Starting phenix.real_space_refine on Tue Jul 23 07:37:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q84_18246/07_2024/8q84_18246.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q84_18246/07_2024/8q84_18246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q84_18246/07_2024/8q84_18246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q84_18246/07_2024/8q84_18246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q84_18246/07_2024/8q84_18246.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q84_18246/07_2024/8q84_18246.cif" } resolution = 3.15 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= 0.004 sd= 0.040 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 80 5.16 5 C 13453 2.51 5 N 3918 2.21 5 O 4351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ASP 72": "OD1" <-> "OD2" Residue "I GLU 96": "OE1" <-> "OE2" Residue "I GLU 113": "OE1" <-> "OE2" Residue "I ASP 136": "OD1" <-> "OD2" Residue "J ASP 108": "OD1" <-> "OD2" Residue "J ASP 146": "OD1" <-> "OD2" Residue "K GLU 75": "OE1" <-> "OE2" Residue "K GLU 122": "OE1" <-> "OE2" Residue "L GLU 22": "OE1" <-> "OE2" Residue "M GLU 2": "OE1" <-> "OE2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "N ASP 22": "OD1" <-> "OD2" Residue "N ASP 27": "OD1" <-> "OD2" Residue "N GLU 32": "OE1" <-> "OE2" Residue "O TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "O TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 119": "OD1" <-> "OD2" Residue "O GLU 189": "OE1" <-> "OE2" Residue "O PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "P GLU 51": "OE1" <-> "OE2" Residue "P ASP 55": "OD1" <-> "OD2" Residue "R PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 69": "OE1" <-> "OE2" Residue "U GLU 89": "OE1" <-> "OE2" Residue "U ASP 93": "OD1" <-> "OD2" Residue "U GLU 96": "OE1" <-> "OE2" Residue "U ASP 120": "OD1" <-> "OD2" Residue "U GLU 135": "OE1" <-> "OE2" Residue "V TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 135": "OD1" <-> "OD2" Residue "W GLU 34": "OE1" <-> "OE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "W ASP 47": "OD1" <-> "OD2" Residue "W ASP 57": "OD1" <-> "OD2" Residue "X GLU 58": "OE1" <-> "OE2" Residue "X ASP 64": "OD1" <-> "OD2" Residue "X GLU 74": "OE1" <-> "OE2" Residue "Y GLU 25": "OE1" <-> "OE2" Residue "Z GLU 2": "OE1" <-> "OE2" Residue "Z ASP 22": "OD1" <-> "OD2" Residue "Z ASP 27": "OD1" <-> "OD2" Residue "Z TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 51": "OD1" <-> "OD2" Residue "Z GLU 61": "OE1" <-> "OE2" Residue "a ASP 17": "OD1" <-> "OD2" Residue "a PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 182": "OE1" <-> "OE2" Residue "a PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 8": "OE1" <-> "OE2" Residue "b GLU 11": "OE1" <-> "OE2" Residue "b GLU 16": "OE1" <-> "OE2" Residue "b ASP 25": "OD1" <-> "OD2" Residue "b GLU 48": "OE1" <-> "OE2" Residue "c GLU 18": "OE1" <-> "OE2" Residue "c GLU 39": "OE1" <-> "OE2" Residue "d GLU 13": "OE1" <-> "OE2" Residue "d GLU 24": "OE1" <-> "OE2" Residue "d GLU 31": "OE1" <-> "OE2" Residue "d PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 52": "OE1" <-> "OE2" Residue "d TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 64": "OE1" <-> "OE2" Residue "d GLU 65": "OE1" <-> "OE2" Residue "d GLU 67": "OE1" <-> "OE2" Residue "d ASP 75": "OD1" <-> "OD2" Residue "d GLU 87": "OE1" <-> "OE2" Residue "d ASP 89": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 21802 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 1463 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 282} Link IDs: {'PTRANS': 2, 'TRANS': 291} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 966 Unresolved non-hydrogen angles: 1196 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 15, 'TYR:plan': 3, 'ASN:plan1': 20, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 39, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 490 Chain: "B" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1180 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 230} Link IDs: {'PTRANS': 1, 'TRANS': 235} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 785 Unresolved non-hydrogen angles: 987 Unresolved non-hydrogen dihedrals: 617 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 17, 'ASP:plan': 18, 'PHE:plan': 5, 'GLU:plan': 30, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 398 Chain: "F" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 1463 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 282} Link IDs: {'PTRANS': 2, 'TRANS': 291} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 966 Unresolved non-hydrogen angles: 1196 Unresolved non-hydrogen dihedrals: 778 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 15, 'TYR:plan': 3, 'ASN:plan1': 20, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 39, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 490 Chain: "G" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1175 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 229} Link IDs: {'PTRANS': 1, 'TRANS': 234} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 782 Unresolved non-hydrogen angles: 983 Unresolved non-hydrogen dihedrals: 615 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 17, 'ASP:plan': 18, 'PHE:plan': 5, 'GLU:plan': 30, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 398 Chain: "I" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 935 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain: "K" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 837 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "L" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 485 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "M" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "N" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 744 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "O" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1929 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "P" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 527 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "Q" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 527 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "R" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 859 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "U" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 757 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "V" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 935 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain: "W" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 837 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "X" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 535 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "Y" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "Z" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "a" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1925 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Chain breaks: 1 Chain: "b" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 561 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "c" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 527 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "d" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 859 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "e" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 82 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Time building chain proxies: 