Starting phenix.real_space_refine on Sun Feb 18 09:53:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mly_23913/02_2024/7mly_23913_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mly_23913/02_2024/7mly_23913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mly_23913/02_2024/7mly_23913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mly_23913/02_2024/7mly_23913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mly_23913/02_2024/7mly_23913_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mly_23913/02_2024/7mly_23913_trim_updated.pdb" } resolution = 2.7 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= 0.024 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 135 5.16 5 C 13597 2.51 5 N 3398 2.21 5 O 3852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 31": "NH1" <-> "NH2" Residue "G ARG 40": "NH1" <-> "NH2" Residue "F ARG 31": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "M TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "H ARG 31": "NH1" <-> "NH2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D ARG 309": "NH1" <-> "NH2" Residue "D ARG 390": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 72": "NH1" <-> "NH2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 309": "NH1" <-> "NH2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C ARG 119": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C ARG 309": "NH1" <-> "NH2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "C ARG 399": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 145": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E ARG 241": "NH1" <-> "NH2" Residue "E ARG 450": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20982 Number of models: 1 Model: "" Number of chains: 23 Chain: "J" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 766 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "K" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 782 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "F" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "M" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 783 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "I" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 783 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "D" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2724 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 319} Chain breaks: 1 Chain: "A" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2771 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 324} Chain breaks: 1 Chain: "B" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2732 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2819 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2686 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 314} Chain breaks: 1 Chain: "T" 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: "Z" 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: "f" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "l" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 66 Unusual residues: {'D10': 1, 'DD9': 1, 'HP6': 2, 'LNK': 2, 'MYS': 1, 'NBU': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 85 Unusual residues: {'D12': 1, 'DD9': 1, 'HEX': 1, 'HP6': 2, 'LNK': 2, 'OCT': 3} Inner-chain residues flagged as termini: ['pdbres="GLY A 502 "'] Classifications: {'peptide': 2, 'undetermined': 10} Modifications used: {'COO': 2} Link IDs: {'TRANS': 1, None: 10} Not linked: pdbres="GLY A 502 " pdbres="D12 A 503 " Not linked: pdbres="D12 A 503 " pdbres="HP6 A 504 " Not linked: pdbres="HP6 A 504 " pdbres="HP6 A 505 " Not linked: pdbres="HP6 A 505 " pdbres="LNK A 506 " Not linked: pdbres="LNK A 506 " pdbres="OCT A 507 " ... (remaining 5 not shown) Chain breaks: 1 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 56 Unusual residues: {'DD9': 1, 'HEX': 1, 'HP6': 2, 'LNK': 2, 'NBU': 3} Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 57 Unusual residues: {'D12': 1, 'HEX': 1, 'LNK': 2, 'NBU': 4, 'OCT': 1} Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Chain: "E" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 47 Unusual residues: {'HP6': 3, 'LNK': 2, 'UND': 1} Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Time building chain proxies: 11.61, per 1000 atoms: 0.55 Number of scatterers: 20982 At special positions: 0 Unit cell: (154.462, 130.508, 141.246, 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 135 16.00 O 3852 8.00 N 3398 7.00 C 13597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.04 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.04 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.04 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " 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 ALPHA1-2 " MAN T 4 " - " MAN T 5 " ALPHA1-3 " BMA T 3 " - " MAN T 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA Z 3 " - " MAN Z 5 " " BMA f 3 " - " MAN f 4 " " BMA l 3 " - " MAN l 4 " BETA1-4 " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " NAG-ASN " NAG T 1 " - " ASN D 38 " " NAG Z 1 " - " ASN A 38 " " NAG f 1 " - " ASN B 38 " " NAG l 1 " - " ASN C 38 " " NAG r 1 " - " ASN E 220 " Time building additional restraints: 9.10 Conformation dependent library (CDL) restraints added in 3.8 seconds 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4786 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 44 sheets defined 23.4% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.80 Creating SS restraints... Processing helix chain 'J' and resid 80 through 82 No H-bonds generated for 'chain 'J' and resid 80 through 82' Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'M' and resid 80 through 82 No H-bonds generated for 'chain 'M' and resid 80 through 82' Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'D' and resid 11 through 17 removed outlier: 4.110A pdb=" N LEU D 14 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 17 " --> pdb=" O LEU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.690A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 228 through 243 removed outlier: 3.888A pdb=" N TRP D 239 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE D 240 " --> pdb=" O ILE D 236 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N SER D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TRP D 243 " --> pdb=" O TRP D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 271 removed outlier: 3.747A pdb=" N VAL D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 307 removed outlier: 3.900A pdb=" N VAL D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 