 5693.36 seconds wall clock time: 101 minutes 36.33 seconds (6096.33 seconds total)