13.46, per 1000 atoms: 0.62 Number of scatterers: 21802 At special positions: 0 Unit cell: (296.8, 157.94, 263.94, 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 80 16.00 O 4351 8.00 N 3918 7.00 C 13453 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 9.96 Conformation dependent library (CDL) restraints added in 4.2 seconds 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6022 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 8 sheets defined 86.9% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 372 through 393 removed outlier: 4.420A pdb=" N GLY A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.757A pdb=" N ASN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 479 removed outlier: 3.794A pdb=" N GLN A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 removed outlier: 3.619A pdb=" N LEU A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.846A pdb=" N LEU A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 663 Processing helix chain 'B' and resid 212 through 244 removed outlier: 3.543A pdb=" N GLU B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER B 239 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 244 " --> pdb=" O ASN B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 Processing helix chain 'B' and resid 252 through 307 removed outlier: 3.708A pdb=" N SER B 256 " --> pdb=" O MET B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 337 Processing helix chain 'B' and resid 339 through 386 Processing helix chain 'B' and resid 386 through 401 Processing helix chain 'B' and resid 405 through 446 removed outlier: 3.547A pdb=" N ASN B 444 " --> pdb=" O ASN B 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 393 removed outlier: 4.527A pdb=" N GLY F 376 " --> pdb=" O GLN F 372 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS F 393 " --> pdb=" O GLU F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.841A pdb=" N ASN F 398 " --> pdb=" O ALA F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 479 removed outlier: 3.874A pdb=" N GLN F 421 " --> pdb=" O GLU F 417 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU F 422 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU F 479 " --> pdb=" O SER F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 489 removed outlier: 3.776A pdb=" N LEU F 488 " --> pdb=" O ASN F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 499 Processing helix chain 'F' and resid 506 through 511 removed outlier: 3.743A pdb=" N LEU F 510 " --> pdb=" O SER F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 663 Processing helix chain 'G' and resid 213 through 244 removed outlier: 4.057A pdb=" N LEU G 237 " --> pdb=" O GLN G 233 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU G 238 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER G 239 " --> pdb=" O VAL G 235 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN G 240 " --> pdb=" O GLU G 236 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU G 244 " --> pdb=" O ASN G 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 248 Processing helix chain 'G' and resid 252 through 307 removed outlier: 3.735A pdb=" N SER G 256 " --> pdb=" O MET G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 337 Processing helix chain 'G' and resid 339 through 386 Processing helix chain 'G' and resid 386 through 401 Processing helix chain 'G' and resid 405 through 446 removed outlier: 3.559A pdb=" N ASN G 444 " --> pdb=" O ASN G 440 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET G 446 " --> pdb=" O TYR G 442 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 110 Proline residue: I 65 - end of helix Processing helix chain 'I' and resid 120 through 151 Processing helix chain 'J' and resid 61 through 126 removed outlier: 4.433A pdb=" N LEU J 89 " --> pdb=" O LEU J 85 " (cutoff:3.500A) Proline residue: J 90 - end of helix removed outlier: 3.655A pdb=" N ASP J 126 " --> pdb=" O LYS J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 143 removed outlier: 3.817A pdb=" N LEU J 130 " --> pdb=" O ASP J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 176 Processing helix chain 'K' and resid 3 through 54 Processing helix chain 'K' and resid 54 through 67 removed outlier: 3.800A pdb=" N SER K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 73 removed outlier: 3.545A pdb=" N GLN K 72 " --> pdb=" O LEU K 68 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR K 73 " --> pdb=" O GLY K 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 68 through 73' Processing helix chain 'K' and resid 74 through 79 removed outlier: 3.602A pdb=" N TYR K 78 " --> pdb=" O GLU K 75 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU K 79 " --> pdb=" O GLY K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 Processing helix chain 'L' and resid 16 through 57 Processing helix chain 'L' and resid 58 through 67 removed outlier: 3.958A pdb=" N VAL L 62 " --> pdb=" O GLU L 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 65 removed outlier: 3.695A pdb=" N GLN M 7 " --> pdb=" O ASN M 3 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ASN M 43 " --> pdb=" O ASN M 39 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU M 45 " --> pdb=" O ASN M 41 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR M 65 " --> pdb=" O ASN M 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 6 through 35 Processing helix chain 'N' and resid 53 through 65 removed outlier: 3.827A pdb=" N ASP N 59 " --> pdb=" O GLN N 55 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS N 63 " --> pdb=" O ASP N 59 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY N 65 " --> pdb=" O GLU N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 94 removed outlier: 3.753A pdb=" N LYS N 72 " --> pdb=" O GLY N 68 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS N 94 " --> pdb=" O GLY N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 22 Processing helix chain 'O' and resid 28 through 38 removed outlier: 3.568A pdb=" N ASN O 32 " --> pdb=" O GLY O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 51 removed outlier: 3.811A pdb=" N ARG O 45 " --> pdb=" O LYS O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 63 Processing helix chain 'O' and resid 81 through 99 Processing helix chain 'O' and resid 111 through 125 removed outlier: 3.521A pdb=" N TYR O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS O 118 " --> pdb=" O VAL O 114 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU O 121 " --> pdb=" O ASN O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 168 Processing helix chain 'O' and resid 171 through 184 Processing helix chain 'O' and resid 206 through 221 Processing helix chain 'O' and resid 223 through 265 removed outlier: 3.647A pdb=" N LEU O 253 " --> pdb=" O LYS O 249 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 57 removed outlier: 3.698A pdb=" N GLU P 11 " --> pdb=" O GLU P 7 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE P 40 " --> pdb=" O THR P 36 " (cutoff:3.500A) Proline residue: P 41 - end of helix Processing helix chain 'P' and resid 57 through 69 removed outlier: 4.271A pdb=" N THR P 67 " --> pdb=" O MET P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 40 removed outlier: 3.591A pdb=" N HIS Q 14 " --> pdb=" O ASN Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 63 Processing helix chain 'R' and resid 2 through 40 Proline residue: R 32 - end of helix removed outlier: 4.112A pdb=" N MET R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 