298 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 414 removed outlier: 3.505A pdb=" N SER D 398 " --> pdb=" O ILE D 394 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG D 399 " --> pdb=" O ASP D 395 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix removed outlier: 3.846A pdb=" N TRP D 414 " --> pdb=" O ASN D 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 17 removed outlier: 3.658A pdb=" N LEU A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.554A pdb=" N ILE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TRP A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 271 removed outlier: 3.888A pdb=" N THR A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 removed outlier: 3.613A pdb=" N VAL A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 417 removed outlier: 4.144A pdb=" N ARG A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Proline residue: A 403 - end of helix removed outlier: 3.689A pdb=" N TRP A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 17 removed outlier: 3.669A pdb=" N ASP B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 223 through 226 No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 228 through 242 removed outlier: 4.046A pdb=" N TRP B 239 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N SER B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 270 removed outlier: 3.550A pdb=" N SER B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 308 removed outlier: 3.649A pdb=" N VAL B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA B 297 " --> pdb=" O PHE B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 396 removed outlier: 4.186A pdb=" N ASP B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 417 Proline residue: B 403 - end of helix removed outlier: 3.669A pdb=" N LEU B 407 " --> pdb=" O PRO B 403 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR B 417 " --> pdb=" O TYR B 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 87 through 90 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.531A pdb=" N ILE C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 249 through 272 removed outlier: 3.772A pdb=" N LEU C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 258 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARG C 271 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 313 removed outlier: 3.880A pdb=" N VAL C 289 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 298 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 383 No H-bonds generated for 'chain 'C' and resid 381 through 383' Processing helix chain 'C' and resid 388 through 416 removed outlier: 4.288A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix removed outlier: 3.730A pdb=" N LEU C 407 " --> pdb=" O PRO C 403 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TRP C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 415 " --> pdb=" O MET C 411 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 42 removed outlier: 4.253A pdb=" N ASN E 39 " --> pdb=" O ASN E 36 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ARG E 40 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU E 42 " --> pdb=" O ASN E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 110 through 115 removed outlier: 3.595A pdb=" N TYR E 113 " --> pdb=" O PRO E 110 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYS E 114 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 248 No H-bonds generated for 'chain 'E' and resid 245 through 248' Processing helix chain 'E' and resid 252 through 266 removed outlier: 3.742A pdb=" N TRP E 263 " --> pdb=" O VAL E 259 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 264 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N SER E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 297 removed outlier: 3.505A pdb=" N VAL E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) Proline residue: E 278 - end of helix removed outlier: 4.033A pdb=" N SER E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA E 295 " --> pdb=" O CYS E 291 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU E 297 " --> pdb=" O THR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 332 removed outlier: 3.572A pdb=" N LEU E 311 " --> pdb=" O LEU E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 473 removed outlier: 4.440A pdb=" N ALA E 457 " --> pdb=" O TYR E 454 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU E 458 " --> pdb=" O ALA E 455 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE E 459 " --> pdb=" O ARG E 456 " (cutoff:3.500A) Proline residue: E 460 - end of helix removed outlier: 3.595A pdb=" N PHE E 463 " --> pdb=" O PRO E 460 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 464 " --> pdb=" O PHE E 461 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE E 465 " --> pdb=" O CYS E 462 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL E 468 " --> pdb=" O PHE E 465 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TRP E 471 " --> pdb=" O VAL E 468 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER E 472 " --> pdb=" O ILE E 469 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'J' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'J' and resid 19 through 22 removed outlier: 3.549A pdb=" N ILE J 21 " --> pdb=" O LEU J 73 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR J 72 " --> pdb=" O SER J 65 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'J' and resid 85 through 90 removed outlier: 3.518A pdb=" N LEU J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.504A pdb=" N THR G 78 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 112 through 114 removed outlier: 6.309A pdb=" N LYS G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N TRP G 47 " --> pdb=" O LYS G 38 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 19 through 22 removed outlier: 3.702A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE K 75 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR K 72 " --> pdb=" O SER K 65 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 85 through 89 removed outlier: 3.664A pdb=" N LEU K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 4 through 6 Processing sheet with id= I, first strand: chain 'F' and resid 112 through 114 removed outlier: 6.307A pdb=" N LYS F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N TRP F 47 " --> pdb=" O LYS F 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'M' and resid 85 through 89 removed outlier: 3.890A pdb=" N LEU M 85 " --> pdb=" O GLN M 38 