65 Processing helix chain 'R' and resid 65 through 108 Processing helix chain 'U' and resid 58 through 111 Proline residue: U 65 - end of helix removed outlier: 3.556A pdb=" N CYS U 111 " --> pdb=" O SER U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 120 through 151 Processing helix chain 'V' and resid 61 through 126 removed outlier: 4.450A pdb=" N LEU V 89 " --> pdb=" O LEU V 85 " (cutoff:3.500A) Proline residue: V 90 - end of helix removed outlier: 3.809A pdb=" N ASP V 126 " --> pdb=" O LYS V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 126 through 143 Processing helix chain 'V' and resid 146 through 150 Processing helix chain 'V' and resid 151 through 176 Processing helix chain 'W' and resid 3 through 67 removed outlier: 4.562A pdb=" N ASN W 55 " --> pdb=" O GLN W 51 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TRP W 56 " --> pdb=" O LEU W 52 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP W 57 " --> pdb=" O MET W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 73 Processing helix chain 'W' and resid 75 through 79 removed outlier: 3.812A pdb=" N GLU W 79 " --> pdb=" O GLY W 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 84 Processing helix chain 'X' and resid 14 through 57 Processing helix chain 'X' and resid 58 through 67 removed outlier: 4.080A pdb=" N VAL X 62 " --> pdb=" O GLU X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 80 Processing helix chain 'Y' and resid 4 through 42 removed outlier: 4.041A pdb=" N VAL Y 8 " --> pdb=" O PRO Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 65 Processing helix chain 'Z' and resid 6 through 35 Processing helix chain 'Z' and resid 53 through 65 removed outlier: 3.922A pdb=" N ASP Z 59 " --> pdb=" O GLN Z 55 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS Z 63 " --> pdb=" O ASP Z 59 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY Z 65 " --> pdb=" O GLU Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 94 removed outlier: 3.827A pdb=" N LYS Z 72 " --> pdb=" O GLY Z 68 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL Z 75 " --> pdb=" O LEU Z 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 22 Processing helix chain 'a' and resid 29 through 37 Processing helix chain 'a' and resid 40 through 51 Processing helix chain 'a' and resid 56 through 63 Processing helix chain 'a' and resid 81 through 99 Processing helix chain 'a' and resid 111 through 125 removed outlier: 4.221A pdb=" N LYS a 118 " --> pdb=" O VAL a 114 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU a 121 " --> pdb=" O ASN a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 158 through 168 Processing helix chain 'a' and resid 171 through 183 Processing helix chain 'a' and resid 206 through 221 Processing helix chain 'a' and resid 223 through 265 removed outlier: 4.272A pdb=" N SER a 242 " --> pdb=" O GLU a 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 38 Processing helix chain 'b' and resid 38 through 57 Processing helix chain 'b' and resid 57 through 69 Processing helix chain 'c' and resid 2 through 39 Processing helix chain 'c' and resid 44 through 63 Processing helix chain 'd' and resid 2 through 40 Proline residue: d 32 - end of helix removed outlier: 3.741A pdb=" N THR d 39 " --> pdb=" O ASN d 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 65 Processing helix chain 'd' and resid 65 through 108 Processing sheet with id=AA1, first strand: chain 'I' and resid 112 through 114 Processing sheet with id=AA2, first strand: chain 'O' and resid 52 through 54 Processing sheet with id=AA3, first strand: chain 'O' and resid 64 through 67 Processing sheet with id=AA4, first strand: chain 'O' and resid 185 through 189 Processing sheet with id=AA5, first strand: chain 'U' and resid 112 through 113 Processing sheet with id=AA6, first strand: chain 'a' and resid 52 through 54 removed outlier: 3.660A pdb=" N ILE W 127 " --> pdb=" O ARG d 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 64 through 67 Processing sheet with id=AA8, first strand: chain 'a' and resid 185 through 189 2257 hydrogen bonds defined for protein. 6720 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: 7.33 Time building geometry restraints manager: 10.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5190 1.33 - 1.45: 3923 1.45 - 1.58: 12737 1.58 - 1.70: 0 1.70 - 1.82: 142 Bond restraints: 21992 Sorted by residual: bond pdb=" N LYS N 72 " pdb=" CA LYS N 72 " ideal model delta sigma weight residual 1.459 1.405 0.054 1.17e-02 7.31e+03 2.13e+01 bond pdb=" C LEU N 71 " pdb=" N LYS N 72 " ideal model delta sigma weight residual 1.334 1.298 0.036 1.23e-02 6.61e+03 8.47e+00 bond pdb=" CA LYS N 72 " pdb=" CB LYS N 72 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.57e-02 4.06e+03 7.95e+00 bond pdb=" C LYS N 72 " pdb=" O LYS N 72 " ideal model delta sigma weight residual 1.236 1.211 0.025 1.15e-02 7.56e+03 4.89e+00 bond pdb=" CA LYS N 72 " pdb=" C LYS N 72 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.24e-02 6.50e+03 2.98e+00 ... (remaining 21987 not shown) Histogram of bond angle deviations from ideal: 98.86 - 105.88: 225 105.88 - 112.91: 12272 112.91 - 119.94: 7018 119.94 - 126.96: 10239 126.96 - 133.99: 123 Bond angle restraints: 29877 Sorted by residual: angle pdb=" CA MET I 143 " pdb=" CB MET I 143 " pdb=" CG MET I 143 " ideal model delta sigma weight residual 114.10 123.86 -9.76 2.00e+00 2.50e-01 2.38e+01 angle pdb=" CA MET U 143 " pdb=" CB MET U 143 " pdb=" CG MET U 143 " ideal model delta sigma weight residual 114.10 123.43 -9.33 2.00e+00 2.50e-01 2.17e+01 angle pdb=" CA ARG d 57 " pdb=" CB ARG d 57 " pdb=" CG ARG d 57 " ideal model delta sigma weight residual 114.10 122.47 -8.37 2.00e+00 2.50e-01 1.75e+01 angle pdb=" CA TYR Z 16 " pdb=" CB TYR Z 16 " pdb=" CG TYR Z 16 " ideal model delta sigma weight residual 113.90 121.42 -7.52 1.80e+00 3.09e-01 1.75e+01 angle pdb=" CA GLN d 85 " pdb=" CB GLN d 85 " pdb=" CG GLN d 85 " ideal model delta sigma weight residual 114.10 122.27 -8.17 2.00e+00 2.50e-01 1.67e+01 ... (remaining 29872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 12030 17.22 - 34.43: 1131 34.43 - 51.65: 316 51.65 - 68.86: 57 68.86 - 86.08: 27 Dihedral angle restraints: 13561 sinusoidal: 4396 harmonic: 9165 Sorted by residual: dihedral pdb=" CA ILE Z 53 " pdb=" C ILE Z 53 " pdb=" N LEU Z 54 " pdb=" CA LEU Z 54 " ideal model delta harmonic sigma weight residual -180.00 -154.92 -25.08 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA LEU I 63 " pdb=" C LEU I 63 " pdb=" N LEU I 64 " pdb=" CA LEU I 64 " ideal model delta harmonic sigma weight residual -180.00 -161.68 -18.32 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA ASP O 119 " pdb=" CB ASP O 119 " pdb=" CG ASP O 119 " pdb=" OD1 ASP O 119 " ideal model delta sinusoidal sigma weight residual -30.00 -89.96 59.96 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 13558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3265 0.066 - 0.132: 337 0.132 - 0.197: 22 0.197 - 0.263: 3 0.263 - 0.329: 2 Chirality restraints: 3629 Sorted by residual: chirality pdb=" CG LEU R 97 " pdb=" CB LEU R 97 " pdb=" CD1 LEU R 97 " pdb=" CD2 LEU R 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB VAL O 251 " pdb=" CA VAL O 251 " pdb=" CG1 VAL O 251 " pdb=" CG2 VAL O 251 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CG LEU Z 78 " pdb=" CB LEU Z 78 " pdb=" CD1 LEU Z 78 " pdb=" CD2 LEU Z 78 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 3626 not shown) Planarity restraints: 3977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU I 64 " 0.056 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO I 65 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO I 65 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO I 65 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP U 120 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.08e+00 pdb=" C ASP U 120 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP U 120 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE U 121 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU X 58 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C GLU X 58 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU X 58 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE X 59 " -0.016 2.00e-02 2.50e+03 ... (remaining 3974 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 267 2.62 - 3.19: 21632 3.19 - 3.76: 38930 3.76 - 4.33: 44268 4.33 - 4.90: 72870 Nonbonded interactions: 177967 Sorted by model distance: nonbonded pdb=" O ILE O 247 " pdb=" OH TYR R 95 " model vdw 2.054 2.440 nonbonded pdb=" OG SER W 3 " pdb=" OD1 ASP W 5 " model vdw 2.125 2.440 nonbonded pdb=" OE1 GLU a 182 " pdb=" ND2 ASN a 183 " model vdw 2.143 2.520 nonbonded pdb=" NZ LYS V 79 " pdb=" OD2 ASP Z 22 " model vdw 2.182 2.520 nonbonded pdb=" OE2 GLU U 96 " pdb=" N ILE a 29 " model vdw 2.185 2.520 ... (remaining 177962 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' selection = chain 'F' } ncs_group { reference = (chain 'B' and resid 212 through 447) selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'W' } ncs_group { reference = chain 'L' selection = (chain 'X' and resid 15 through 75) } ncs_group { reference = chain 'M' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = (chain 'Z' and resid 3 through 94) } ncs_group { reference = (chain 'O' and resid 3 through 265) selection = chain 'a' } ncs_group { reference = chain 'P' selection = (chain 'b' and resid 5 through 69) } ncs_group { reference = chain 'Q' selection = chain 'c' } ncs_group { reference = chain 'R' selection = chain 'd' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 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: 0.980 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 61.200 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 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 : 0.003 0.054 21992 Z= 0.224 Angle : 0.740 12.988 29877 Z= 0.400 Chirality : 0.040 0.329 3629 Planarity : 0.004 0.085 3977 Dihedral : 15.742 86.080 7539 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 0.58 % Allowed : 22.99 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 3.51 (0.15), residues: 3057 helix: 2.80 (0.10), residues: 2543 sheet: 0.06 (0.97), residues: 32 loop : -0.32 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 59 HIS 0.006 0.001 HIS a 31 PHE 0.022 0.002 PHE M 60 TYR 0.045 0.002 TYR Z 16 ARG 0.017 0.001 ARG O 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 377 time to evaluate : 2.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 65 GLN cc_start: 0.8449 (tt0) cc_final: 0.7800 (tp40) REVERT: Q 6 GLN cc_start: 0.9398 (mt0) cc_final: 0.9067 (mm-40) REVERT: U 66 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8769 (mmmm) REVERT: W 41 GLU cc_start: 0.8434 (tp30) cc_final: 0.8067 (tp30) REVERT: W 47 ASP cc_start: 0.8972 (t0) cc_final: 0.8651 (p0) REVERT: Z 11 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8235 (tm-30) REVERT: a 168 PHE cc_start: 0.8271 (m-80) cc_final: 0.7960 (m-80) REVERT: a 201 PHE cc_start: 0.8544 (t80) cc_final: 0.8290 (t80) outliers start: 11 outliers final: 6 residues processed: 380 average time/residue: 0.3268 time to fit residues: 191.2173 Evaluate side-chains 318 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 312 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain V residue 144 THR Chi-restraints excluded: chain W residue 72 GLN Chi-restraints excluded: chain Y residue 66 ASN Chi-restraints excluded: chain d residue 98 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 4.9990 chunk 227 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 77 optimal weight: 30.0000 chunk 153 optimal weight: 0.9980 chunk 121 optimal weight: 0.3980 chunk 235 optimal weight: 0.7980 chunk 90 optimal weight: 30.0000 chunk 142 optimal weight: 0.7980 chunk 175 optimal weight: 0.2980 chunk 272 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 31 GLN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN W 72 GLN ** Y 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 22 GLN c 6 GLN c 36 GLN c 44 GLN d 105 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21992 Z= 0.190 Angle : 0.588 10.937 29877 Z= 0.307 Chirality : 0.037 0.268 3629 Planarity : 0.004 0.072 3977 Dihedral : 4.307 43.885 3251 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.51 % Rotamer: Outliers : 3.16 % Allowed : 19.04 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 3.97 (0.15), residues: 3057 helix: 3.14 (0.10), residues: 2543 sheet: -0.09 (0.92), residues: 32 loop : -0.25 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 59 HIS 0.006 0.001 HIS a 31 PHE 0.032 0.002 PHE a 246 TYR 0.041 0.001 TYR Z 16 ARG 0.006 0.001 ARG X 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 349 time to evaluate : 2.750 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: K 19 GLN cc_start: 0.8405 (mt0) cc_final: 0.8158 (mt0) REVERT: K 71 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8626 (mp) REVERT: K 77 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8198 (t0) REVERT: K 85 ASP cc_start: 0.8354 (t0) cc_final: 0.8114 (t0) REVERT: N 83 LYS cc_start: 0.9360 (tppp) cc_final: 0.9059 (tppp) REVERT: N 87 GLU cc_start: 0.8756 (pp20) cc_final: 0.8534 (pp20) REVERT: P 65 GLN cc_start: 0.8382 (tt0) cc_final: 0.7747 (tp40) REVERT: Q 6 GLN cc_start: 0.9366 (mt0) cc_final: 0.9110 (mm-40) REVERT: Q 33 MET cc_start: 0.8955 (tmm) cc_final: 0.8729 (tmm) REVERT: U 66 LYS cc_start: 0.9208 (mmtt) cc_final: 0.8850 (mmmm) REVERT: U 123 ASP cc_start: 0.9036 (t0) cc_final: 0.8695 (t0) REVERT: V 140 GLU cc_start: 0.7374 (mp0) cc_final: 0.6857 (pm20) REVERT: W 79 GLU cc_start: 0.7989 (mp0) cc_final: 0.7724 (mp0) REVERT: X 58 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8192 (tm-30) REVERT: Z 13 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8576 (mt) REVERT: Z 29 THR cc_start: 0.8518 (m) cc_final: 0.8303 (m) REVERT: Z 35 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: Z 59 ASP cc_start: 0.7993 (t0) cc_final: 0.7773 (t0) REVERT: a 168 PHE cc_start: 0.8442 (m-80) cc_final: 0.8168 (m-80) REVERT: d 98 ASN cc_start: 0.8426 (m110) cc_final: 0.7519 (t0) outliers start: 60 outliers final: 24 residues processed: 389 average time/residue: 0.3143 time to fit residues: 190.5250 Evaluate side-chains 331 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 303 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 77 ASP Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain W residue 5 ASP Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Z residue 13 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 81 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 30.0000 chunk 226 optimal weight: 0.9980 chunk 185 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 272 optimal weight: 2.9990 chunk 294 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 270 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 31 GLN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** V 