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN M 37 " --> pdb=" O LEU M 46 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU M 46 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'M' and resid 62 through 67 removed outlier: 3.720A pdb=" N THR M 72 " --> pdb=" O SER M 65 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= M, first strand: chain 'L' and resid 112 through 114 removed outlier: 6.291A pdb=" N LYS L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TRP L 47 " --> pdb=" O LYS L 38 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER L 57 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 19 through 22 removed outlier: 4.022A pdb=" N VAL I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE I 75 " --> pdb=" O VAL I 19 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR I 72 " --> pdb=" O SER I 65 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 33 through 38 removed outlier: 3.738A pdb=" N LEU I 85 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 3 through 6 Processing sheet with id= Q, first strand: chain 'H' and resid 112 through 114 removed outlier: 6.081A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER H 57 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 166 through 170 removed outlier: 6.383A pdb=" N VAL D 37 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLU D 169 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL D 39 " --> pdb=" O GLU D 169 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 43 through 45 Processing sheet with id= T, first strand: chain 'D' and resid 98 through 100 Processing sheet with id= U, first strand: chain 'D' and resid 116 through 120 removed outlier: 3.518A pdb=" N SER D 129 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG D 119 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 149 through 152 Processing sheet with id= W, first strand: chain 'D' and resid 200 through 202 Processing sheet with id= X, first strand: chain 'A' and resid 166 through 170 removed outlier: 5.901A pdb=" N VAL A 37 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLU A 169 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 39 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 133 " --> pdb=" O HIS A 107 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS A 107 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 43 through 45 Processing sheet with id= Z, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.661A pdb=" N MET A 154 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 217 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.556A pdb=" N ARG A 119 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 166 through 170 removed outlier: 5.875A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU B 169 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL B 39 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 43 through 45 Processing sheet with id= AD, first strand: chain 'B' and resid 98 through 100 Processing sheet with id= AE, first strand: chain 'B' and resid 116 through 120 Processing sheet with id= AF, first strand: chain 'B' and resid 149 through 152 removed outlier: 3.527A pdb=" N GLU B 217 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 200 through 202 Processing sheet with id= AH, first strand: chain 'C' and resid 167 through 170 removed outlier: 6.504A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 43 through 45 Processing sheet with id= AJ, first strand: chain 'C' and resid 62 through 65 Processing sheet with id= AK, first strand: chain 'C' and resid 98 through 100 Processing sheet with id= AL, first strand: chain 'C' and resid 193 through 197 Processing sheet with id= AM, first strand: chain 'C' and resid 200 through 202 Processing sheet with id= AN, first strand: chain 'E' and resid 58 through 62 Processing sheet with id= AO, first strand: chain 'E' and resid 148 through 160 removed outlier: 6.583A pdb=" N PHE E 84 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE E 66 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG E 86 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE E 64 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'E' and resid 121 through 123 Processing sheet with id= AQ, first strand: chain 'E' and resid 172 through 176 Processing sheet with id= AR, first strand: chain 'E' and resid 223 through 225 619 hydrogen bonds defined for protein. 1698 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: 6.70 Time building geometry restraints manager: 9.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3241 1.31 - 1.44: 6108 1.44 - 1.57: 11870 1.57 - 1.70: 1 1.70 - 1.82: 222 Bond restraints: 21442 Sorted by residual: bond pdb=" C ARG D 399 " pdb=" O ARG D 399 " ideal model delta sigma weight residual 1.236 1.185 0.051 1.25e-02 6.40e+03 1.69e+01 bond pdb=" CA ARG D 399 " pdb=" CB ARG D 399 " ideal model delta sigma weight residual 1.529 1.466 0.063 1.64e-02 3.72e+03 1.47e+01 bond pdb=" C1 NAG r 2 " pdb=" O5 NAG r 2 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 BMA l 3 " pdb=" C2 BMA l 3 " ideal model delta sigma weight residual 1.519 1.582 -0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" NE ARG D 399 " pdb=" CZ ARG D 399 " ideal model delta sigma weight residual 1.326 1.294 0.032 1.10e-02 8.26e+03 8.40e+00 ... (remaining 21437 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.66: 638 106.66 - 113.50: 11770 113.50 - 120.34: 7617 120.34 - 127.19: 8651 127.19 - 134.03: 256 Bond angle restraints: 28932 Sorted by residual: angle pdb=" C SER A 308 " pdb=" N ARG A 309 " pdb=" CA ARG A 309 " ideal model delta sigma weight residual 123.20 117.38 5.82 1.38e+00 5.25e-01 1.78e+01 angle pdb=" NE ARG D 399 " pdb=" CZ ARG D 399 " pdb=" NH1 ARG D 399 " ideal model delta sigma weight residual 121.50 117.64 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" N ALA K 51 " pdb=" CA ALA K 51 " pdb=" CB ALA K 51 " ideal model delta sigma weight residual 114.17 110.32 3.85 1.14e+00 7.69e-01 1.14e+01 angle pdb=" N ALA I 51 " pdb=" CA ALA I 51 " pdb=" CB ALA I 51 " ideal model delta sigma weight residual 114.17 110.32 3.85 1.14e+00 7.69e-01 1.14e+01 angle pdb=" N ALA M 51 " pdb=" CA ALA M 51 " pdb=" CB ALA M 51 " ideal model delta sigma weight residual 114.17 110.40 3.77 1.14e+00 7.69e-01 1.09e+01 ... (remaining 28927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.56: 12547 24.56 - 49.12: 279 49.12 - 73.68: 67 73.68 - 98.24: 41 98.24 - 122.81: 46 Dihedral angle restraints: 12980 sinusoidal: 5529 harmonic: 7451 Sorted by residual: dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 152 " pdb=" CB CYS D 152 " ideal model delta sinusoidal sigma weight residual 93.00 39.49 53.51 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CB CYS E 161 " pdb=" SG CYS E 161 " pdb=" SG CYS E 175 " pdb=" CB CYS E 175 " ideal model delta sinusoidal sigma weight residual 93.00 40.48 52.52 1 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 42.64 50.36 1 1.00e+01 1.00e-02 3.48e+01 ... (remaining 12977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3162 0.115 - 0.229: 60 0.229 - 0.344: 10 0.344 - 0.458: 1 0.458 - 0.573: 1 Chirality restraints: 3234 Sorted by residual: chirality pdb=" C1 NAG r 1 " pdb=" ND2 ASN E 220 " pdb=" C2 NAG r 1 " pdb=" O5 NAG r 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" CA ARG D 399 " pdb=" N ARG D 399 " pdb=" C ARG D 399 " pdb=" CB ARG D 399 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" C1 NAG l 1 " pdb=" ND2 ASN C 38 " pdb=" C2 NAG l 1 " pdb=" O5 NAG l 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3231 not shown) Planarity restraints: 3579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 308 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C SER A 308 " -0.053 2.00e-02 2.50e+03 pdb=" O SER A 308 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG A 309 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 98 " -0.007 2.00e-02 2.50e+03 1.41e-02 3.49e+00 pdb=" CG PHE J 98 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE J 98 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE J 98 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE J 98 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE J 98 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE J 98 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 98 " 0.008 2.00e-02 2.50e+03 1.35e-02 3.19e+00 pdb=" CG PHE K 98 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE K 98 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE K 98 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE K 98 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE K 98 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE K 98 " 0.001 2.00e-02 2.50e+03 ... (remaining 3576 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 258 2.61 - 3.18: 19168 3.18 - 3.76: 30512 3.76 - 4.33: 47364 4.33 - 4.90: 75250 Nonbonded interactions: 172552 Sorted by model distance: nonbonded pdb=" O SER I 30 " pdb=" OH TYR I 71 " model vdw 2.040 2.440 nonbonded pdb=" O LEU A 98 " pdb=" OG1 THR B 112 " model vdw 2.046 2.440 nonbonded pdb=" O LYS D 16 " pdb=" OG SER D 22 " model vdw 2.053 2.440 nonbonded pdb=" OG SER J 43 " pdb=" O GLY G 109 " model vdw 2.063 2.440 nonbonded pdb=" O SER J 30 " pdb=" OH TYR J 71 " model vdw 2.067 2.440 ... (remaining 172547 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 9 through 309 or resid 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'B' and (resid 9 through 386 or (resid 387 and (name N or name CA or name \ C or name O or name CB )) or resid 388 through 419)) selection = (chain 'C' and (resid 9 through 309 or resid 386 through 419)) selection = (chain 'D' and (resid 9 through 386 or (resid 387 and (name N or name CA or name \ C or name O or name CB )) or resid 388 through 419)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' } ncs_group { reference = (chain 'I' and resid 2 through 102) selection = chain 'J' selection = (chain 'K' and (resid 2 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB )) or resid 93 through 102)) selection = (chain 'M' and resid 2 through 102) } ncs_group { reference = chain 'T' selection = chain 'Z' } ncs_group { reference = chain 'f' selection = chain 'l' } 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: 9.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 23.540 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 57.660 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 0.004 0.064 21442 Z= 0.249 Angle : 0.697 9.852 28932 Z= 0.340 Chirality : 0.046 0.573 3234 Planarity : 0.004 0.043 3574 Dihedral : 14.567 122.805 8140 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 29.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.13 % Allowed : 1.75 % Favored : 98.12 % 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: -4.16 (0.15), residues: 2522 helix: -2.70 (0.17), residues: 511 sheet: -2.98 (0.15), residues: 759 loop : -2.55 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 108 HIS 0.009 0.001 HIS B 201 PHE 0.030 0.002 PHE J 98 TYR 0.014 0.002 TYR A 301 ARG 0.009 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 463 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.8688 (mt0) cc_final: 0.8439 (pm20) REVERT: F 23 LYS cc_start: 0.9238 (tptp) cc_final: 0.8898 (tppp) REVERT: D 235 VAL cc_start: 0.9654 (t) cc_final: 0.9170 (t) REVERT: D 399 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8082 (mpp80) REVERT: A 220 MET cc_start: 0.7769 (ptm) cc_final: 0.7421 (ttp) REVERT: B 287 MET cc_start: 0.8743 (mmm) cc_final: 0.8405 (mmm) REVERT: C 407 LEU cc_start: 0.9413 (tt) cc_final: 0.9118 (tm) REVERT: C 412 PHE cc_start: 0.8239 (t80) cc_final: 0.7989 (t80) REVERT: E 77 MET cc_start: 0.8871 (mmt) cc_final: 0.8382 (mmm) REVERT: E 263 TRP cc_start: 0.8949 (m-10) cc_final: 0.8738 (m-10) REVERT: E 329 GLN cc_start: 0.8804 (tp40) cc_final: 0.8319 (tp-100) outliers start: 3 outliers final: 0 residues processed: 465 average time/residue: 1.5480 time to fit residues: 802.4980 Evaluate side-chains 264 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 2.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 399 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 211 optimal weight: 0.1980 chunk 190 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 128 optimal weight: 0.0970 chunk 101 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 119 optimal weight: 0.0020 chunk 146 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN M 37 GLN ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 HIS L 5 GLN ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN D 107 HIS D 125 ASN D 150 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN A 125 ASN A 150 GLN A 186 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN A 266 GLN B 107 HIS B 125 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN C 46 ASN C 164 ASN C 177 GLN C 186 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 90 ASN E 138 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21442 Z= 0.228 Angle : 0.786 12.276 28932 Z= 0.367 Chirality : 0.048 0.441 3234 Planarity : 0.004 0.044 3574 Dihedral : 15.428 105.756 3369 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.64 % Allowed : 12.27 % Favored : 85.09 % 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: -3.24 (0.15), residues: 2522 helix: -1.58 (0.20), residues: 532 sheet: -2.32 (0.16), residues: 759 loop : -2.22 (0.17), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 239 HIS 0.006 0.001 HIS A 201 PHE 0.036 0.002 PHE B 409 TYR 0.021 0.002 TYR E 325 ARG 0.008 0.001 ARG M 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 319 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 LYS cc_start: 0.8761 (mmmm) cc_final: 0.8537 (mmpt) REVERT: F 13 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6741 (mmtt) REVERT: D 239 TRP cc_start: 0.8185 (m-10) cc_final: 0.7903 (m-10) REVERT: D 293 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: A 220 MET cc_start: 0.7695 (ptm) cc_final: 0.7327 (ttp) REVERT: B 235 VAL cc_start: 0.9651 (p) cc_final: 0.9405 (m) REVERT: B 412 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.8007 (t80) REVERT: C 239 TRP cc_start: 0.8645 (m-10) cc_final: 0.8431 (m-10) REVERT: C 412 PHE cc_start: 0.8206 (t80) cc_final: 0.7921 (t80) REVERT: E 217 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5793 (pp20) REVERT: E 263 TRP cc_start: 0.9092 (m-10) cc_final: 0.8537 (m-10) REVERT: E 290 GLU cc_start: 0.8600 (tp30) cc_final: 0.8353 (tp30) REVERT: E 329 GLN cc_start: 0.8874 (tp40) cc_final: 0.8387 (tp-100) outliers start: 59 outliers final: 17 residues processed: 355 average time/residue: 1.4530 time to fit residues: 583.1985 Evaluate side-chains 270 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 249 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 217 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 203 optimal weight: 0.5980 chunk 226 optimal weight: 1.9990 chunk 77 optimal weight: 0.0010 chunk 183 optimal weight: 2.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** H 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN A 305 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN C 125 ASN C 177 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 ASN ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21442 Z= 0.284 Angle : 0.757 11.980 28932 Z= 0.352 Chirality : 0.047 0.469 3234 Planarity : 0.004 0.044 3574 Dihedral : 13.675 98.972 3365 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.09 % Allowed : 13.61 % Favored : 83.30 % 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: -2.62 (0.16), residues: 2522 helix: -0.90 (0.22), residues: 532 sheet: -1.89 (0.17), residues: 732 loop : -1.96 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 243 HIS 0.011 0.002 HIS A 201 PHE 0.029 0.002 PHE B 409 TYR 0.016 0.002 TYR E 325 ARG 0.008 0.001 ARG M 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 279 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 9 LYS cc_start: 0.8767 (mmmm) cc_final: 0.8559 (mmpt) REVERT: G 89 GLU cc_start: 0.8499 (mp0) cc_final: 0.8121 (pp20) REVERT: F 74 LYS cc_start: 0.8658 (mttt) cc_final: 0.8413 (mttm) REVERT: M 42 GLN cc_start: 0.8665 (mt0) cc_final: 0.8457 (mt0) REVERT: L 63 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8492 (mtpp) REVERT: H 59 ASN cc_start: 0.8600 (t0) cc_final: 0.8304 (t160) REVERT: D 293 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8468 (m-80) REVERT: A 220 MET cc_start: 0.7809 (ptm) cc_final: 0.7453 (ttp) REVERT: A 305 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8660 (t0) REVERT: B 235 VAL cc_start: 0.9624 (p) cc_final: 0.9392 (m) REVERT: B 412 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.8008 (t80) REVERT: C 226 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7981 (tp-100) REVERT: C 239 TRP cc_start: 0.8697 (m-10) cc_final: 0.8470 (m-10) REVERT: C 263 MET cc_start: 0.9056 (mmm) cc_final: 0.8729 (mmm) REVERT: C 290 CYS cc_start: 0.9069 (m) cc_final: 0.8862 (m) REVERT: E 120 ASP cc_start: 0.8205 (p0) cc_final: 0.7950 (p0) REVERT: E 153 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7823 (mtt) REVERT: E 263 TRP cc_start: 0.9139 (m-10) cc_final: 0.8829 (m-10) REVERT: E 290 GLU cc_start: 0.8738 (tp30) cc_final: 0.8526 (tp30) REVERT: E 329 GLN cc_start: 0.8939 (tp40) cc_final: 0.8455 (tp-100) outliers start: 69 outliers final: 27 residues processed: 320 average time/residue: 1.4032 time to fit residues: 508.6935 Evaluate side-chains 280 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 248 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 284 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 225 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 118 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 229 optimal weight: 0.0070 chunk 242 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 217 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 79 GLN M 37 GLN ** L 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN H 27 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21442 Z= 0.192 Angle : 0.744 12.329 28932 Z= 0.339 Chirality : 0.046 0.437 3234 Planarity : 0.004 0.044 3574 Dihedral : 12.500 95.728 3365 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.00 % Allowed : 15.45 % Favored : 81.55 % 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: -2.32 (0.16), residues: 2522 helix: -0.68 (0.23), residues: 534 sheet: -1.67 (0.17), residues: 747 loop : -1.77 (0.18), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 239 HIS 0.010 0.001 HIS A 201 PHE 0.028 0.001 PHE A 409 TYR 0.017 0.001 TYR E 454 ARG 0.007 0.000 ARG I 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 280 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 89 GLU cc_start: 0.8504 (mp0) cc_final: 0.8121 (pp20) REVERT: G 107 TYR cc_start: 0.8336 (m-80) cc_final: 0.8106 (m-80) REVERT: F 74 LYS cc_start: 0.8636 (mttt) cc_final: 0.8375 (mttm) REVERT: F 82 GLN cc_start: 0.8988 (tt0) cc_final: 0.8535 (tp40) REVERT: M 83 LEU cc_start: 0.8120 (mm) cc_final: 0.7884 (mm) REVERT: I 9 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8499 (mmmt) REVERT: H 59 ASN cc_start: 0.8556 (t0) cc_final: 0.8279 (t160) REVERT: D 287 MET cc_start: 0.8354 (mmm) cc_final: 0.7728 (mtm) REVERT: D 293 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8478 (m-80) REVERT: A 247 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: A 412 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8141 (t80) REVERT: B 235 VAL cc_start: 0.9590 (p) cc_final: 0.9364 (m) REVERT: B 412 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7968 (t80) REVERT: C 226 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7977 (tp-100) REVERT: C 239 TRP cc_start: 0.8711 (m-10) cc_final: 0.8477 (m-10) REVERT: C 263 MET cc_start: 0.9193 (mmm) cc_final: 0.8632 (mmm) REVERT: C 290 CYS cc_start: 0.9202 (m) cc_final: 0.8908 (m) REVERT: C 412 PHE cc_start: 0.8279 (t80) cc_final: 0.8023 (t80) REVERT: E 120 ASP cc_start: 0.8203 (p0) cc_final: 0.7902 (p0) REVERT: E 153 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7821 (mtt) REVERT: E 217 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.6009 (pp20) REVERT: E 263 TRP cc_start: 0.9010 (m-10) cc_final: 0.8705 (m-10) REVERT: E 329 GLN cc_start: 0.8973 (tp40) cc_final: 0.8533 (tp-100) outliers start: 67 outliers final: 30 residues processed: 320 average time/residue: 1.3230 time to fit residues: 481.3484 Evaluate side-chains 289 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 252 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 284 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 202 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN M 37 GLN I 27 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 21442 Z= 0.361 Angle : 0.784 12.261 28932 Z= 0.365 Chirality : 0.047 0.534 3234 Planarity : 0.004 0.046 3574 Dihedral : 11.571 94.572 3365 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 3.76 % Allowed : 16.26 % Favored : 79.98 % 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: -2.07 (0.17), residues: 2522 helix: -0.33 (0.23), residues: 545 sheet: -1.56 (0.17), residues: 746 loop : -1.68 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 243 HIS 0.010 0.002 HIS A 201 PHE 0.025 0.002 PHE A 409 TYR 0.016 0.002 TYR E 231 ARG 0.006 0.001 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 257 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 82 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8416 (mm-40) REVERT: G 89 GLU cc_start: 0.8545 (mp0) cc_final: 0.8171 (pp20) REVERT: K 70 ASP cc_start: 0.8625 (t0) cc_final: 0.8305 (t0) REVERT: F 74 LYS cc_start: 0.8739 (mttt) cc_final: 0.8496 (mttm) REVERT: F 82 GLN cc_start: 0.9030 (tt0) cc_final: 0.8526 (tp40) REVERT: L 63 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8467 (mtpp) REVERT: H 59 ASN cc_start: 0.8630 (t0) cc_final: 0.8377 (t160) REVERT: D 293 PHE cc_start: 0.8998 (OUTLIER) cc_final: 0.8659 (m-80) REVERT: D 392 LYS cc_start: 0.8686 (ptpp) cc_final: 0.8311 (ptpp) REVERT: A 220 MET cc_start: 0.8025 (ptm) cc_final: 0.7663 (ttp) REVERT: A 247 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7787 (m-30) REVERT: A 412 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8200 (t80) REVERT: B 412 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7991 (t80) REVERT: C 226 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8103 (tp-100) REVERT: C 263 MET cc_start: 0.9254 (mmm) cc_final: 0.9052 (mmm) REVERT: C 293 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8401 (m-10) REVERT: C 412 PHE cc_start: 0.8295 (t80) cc_final: 0.7995 (t80) REVERT: E 77 MET cc_start: 0.9026 (mmt) cc_final: 0.8447 (mmm) REVERT: E 153 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7747 (mtt) REVERT: E 217 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6214 (pp20) REVERT: E 263 TRP cc_start: 0.9133 (m-10) cc_final: 0.8773 (m-10) REVERT: E 329 GLN cc_start: 0.9011 (tp40) cc_final: 0.8628 (tp-100) outliers start: 84 outliers final: 39 residues processed: 309 average time/residue: 1.2829 time to fit residues: 454.5419 Evaluate side-chains 288 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 240 time to evaluate : 2.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain E residue 153 MET Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 284 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 81 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 142 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN C 177 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21442 Z= 0.286 Angle : 0.758 11.958 28932 Z= 0.350 Chirality : 0.047 0.515 3234 Planarity : 0.004 0.045 3574 Dihedral : 10.503 93.546 3365 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.90 % Allowed : 17.38 % Favored : 78.73 % 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: -1.88 (0.17), residues: 2522 helix: -0.18 (0.23), residues: 548 sheet: -1.44 (0.18), residues: 746 loop : -1.54 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 239 HIS 0.009 0.002 HIS A 201 PHE 0.025 0.002 PHE A 409 TYR 0.018 0.002 TYR G 107 ARG 0.010 0.001 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 251 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 82 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8380 (mm-40) REVERT: G 89 GLU cc_start: 0.8549 (mp0) cc_final: 0.8193 (pp20) REVERT: G 90 ASP cc_start: 0.8363 (m-30) cc_final: 0.7781 (m-30) REVERT: K 70 ASP cc_start: 0.8617 (t0) cc_final: 0.8304 (t0) REVERT: F 74 LYS cc_start: 0.8723 (mttt) cc_final: 0.8477 (mttm) REVERT: F 82 GLN cc_start: 0.9065 (tt0) cc_final: 0.8586 (tp40) REVERT: L 50 GLU cc_start: 0.8620 (pt0) cc_final: 0.8317 (pt0) REVERT: L 52 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8878 (tt) REVERT: L 74 LYS cc_start: 0.8898 (mppt) cc_final: 0.8515 (mptt) REVERT: H 59 ASN cc_start: 0.8615 (t0) cc_final: 0.8350 (t160) REVERT: D 287 MET cc_start: 0.8255 (mmm) cc_final: 0.7780 (mtm) REVERT: D 293 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8728 (m-80) REVERT: A 29 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.7999 (ptm-80) REVERT: A 220 MET cc_start: 0.7943 (ptm) cc_final: 0.7559 (ttp) REVERT: A 412 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8196 (t80) REVERT: B 56 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8800 (mmm) REVERT: B 412 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.8001 (t80) REVERT: C 226 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8130 (tm-30) REVERT: C 293 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8367 (m-10) REVERT: C 412 PHE cc_start: 0.8224 (t80) cc_final: 0.7972 (t80) REVERT: E 77 MET cc_start: 0.9031 (mmt) cc_final: 0.8501 (mmm) REVERT: E 214 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8060 (pp20) REVERT: E 263 TRP cc_start: 0.9112 (m-10) cc_final: 0.8760 (m-10) REVERT: E 329 GLN cc_start: 0.9013 (tp40) cc_final: 0.8665 (tp-100) outliers start: 87 outliers final: 44 residues processed: 312 average time/residue: 1.2977 time to fit residues: 461.8867 Evaluate side-chains 288 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 234 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 82 ASP Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 