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN ** Y 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 57 HIS c 44 GLN ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21992 Z= 0.333 Angle : 0.641 11.197 29877 Z= 0.335 Chirality : 0.039 0.331 3629 Planarity : 0.004 0.059 3977 Dihedral : 4.114 45.009 3242 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.45 % Favored : 97.48 % Rotamer: Outliers : 4.58 % Allowed : 19.25 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 3.87 (0.15), residues: 3057 helix: 3.06 (0.10), residues: 2565 sheet: -0.56 (0.88), residues: 32 loop : -0.44 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 59 HIS 0.008 0.001 HIS a 31 PHE 0.024 0.002 PHE a 201 TYR 0.034 0.002 TYR a 230 ARG 0.009 0.001 ARG R 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 330 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 72 ASP cc_start: 0.8906 (m-30) cc_final: 0.8623 (m-30) REVERT: K 77 ASP cc_start: 0.8665 (t70) cc_final: 0.8205 (t0) REVERT: K 85 ASP cc_start: 0.8257 (t0) cc_final: 0.7850 (t0) REVERT: M 16 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8948 (tt) REVERT: N 24 LYS cc_start: 0.9317 (mtmm) cc_final: 0.8994 (pttm) REVERT: N 28 GLU cc_start: 0.8900 (tp30) cc_final: 0.8560 (tp30) REVERT: N 83 LYS cc_start: 0.9424 (tppp) cc_final: 0.9138 (tppp) REVERT: O 232 GLN cc_start: 0.9296 (pp30) cc_final: 0.9006 (pp30) REVERT: P 8 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7911 (tm-30) REVERT: U 66 LYS cc_start: 0.9215 (mmtt) cc_final: 0.8947 (mmmm) REVERT: U 123 ASP cc_start: 0.9075 (t0) cc_final: 0.8737 (t0) REVERT: X 58 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8058 (tm-30) REVERT: Z 13 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8539 (mt) REVERT: Z 29 THR cc_start: 0.8561 (m) cc_final: 0.8273 (m) REVERT: Z 35 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.8286 (t80) REVERT: Z 59 ASP cc_start: 0.8025 (t0) cc_final: 0.7664 (t0) REVERT: a 168 PHE cc_start: 0.8472 (m-80) cc_final: 0.8235 (m-80) REVERT: b 58 GLU cc_start: 0.8460 (tp30) cc_final: 0.8069 (tm-30) REVERT: d 98 ASN cc_start: 0.8490 (m110) cc_final: 0.7695 (t0) REVERT: d 108 MET cc_start: 0.2545 (tmm) cc_final: 0.2049 (pmm) REVERT: e 17 TYR cc_start: 0.8599 (t80) cc_final: 0.8399 (t80) outliers start: 87 outliers final: 55 residues processed: 388 average time/residue: 0.3065 time to fit residues: 187.3728 Evaluate side-chains 352 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 294 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 100 SER Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain K residue 116 ASP Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 59 ILE Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 115 SER Chi-restraints excluded: chain V residue 143 ASN Chi-restraints excluded: chain W residue 5 ASP Chi-restraints excluded: chain W residue 6 GLU Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 66 ASN Chi-restraints excluded: chain Y residue 69 LYS Chi-restraints excluded: chain Z residue 13 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 85 GLU Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 57 HIS Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 204 ASP Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 40.0000 chunk 205 optimal weight: 0.7980 chunk 141 optimal weight: 0.5980 chunk 30 optimal weight: 50.0000 chunk 130 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 273 optimal weight: 4.9990 chunk 289 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 259 optimal weight: 10.0000 chunk 78 optimal weight: 50.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 ASN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 46 ASN a 57 HIS ** d 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21992 Z= 0.189 Angle : 0.574 12.016 29877 Z= 0.300 Chirality : 0.036 0.263 3629 Planarity : 0.003 0.056 3977 Dihedral : 4.031 45.720 3242 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.49 % Favored : 97.45 % Rotamer: Outliers : 3.37 % Allowed : 21.78 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 4.09 (0.15), residues: 3057 helix: 3.21 (0.10), residues: 2567 sheet: -0.29 (0.79), residues: 42 loop : -0.32 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 59 HIS 0.009 0.001 HIS a 57 PHE 0.025 0.002 PHE O 168 TYR 0.026 0.001 TYR Z 16 ARG 0.009 0.001 ARG R 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 337 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8264 (pp) REVERT: J 72 ASP cc_start: 0.8905 (m-30) cc_final: 0.8600 (m-30) REVERT: K 12 ARG cc_start: 0.8219 (mpp80) cc_final: 0.7914 (mtt90) REVERT: K 20 LYS cc_start: 0.8421 (mttm) cc_final: 0.8045 (mmtp) REVERT: K 85 ASP cc_start: 0.8247 (t0) cc_final: 0.7768 (t0) REVERT: M 16 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8878 (tt) REVERT: N 24 LYS cc_start: 0.9271 (mtmm) cc_final: 0.8930 (pttm) REVERT: N 83 LYS cc_start: 0.9382 (tppp) cc_final: 0.9028 (tppt) REVERT: O 232 GLN cc_start: 0.9299 (pp30) cc_final: 0.9017 (pp30) REVERT: P 8 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7855 (tm-30) REVERT: Q 33 MET cc_start: 0.8900 (tmm) cc_final: 0.8491 (tmm) REVERT: R 1 MET cc_start: 0.8014 (mmm) cc_final: 0.7585 (mmm) REVERT: U 61 GLN cc_start: 0.8902 (mm110) cc_final: 0.8542 (mm-40) REVERT: U 66 LYS cc_start: 0.9210 (mmtt) cc_final: 0.8919 (mmmm) REVERT: U 123 ASP cc_start: 0.9004 (t0) cc_final: 0.8667 (t0) REVERT: X 58 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8224 (tm-30) REVERT: X 60 GLN cc_start: 0.8665 (tp40) cc_final: 0.8335 (pm20) REVERT: Y 6 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7873 (mm-30) REVERT: Z 19 LEU cc_start: 0.9398 (tt) cc_final: 0.9172 (mm) REVERT: Z 29 THR cc_start: 0.8512 (m) cc_final: 0.8276 (m) REVERT: Z 35 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8181 (t80) REVERT: Z 59 ASP cc_start: 0.8134 (t0) cc_final: 0.7903 (t0) REVERT: a 168 PHE cc_start: 0.8541 (m-80) cc_final: 0.8304 (m-80) REVERT: b 8 GLU cc_start: 0.7831 (tp30) cc_final: 0.7448 (tp30) REVERT: d 75 ASP cc_start: 0.9538 (t0) cc_final: 0.9215 (p0) REVERT: d 98 ASN cc_start: 0.8589 (m110) cc_final: 0.7878 (t0) REVERT: d 108 MET cc_start: 0.2404 (tmm) cc_final: 0.1869 (pmm) outliers start: 64 outliers final: 39 residues processed: 379 average time/residue: 0.3217 time to fit residues: 190.8275 Evaluate side-chains 338 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 296 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 143 ASN Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 5 ASP Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 66 ASN Chi-restraints excluded: chain Z residue 31 LYS Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 57 HIS Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 204 ASP Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 57 ARG Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.0870 chunk 164 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 0 optimal weight: 80.0000 chunk 148 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 73 optimal weight: 50.0000 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 46 ASN ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 46 ASN a 57 HIS ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21992 Z= 0.191 Angle : 0.581 9.911 29877 Z= 0.304 Chirality : 0.036 0.260 3629 Planarity : 0.003 0.058 3977 Dihedral : 3.977 46.310 3242 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.29 % Favored : 97.64 % Rotamer: Outliers : 3.21 % Allowed : 22.62 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 4.22 (0.15), residues: 3057 helix: 3.31 (0.10), residues: 2560 sheet: -0.21 (0.79), residues: 42 loop : -0.28 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 59 HIS 0.009 0.001 HIS a 57 PHE 0.022 0.002 PHE M 60 TYR 0.029 0.001 TYR Z 16 ARG 0.008 0.001 ARG R 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 333 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 63 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8187 (pp) REVERT: I 69 GLU cc_start: 0.9058 (pm20) cc_final: 0.8640 (pm20) REVERT: J 72 ASP cc_start: 0.8937 (m-30) cc_final: 0.8698 (m-30) REVERT: K 12 ARG cc_start: 0.8249 (mpp80) cc_final: 0.7981 (mtt90) REVERT: K 20 LYS cc_start: 0.8405 (mttm) cc_final: 0.8042 (mmtp) REVERT: K 85 ASP cc_start: 0.8266 (t0) cc_final: 0.7758 (t0) REVERT: M 16 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8865 (tt) REVERT: N 24 LYS cc_start: 0.9270 (mtmm) cc_final: 0.8900 (pttm) REVERT: N 28 GLU cc_start: 0.8816 (tp30) cc_final: 0.8520 (tp30) REVERT: N 83 LYS cc_start: 0.9412 (tppp) cc_final: 0.8944 (tppt) REVERT: O 230 TYR cc_start: 0.8944 (t80) cc_final: 0.8639 (t80) REVERT: O 232 GLN cc_start: 0.9320 (pp30) cc_final: 0.9039 (pp30) REVERT: P 8 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7872 (tm-30) REVERT: Q 33 MET cc_start: 0.9004 (tmm) cc_final: 0.8603 (tmm) REVERT: R 1 MET cc_start: 0.8021 (mmm) cc_final: 0.7671 (mmm) REVERT: U 61 GLN cc_start: 0.8912 (mm110) cc_final: 0.8653 (mm110) REVERT: U 66 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8909 (mmmm) REVERT: U 112 VAL cc_start: 0.8938 (t) cc_final: 0.8702 (p) REVERT: U 123 ASP cc_start: 0.9025 (t0) cc_final: 0.8791 (t0) REVERT: V 148 ASP cc_start: 0.8715 (t0) cc_final: 0.8384 (p0) REVERT: W 40 LYS cc_start: 0.8899 (tppt) cc_final: 0.8672 (tptp) REVERT: X 58 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8085 (tm-30) REVERT: Y 6 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7944 (mm-30) REVERT: Z 29 THR cc_start: 0.8465 (m) cc_final: 0.8226 (m) REVERT: Z 35 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8150 (t80) REVERT: Z 58 ARG cc_start: 0.6362 (mmt90) cc_final: 0.5937 (mmt180) REVERT: Z 59 ASP cc_start: 0.8141 (t0) cc_final: 0.7906 (t0) REVERT: Z 83 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9080 (pttm) REVERT: a 168 PHE cc_start: 0.8515 (m-80) cc_final: 0.8246 (m-80) REVERT: b 8 GLU cc_start: 0.7870 (tp30) cc_final: 0.7401 (tp30) REVERT: d 75 ASP cc_start: 0.9520 (t0) cc_final: 0.9194 (p0) REVERT: d 98 ASN cc_start: 0.8593 (m110) cc_final: 0.7871 (t0) outliers start: 61 outliers final: 46 residues processed: 375 average time/residue: 0.3156 time to fit residues: 185.5781 Evaluate side-chains 357 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 307 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 143 ASN Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 5 ASP Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 66 ASN Chi-restraints excluded: chain Y residue 69 LYS Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 74 SER Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 57 HIS Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 10.0000 chunk 261 optimal weight: 0.0970 chunk 57 optimal weight: 9.9990 chunk 170 optimal weight: 0.0980 chunk 71 optimal weight: 50.0000 chunk 290 optimal weight: 0.8980 chunk 240 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 24 optimal weight: 50.0000 chunk 96 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 46 ASN ** M 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 127 GLN X 46 ASN ** a 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21992 Z= 0.179 Angle : 0.581 9.172 29877 Z= 0.305 Chirality : 0.036 0.257 3629 Planarity : 0.003 0.058 3977 Dihedral : 3.950 46.620 3242 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 3.47 % Allowed : 22.99 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 4.28 (0.15), residues: 3057 helix: 3.34 (0.10), residues: 2566 sheet: -0.21 (0.78), residues: 42 loop : -0.28 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 59 HIS 0.007 0.001 HIS a 31 PHE 0.022 0.002 PHE M 60 TYR 0.028 0.001 TYR Z 16 ARG 0.007 0.000 ARG R 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 342 time to evaluate : 3.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 69 GLU cc_start: 0.8883 (pm20) cc_final: 0.8560 (pm20) REVERT: I 112 VAL cc_start: 0.9016 (t) cc_final: 0.8739 (p) REVERT: J 72 ASP cc_start: 0.8980 (m-30) cc_final: 0.8717 (m-30) REVERT: K 12 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7995 (mtt90) REVERT: K 20 LYS cc_start: 0.8342 (mttm) cc_final: 0.7920 (mmtp) REVERT: K 85 ASP cc_start: 0.8274 (t0) cc_final: 0.7784 (t0) REVERT: N 24 LYS cc_start: 0.9260 (mtmm) cc_final: 0.8892 (pttm) REVERT: N 35 TYR cc_start: 0.6362 (m-80) cc_final: 0.6060 (m-80) REVERT: O 205 PHE cc_start: 0.4564 (OUTLIER) cc_final: 0.2308 (t80) REVERT: O 230 TYR cc_start: 0.8978 (t80) cc_final: 0.8656 (t80) REVERT: O 232 GLN cc_start: 0.9339 (pp30) cc_final: 0.9042 (pp30) REVERT: O 237 TYR cc_start: 0.7773 (t80) cc_final: 0.7384 (t80) REVERT: Q 33 MET cc_start: 0.9030 (tmm) cc_final: 0.8585 (tmm) REVERT: U 61 GLN cc_start: 0.8881 (mm110) cc_final: 0.8603 (mm110) REVERT: U 66 LYS cc_start: 0.9195 (mmtt) cc_final: 0.8949 (mmmm) REVERT: U 123 ASP cc_start: 0.9054 (t0) cc_final: 0.8827 (t0) REVERT: V 98 GLU cc_start: 0.8646 (tp30) cc_final: 0.8383 (tp30) REVERT: V 148 ASP cc_start: 0.8706 (t0) cc_final: 0.8365 (p0) REVERT: W 41 GLU cc_start: 0.8388 (tp30) cc_final: 0.8134 (tp30) REVERT: W 126 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6919 (tmm-80) REVERT: X 58 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8110 (tm-30) REVERT: Y 6 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7991 (mm-30) REVERT: Y 40 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8264 (ttp80) REVERT: Z 29 THR cc_start: 0.8384 (m) cc_final: 0.8123 (m) REVERT: Z 35 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8125 (t80) REVERT: Z 58 ARG cc_start: 0.6444 (mmt90) cc_final: 0.5936 (mmt180) REVERT: Z 83 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9050 (pttm) REVERT: a 168 PHE cc_start: 0.8562 (m-80) cc_final: 0.8324 (m-80) REVERT: b 8 GLU cc_start: 0.7858 (tp30) cc_final: 0.7377 (tp30) REVERT: c 24 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8129 (tm-30) REVERT: d 20 LYS cc_start: 0.9134 (tppt) cc_final: 0.8715 (tppt) REVERT: d 98 ASN cc_start: 0.8569 (m110) cc_final: 0.7970 (t0) REVERT: d 108 MET cc_start: 0.2628 (ppp) cc_final: 0.2104 (pmm) outliers start: 66 outliers final: 44 residues processed: 388 average time/residue: 0.3281 time to fit residues: 196.8382 Evaluate side-chains 360 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 311 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain I residue 147 ASN Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 12 ARG Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 205 PHE Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 143 ASN Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 5 ASP Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain W residue 126 ARG Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 48 SER Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 66 ASN Chi-restraints excluded: chain Y residue 69 LYS Chi-restraints excluded: chain Z residue 31 LYS Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 57 ARG Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 165 optimal weight: 0.7980 chunk 211 optimal weight: 0.9980 chunk 164 optimal weight: 0.5980 chunk 244 optimal weight: 0.0670 chunk 162 optimal weight: 0.8980 chunk 289 optimal weight: 0.9980 chunk 180 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 46 ASN ** M 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 46 ASN ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 98 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21992 Z= 0.183 Angle : 0.602 13.229 29877 Z= 0.316 Chirality : 0.037 0.256 3629 Planarity : 0.003 0.050 3977 Dihedral : 3.918 46.798 3242 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.22 % Favored : 97.71 % Rotamer: Outliers : 3.16 % Allowed : 23.78 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 4.31 (0.15), residues: 3057 helix: 3.36 (0.10), residues: 2567 sheet: -0.16 (0.78), residues: 42 loop : -0.25 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 59 HIS 0.006 0.001 HIS a 31 PHE 0.021 0.002 PHE M 60 TYR 0.025 0.001 TYR Z 16 ARG 0.007 0.000 ARG R 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 342 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 69 GLU cc_start: 0.8914 (pm20) cc_final: 0.8580 (pm20) REVERT: I 112 VAL cc_start: 0.9034 (t) cc_final: 0.8767 (p) REVERT: J 72 ASP cc_start: 0.8972 (m-30) cc_final: 0.8710 (m-30) REVERT: K 8 ILE cc_start: 0.7487 (mm) cc_final: 0.7079 (mm) REVERT: K 20 LYS cc_start: 0.8346 (mttm) cc_final: 0.7916 (mmtp) REVERT: K 85 ASP cc_start: 0.8223 (t0) cc_final: 0.7722 (t0) REVERT: O 205 PHE cc_start: 0.4018 (OUTLIER) cc_final: 0.3658 (t80) REVERT: O 230 TYR cc_start: 0.8962 (t80) cc_final: 0.8541 (t80) REVERT: O 232 GLN cc_start: 0.9270 (pp30) cc_final: 0.8964 (pp30) REVERT: O 237 TYR cc_start: 0.7752 (t80) cc_final: 0.7355 (t80) REVERT: Q 6 GLN cc_start: 0.9340 (mt0) cc_final: 0.9119 (mm-40) REVERT: Q 33 MET cc_start: 0.9050 (tmm) cc_final: 0.8849 (tmm) REVERT: U 61 GLN cc_start: 0.8876 (mm110) cc_final: 0.8603 (mm110) REVERT: U 66 LYS cc_start: 0.9183 (mmtt) cc_final: 0.8952 (mmmm) REVERT: U 123 ASP cc_start: 0.9050 (t0) cc_final: 0.8850 (t0) REVERT: V 98 GLU cc_start: 0.8703 (tp30) cc_final: 0.8408 (tp30) REVERT: V 148 ASP cc_start: 0.8739 (t0) cc_final: 0.8408 (p0) REVERT: W 41 GLU cc_start: 0.8440 (tp30) cc_final: 0.8130 (tp30) REVERT: W 126 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6933 (tmm-80) REVERT: X 58 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8093 (tm-30) REVERT: Y 6 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8016 (mm-30) REVERT: Z 29 THR cc_start: 0.8351 (m) cc_final: 0.8099 (m) REVERT: Z 35 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8112 (t80) REVERT: Z 58 ARG cc_start: 0.6449 (mmt90) cc_final: 0.5951 (mmt180) REVERT: Z 83 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.9034 (pttm) REVERT: a 168 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8335 (m-80) REVERT: b 8 GLU cc_start: 0.7901 (tp30) cc_final: 0.7411 (tp30) REVERT: c 24 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8145 (tm-30) REVERT: d 20 LYS cc_start: 0.9137 (tppt) cc_final: 0.8721 (tppt) REVERT: d 75 ASP cc_start: 0.9513 (t0) cc_final: 0.9020 (m-30) REVERT: d 98 ASN cc_start: 0.8537 (m-40) cc_final: 0.7782 (t0) REVERT: d 108 MET cc_start: 0.2749 (ppp) cc_final: 0.2196 (pmm) outliers start: 60 outliers final: 44 residues processed: 379 average time/residue: 0.3177 time to fit residues: 187.6577 Evaluate side-chains 363 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 314 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 205 PHE Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 143 ASN Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 5 ASP Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain W residue 126 ARG Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 66 ASN Chi-restraints excluded: chain Y residue 69 LYS Chi-restraints excluded: chain Z residue 19 LEU Chi-restraints excluded: chain Z residue 31 LYS Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 172 optimal weight: 9.9990 chunk 87 optimal weight: 30.0000 chunk 56 optimal weight: 0.0040 chunk 183 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 26 optimal weight: 50.0000 chunk 227 optimal weight: 0.9980 chunk 263 optimal weight: 6.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 46 ASN ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21992 Z= 0.192 Angle : 0.617 10.434 29877 Z= 0.324 Chirality : 0.037 0.252 3629 Planarity : 0.004 0.093 3977 Dihedral : 3.922 46.578 3242 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.22 % Favored : 97.71 % Rotamer: Outliers : 3.05 % Allowed : 24.36 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 4.31 (0.15), residues: 3057 helix: 3.37 (0.10), residues: 2564 sheet: -0.12 (0.79), residues: 42 loop : -0.30 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 59 HIS 0.007 0.001 HIS a 31 PHE 0.062 0.002 PHE a 246 TYR 0.028 0.001 TYR Z 16 ARG 0.016 0.001 ARG K 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 338 time to evaluate : 2.584 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: I 69 GLU cc_start: 0.8875 (pm20) cc_final: 0.8477 (pm20) REVERT: I 112 VAL cc_start: 0.9017 (t) cc_final: 0.8755 (p) REVERT: J 72 ASP cc_start: 0.8937 (m-30) cc_final: 0.8664 (m-30) REVERT: K 20 LYS cc_start: 0.8373 (mttm) cc_final: 0.7918 (mmtp) REVERT: K 85 ASP cc_start: 0.8280 (t0) cc_final: 0.7778 (t0) REVERT: O 57 HIS cc_start: 0.8343 (p-80) cc_final: 0.8105 (p-80) REVERT: O 230 TYR cc_start: 0.8950 (t80) cc_final: 0.8443 (t80) REVERT: O 232 GLN cc_start: 0.9185 (pp30) cc_final: 0.8915 (pp30) REVERT: O 234 TYR cc_start: 0.9303 (t80) cc_final: 0.9101 (t80) REVERT: O 237 TYR cc_start: 0.7805 (t80) cc_final: 0.7361 (t80) REVERT: Q 6 GLN cc_start: 0.9337 (mt0) cc_final: 0.9084 (mm-40) REVERT: Q 33 MET cc_start: 0.9067 (tmm) cc_final: 0.8603 (tmm) REVERT: R 20 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8848 (tptp) REVERT: U 61 GLN cc_start: 0.8872 (mm110) cc_final: 0.8577 (mm110) REVERT: V 140 GLU cc_start: 0.7052 (mp0) cc_final: 0.6623 (pm20) REVERT: V 148 ASP cc_start: 0.8733 (t0) cc_final: 0.8399 (p0) REVERT: W 41 GLU cc_start: 0.8449 (tp30) cc_final: 0.8138 (tp30) REVERT: W 126 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6932 (tmm-80) REVERT: X 58 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8212 (tm-30) REVERT: X 60 GLN cc_start: 0.8669 (tp40) cc_final: 0.8395 (pm20) REVERT: Y 6 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8044 (mm-30) REVERT: Z 29 THR cc_start: 0.8252 (m) cc_final: 0.7997 (m) REVERT: Z 35 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.8095 (t80) REVERT: Z 58 ARG cc_start: 0.6438 (mmt90) cc_final: 0.5863 (mtt180) REVERT: Z 83 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.9052 (pttm) REVERT: a 168 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: b 8 GLU cc_start: 0.7908 (tp30) cc_final: 0.7397 (tp30) REVERT: c 24 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8181 (tm-30) REVERT: d 20 LYS cc_start: 0.9135 (tppt) cc_final: 0.8721 (tppt) REVERT: d 75 ASP cc_start: 0.9514 (t0) cc_final: 0.9053 (m-30) REVERT: d 98 ASN cc_start: 0.8434 (m-40) cc_final: 0.7613 (t0) REVERT: d 108 MET cc_start: 0.3100 (ppp) cc_final: 0.2469 (pmm) outliers start: 58 outliers final: 44 residues processed: 376 average time/residue: 0.3119 time to fit residues: 184.3552 Evaluate side-chains 364 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 316 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 