284 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 234 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 241 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 HIS M 42 GLN ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 HIS ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 ASN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21442 Z= 0.310 Angle : 0.775 12.066 28932 Z= 0.359 Chirality : 0.047 0.520 3234 Planarity : 0.004 0.045 3574 Dihedral : 9.895 90.561 3365 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.76 % Allowed : 18.32 % Favored : 77.92 % 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: -1.76 (0.17), residues: 2522 helix: 0.01 (0.23), residues: 551 sheet: -1.40 (0.18), residues: 746 loop : -1.49 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 243 HIS 0.009 0.002 HIS A 201 PHE 0.025 0.002 PHE A 409 TYR 0.017 0.002 TYR G 107 ARG 0.008 0.001 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 244 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 82 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8409 (mm-40) REVERT: G 89 GLU cc_start: 0.8564 (mp0) cc_final: 0.8230 (pp20) REVERT: K 70 ASP cc_start: 0.8647 (t0) cc_final: 0.8350 (t0) REVERT: F 74 LYS cc_start: 0.8730 (mttt) cc_final: 0.8487 (mttm) REVERT: F 89 GLU cc_start: 0.8334 (mp0) cc_final: 0.8116 (pm20) REVERT: L 74 LYS cc_start: 0.8860 (mppt) cc_final: 0.8523 (mptt) REVERT: H 59 ASN cc_start: 0.8630 (t0) cc_final: 0.8374 (t160) REVERT: D 103 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7598 (pt0) REVERT: D 287 MET cc_start: 0.8360 (mmm) cc_final: 0.7822 (mtm) REVERT: D 293 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8820 (m-80) REVERT: A 29 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.7957 (ptm-80) REVERT: A 220 MET cc_start: 0.7958 (ptm) cc_final: 0.7543 (ttp) REVERT: A 412 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8163 (t80) REVERT: B 56 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8812 (mmm) REVERT: B 239 TRP cc_start: 0.8219 (m-10) cc_final: 0.7594 (m-10) REVERT: B 412 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.7998 (t80) REVERT: C 226 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: C 239 TRP cc_start: 0.8663 (m-10) cc_final: 0.8232 (m-90) REVERT: C 263 MET cc_start: 0.9202 (mmm) cc_final: 0.8646 (mmm) REVERT: C 293 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8383 (m-10) REVERT: C 412 PHE cc_start: 0.8208 (t80) cc_final: 0.7867 (t80) REVERT: E 77 MET cc_start: 0.9039 (mmt) cc_final: 0.8503 (mmm) REVERT: E 214 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8112 (pp20) REVERT: E 217 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6274 (pp20) REVERT: E 263 TRP cc_start: 0.9137 (m-10) cc_final: 0.8806 (m-10) REVERT: E 329 GLN cc_start: 0.9034 (tp40) cc_final: 0.8703 (tp-100) outliers start: 84 outliers final: 49 residues processed: 304 average time/residue: 1.3174 time to fit residues: 456.3459 Evaluate side-chains 291 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 231 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 284 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 149 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 chunk 119 optimal weight: 0.0870 chunk 22 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 HIS ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21442 Z= 0.195 Angle : 0.755 12.424 28932 Z= 0.346 Chirality : 0.046 0.474 3234 Planarity : 0.003 0.045 3574 Dihedral : 9.212 85.013 3365 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.27 % Allowed : 18.94 % Favored : 77.79 % 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: -1.60 (0.17), residues: 2522 helix: 0.07 (0.24), residues: 551 sheet: -1.24 (0.18), residues: 746 loop : -1.41 (0.18), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 243 HIS 0.008 0.001 HIS A 201 PHE 0.024 0.001 PHE A 409 TYR 0.016 0.001 TYR E 325 ARG 0.008 0.000 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 252 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 89 GLU cc_start: 0.8540 (mp0) cc_final: 0.8241 (pp20) REVERT: G 90 ASP cc_start: 0.8307 (m-30) cc_final: 0.7719 (m-30) REVERT: K 70 ASP cc_start: 0.8642 (t0) cc_final: 0.8352 (t0) REVERT: F 74 LYS cc_start: 0.8711 (mttt) cc_final: 0.8475 (mttt) REVERT: L 74 LYS cc_start: 0.8837 (mppt) cc_final: 0.8474 (mptt) REVERT: I 75 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7319 (tp) REVERT: H 59 ASN cc_start: 0.8597 (t0) cc_final: 0.8311 (t160) REVERT: D 56 MET cc_start: 0.8755 (tpp) cc_final: 0.8389 (mmm) REVERT: D 103 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7547 (pt0) REVERT: D 287 MET cc_start: 0.8317 (mmm) cc_final: 0.7701 (mtm) REVERT: D 293 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8815 (m-80) REVERT: A 29 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8051 (ptm-80) REVERT: A 220 MET cc_start: 0.7936 (ptm) cc_final: 0.7570 (ttp) REVERT: A 287 MET cc_start: 0.8355 (mmm) cc_final: 0.8153 (mtp) REVERT: A 412 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8102 (t80) REVERT: B 239 TRP cc_start: 0.8120 (m-10) cc_final: 0.7565 (m-10) REVERT: C 226 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: C 239 TRP cc_start: 0.8646 (m-10) cc_final: 0.8214 (m-90) REVERT: C 263 MET cc_start: 0.9202 (mmm) cc_final: 0.8850 (mmm) REVERT: C 412 PHE cc_start: 0.8043 (t80) cc_final: 0.7801 (t80) REVERT: E 77 MET cc_start: 0.9054 (mmt) cc_final: 0.8543 (mmm) REVERT: E 263 TRP cc_start: 0.9074 (m-10) cc_final: 0.8745 (m-10) REVERT: E 329 GLN cc_start: 0.9033 (tp40) cc_final: 0.8674 (tp-100) outliers start: 73 outliers final: 40 residues processed: 303 average time/residue: 1.2432 time to fit residues: 432.4484 Evaluate side-chains 277 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 231 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 284 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 220 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 203 optimal weight: 0.7980 chunk 213 optimal weight: 7.9990 chunk 224 optimal weight: 0.0060 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN F 6 GLN ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21442 Z= 0.307 Angle : 0.798 13.002 28932 Z= 0.368 Chirality : 0.047 0.514 3234 Planarity : 0.004 0.053 3574 Dihedral : 8.717 79.472 3365 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.82 % Allowed : 19.30 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.17), residues: 2522 helix: 0.14 (0.23), residues: 562 sheet: -1.25 (0.18), residues: 753 loop : -1.41 (0.19), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 243 HIS 0.010 0.002 HIS A 201 PHE 0.023 0.002 PHE A 409 TYR 0.019 0.002 TYR G 107 ARG 0.011 0.001 ARG I 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 232 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 89 GLU cc_start: 0.8565 (mp0) cc_final: 0.8266 (pp20) REVERT: G 90 ASP cc_start: 0.8365 (m-30) cc_final: 0.7806 (m-30) REVERT: F 74 LYS cc_start: 0.8744 (mttt) cc_final: 0.8500 (mttm) REVERT: H 59 ASN cc_start: 0.8608 (t0) cc_final: 0.8345 (t160) REVERT: D 103 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: D 140 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8123 (mpp) REVERT: D 287 MET cc_start: 0.8410 (mmm) cc_final: 0.7771 (mtm) REVERT: D 392 LYS cc_start: 0.8748 (pttt) cc_final: 0.8510 (ptpp) REVERT: A 29 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.7915 (ptm-80) REVERT: A 220 MET cc_start: 0.7969 (ptm) cc_final: 0.7564 (ttp) REVERT: A 412 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8152 (t80) REVERT: B 239 TRP cc_start: 0.8139 (m-10) cc_final: 0.7578 (m-10) REVERT: B 412 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7956 (t80) REVERT: C 226 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: C 227 MET cc_start: 0.8655 (mmt) cc_final: 0.8321 (mmm) REVERT: C 239 TRP cc_start: 0.8734 (m-10) cc_final: 0.8305 (m-90) REVERT: C 263 MET cc_start: 0.9216 (mmm) cc_final: 0.8565 (mmm) REVERT: C 412 PHE cc_start: 0.8121 (t80) cc_final: 0.7855 (t80) REVERT: E 77 MET cc_start: 0.9064 (mmt) cc_final: 0.8531 (mmm) REVERT: E 217 GLU cc_start: 0.6783 (pp20) cc_final: 0.6562 (pp20) REVERT: E 263 TRP cc_start: 0.9131 (m-10) cc_final: 0.8788 (m-10) REVERT: E 329 GLN cc_start: 0.9056 (tp40) cc_final: 0.8689 (tp-100) outliers start: 63 outliers final: 45 residues processed: 276 average time/residue: 1.3468 time to fit residues: 423.2063 Evaluate side-chains 275 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 224 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 17 ASP Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain D residue 18 MET Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 412 PHE Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 148 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 145 optimal weight: 0.0970 chunk 113 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 250 optimal weight: 0.0170 chunk 230 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 153 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 79 GLN F 3 GLN ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21442 Z= 0.188 Angle : 0.786 18.778 28932 Z= 0.356 Chirality : 0.046 0.460 3234 Planarity : 0.004 0.076 3574 Dihedral : 8.173 71.311 3365 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.15 % Allowed : 19.88 % Favored : 77.97 % 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: -1.49 (0.17), residues: 2522 helix: 0.12 (0.23), residues: 561 sheet: -1.05 (0.18), residues: 747 loop : -1.42 (0.18), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 243 HIS 0.008 0.001 HIS A 201 PHE 0.023 0.001 PHE A 409 TYR 0.017 0.001 TYR E 454 ARG 0.024 0.001 ARG K 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5044 Ramachandran restraints generated. 2522 Oldfield, 0 Emsley, 2522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 247 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 11 MET cc_start: 0.7144 (mpp) cc_final: 0.6831 (mpm) REVERT: G 89 GLU cc_start: 0.8548 (mp0) cc_final: 0.8290 (pp20) REVERT: G 90 ASP cc_start: 0.8279 (m-30) cc_final: 0.7775 (m-30) REVERT: F 74 LYS cc_start: 0.8735 (mttt) cc_final: 0.8490 (mttm) REVERT: F 82 GLN cc_start: 0.8986 (tt0) cc_final: 0.8615 (tp40) REVERT: L 63 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8579 (mtpp) REVERT: L 74 LYS cc_start: 0.8773 (mppt) cc_final: 0.8368 (mptt) REVERT: H 59 ASN cc_start: 0.8546 (t0) cc_final: 0.8276 (t160) REVERT: D 56 MET cc_start: 0.8689 (tpp) cc_final: 0.8382 (mmm) REVERT: D 103 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7514 (pt0) REVERT: D 287 MET cc_start: 0.8340 (mmm) cc_final: 0.7716 (mtm) REVERT: D 392 LYS cc_start: 0.8722 (pttt) cc_final: 0.8475 (ptpp) REVERT: A 29 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8102 (ptm-80) REVERT: A 220 MET cc_start: 0.7915 (ptm) cc_final: 0.7513 (ttp) REVERT: A 412 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8139 (t80) REVERT: B 239 TRP cc_start: 0.8006 (m-10) cc_final: 0.7491 (m-10) REVERT: C 226 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: C 227 MET cc_start: 0.8592 (mmt) cc_final: 0.8229 (mmm) REVERT: C 239 TRP cc_start: 0.8684 (m-10) cc_final: 0.8293 (m-90) REVERT: C 412 PHE cc_start: 0.8041 (t80) cc_final: 0.7815 (t80) REVERT: E 77 MET cc_start: 0.9041 (mmt) cc_final: 0.8537 (mmm) REVERT: E 263 TRP cc_start: 0.9067 (m-10) cc_final: 0.8789 (m-10) REVERT: E 281 ILE cc_start: 0.9505 (pt) cc_final: 0.9242 (pp) REVERT: E 329 GLN cc_start: 0.9082 (tp40) cc_final: 0.8644 (tp-100) outliers start: 48 outliers final: 32 residues processed: 279 average time/residue: 1.3408 time to fit residues: 428.5989 Evaluate side-chains 267 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 231 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 98 MET Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 85 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain A residue 29 ARG Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 402 PHE Chi-restraints excluded: chain A residue 412 PHE Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 251 random chunks: chunk 158 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN ** L 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.065832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.049989 restraints weight = 78142.137| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.57 r_work: 0.2955 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21442 Z= 0.260 Angle : 0.791 12.486 28932 Z= 0.362 Chirality : 0.046 0.503 3234 Planarity : 0.004 0.057 3574 Dihedral : 7.805 64.189 3365 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.24 % Allowed : 20.24 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.17), residues: 2522 helix: 0.17 (0.23), residues: 563 sheet: -1.04 (0.18), residues: 753 loop : -1.40 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 243 HIS 0.008 0.001 HIS A 201 PHE 0.027 0.001 PHE D 295 TYR 0.016 0.001 TYR G 107 ARG 0.014 0.001 ARG K 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8239.56 seconds wall clock time: 148 minutes 8.11 seconds (8888.11 seconds total)