5 ASP Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain W residue 126 ARG Chi-restraints excluded: chain X residue 46 ASN Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 66 ASN Chi-restraints excluded: chain Z residue 31 LYS Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.9990 chunk 252 optimal weight: 4.9990 chunk 269 optimal weight: 0.5980 chunk 276 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 chunk 254 optimal weight: 7.9990 chunk 268 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 ASN X 46 ASN ** a 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21992 Z= 0.222 Angle : 0.644 10.846 29877 Z= 0.338 Chirality : 0.038 0.263 3629 Planarity : 0.004 0.055 3977 Dihedral : 3.921 47.947 3242 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.29 % Favored : 97.64 % Rotamer: Outliers : 3.37 % Allowed : 24.57 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 4.31 (0.15), residues: 3057 helix: 3.36 (0.10), residues: 2567 sheet: -0.08 (0.80), residues: 42 loop : -0.29 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 221 HIS 0.009 0.001 HIS N 38 PHE 0.043 0.002 PHE a 246 TYR 0.025 0.001 TYR Z 16 ARG 0.010 0.001 ARG K 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 334 time to evaluate : 2.663 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: I 69 GLU cc_start: 0.8991 (pm20) cc_final: 0.8577 (pm20) REVERT: I 112 VAL cc_start: 0.9015 (t) cc_final: 0.8750 (p) REVERT: J 72 ASP cc_start: 0.8950 (m-30) cc_final: 0.8678 (m-30) REVERT: K 12 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7942 (mtt90) REVERT: K 20 LYS cc_start: 0.8426 (mttm) cc_final: 0.7950 (mmtp) REVERT: K 85 ASP cc_start: 0.8347 (t0) cc_final: 0.7846 (t0) REVERT: O 57 HIS cc_start: 0.8351 (p-80) cc_final: 0.8117 (p-80) REVERT: O 226 PHE cc_start: 0.8399 (m-80) cc_final: 0.7613 (m-80) REVERT: O 230 TYR cc_start: 0.8972 (t80) cc_final: 0.8528 (t80) REVERT: O 232 GLN cc_start: 0.9214 (pp30) cc_final: 0.8921 (pp30) REVERT: O 237 TYR cc_start: 0.7835 (t80) cc_final: 0.7598 (t80) REVERT: Q 33 MET cc_start: 0.9068 (tmm) cc_final: 0.8603 (tmm) REVERT: R 1 MET cc_start: 0.7856 (mmm) cc_final: 0.7376 (mmm) REVERT: R 20 LYS cc_start: 0.9129 (mmmt) cc_final: 0.8853 (tptp) REVERT: U 61 GLN cc_start: 0.8859 (mm110) cc_final: 0.8567 (mm110) REVERT: U 69 GLU cc_start: 0.8881 (pt0) cc_final: 0.8650 (pt0) REVERT: V 140 GLU cc_start: 0.6999 (mp0) cc_final: 0.6341 (pm20) REVERT: V 148 ASP cc_start: 0.8729 (t0) cc_final: 0.8391 (p0) REVERT: W 41 GLU cc_start: 0.8464 (tp30) cc_final: 0.8149 (tp30) REVERT: W 126 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7010 (tmm-80) REVERT: X 58 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7988 (tm-30) REVERT: Y 6 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8148 (mm-30) REVERT: Z 29 THR cc_start: 0.8208 (m) cc_final: 0.7979 (m) REVERT: Z 35 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8100 (t80) REVERT: Z 58 ARG cc_start: 0.6450 (mmt90) cc_final: 0.5874 (mtt180) REVERT: a 19 MET cc_start: 0.8655 (mmp) cc_final: 0.8447 (mmm) REVERT: a 168 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: b 8 GLU cc_start: 0.7944 (tp30) cc_final: 0.7434 (tp30) REVERT: c 24 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8178 (tm-30) REVERT: d 20 LYS cc_start: 0.9142 (tppt) cc_final: 0.8726 (tppt) REVERT: d 75 ASP cc_start: 0.9527 (t0) cc_final: 0.9075 (m-30) REVERT: d 98 ASN cc_start: 0.8400 (m-40) cc_final: 0.7533 (t0) REVERT: d 108 MET cc_start: 0.3425 (ppp) cc_final: 0.2782 (pmm) outliers start: 64 outliers final: 51 residues processed: 380 average time/residue: 0.3243 time to fit residues: 190.6032 Evaluate side-chains 372 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 318 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 51 CYS Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain V residue 153 HIS Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 5 ASP Chi-restraints excluded: chain W residue 124 MET Chi-restraints excluded: chain W residue 126 ARG Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 66 ASN Chi-restraints excluded: chain Y residue 69 LYS Chi-restraints excluded: chain Z residue 31 LYS Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain d residue 81 MET Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 1.9990 chunk 284 optimal weight: 0.7980 chunk 173 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 298 optimal weight: 9.9990 chunk 275 optimal weight: 6.9990 chunk 237 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 45 ASN ** a 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21992 Z= 0.223 Angle : 0.661 11.996 29877 Z= 0.346 Chirality : 0.038 0.263 3629 Planarity : 0.004 0.059 3977 Dihedral : 3.945 47.996 3242 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 2.89 % Allowed : 24.93 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.30 (0.15), residues: 3057 helix: 3.35 (0.10), residues: 2567 sheet: -0.03 (0.81), residues: 42 loop : -0.26 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP a 221 HIS 0.006 0.001 HIS a 31 PHE 0.036 0.002 PHE a 246 TYR 0.025 0.001 TYR Z 16 ARG 0.013 0.001 ARG K 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6114 Ramachandran restraints generated. 3057 Oldfield, 0 Emsley, 3057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 325 time to evaluate : 2.297 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: I 69 GLU cc_start: 0.8981 (pm20) cc_final: 0.8565 (pm20) REVERT: I 112 VAL cc_start: 0.9005 (t) cc_final: 0.8742 (p) REVERT: J 72 ASP cc_start: 0.8968 (m-30) cc_final: 0.8697 (m-30) REVERT: K 20 LYS cc_start: 0.8442 (mttm) cc_final: 0.8086 (mttm) REVERT: K 85 ASP cc_start: 0.8348 (t0) cc_final: 0.7826 (t0) REVERT: O 57 HIS cc_start: 0.8362 (p-80) cc_final: 0.8132 (p-80) REVERT: O 221 TRP cc_start: 0.8427 (m-90) cc_final: 0.7736 (m-90) REVERT: O 226 PHE cc_start: 0.8332 (m-80) cc_final: 0.7566 (m-80) REVERT: O 230 TYR cc_start: 0.8922 (t80) cc_final: 0.8470 (t80) REVERT: O 232 GLN cc_start: 0.9180 (pp30) cc_final: 0.8908 (pp30) REVERT: O 237 TYR cc_start: 0.7839 (t80) cc_final: 0.7587 (t80) REVERT: Q 33 MET cc_start: 0.9071 (tmm) cc_final: 0.8607 (tmm) REVERT: R 1 MET cc_start: 0.7930 (mmm) cc_final: 0.7483 (mmm) REVERT: R 20 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8854 (tptp) REVERT: U 61 GLN cc_start: 0.8839 (mm110) cc_final: 0.8553 (mm110) REVERT: U 69 GLU cc_start: 0.8880 (pt0) cc_final: 0.8651 (pt0) REVERT: V 140 GLU cc_start: 0.7000 (mp0) cc_final: 0.6371 (pm20) REVERT: V 148 ASP cc_start: 0.8725 (t0) cc_final: 0.8388 (p0) REVERT: W 41 GLU cc_start: 0.8509 (tp30) cc_final: 0.8182 (tp30) REVERT: W 126 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7039 (tmm-80) REVERT: X 58 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8182 (tm-30) REVERT: Y 6 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8159 (mm-30) REVERT: Z 29 THR cc_start: 0.8200 (m) cc_final: 0.7983 (m) REVERT: Z 35 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.8096 (t80) REVERT: Z 58 ARG cc_start: 0.6450 (mmt90) cc_final: 0.5875 (mtt180) REVERT: a 19 MET cc_start: 0.8655 (mmp) cc_final: 0.8440 (mmm) REVERT: a 168 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: a 221 TRP cc_start: 0.7833 (m-90) cc_final: 0.7600 (m-90) REVERT: b 8 GLU cc_start: 0.7984 (tp30) cc_final: 0.7479 (tp30) REVERT: c 24 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8184 (tm-30) REVERT: d 20 LYS cc_start: 0.9139 (tppt) cc_final: 0.8727 (tppt) REVERT: d 75 ASP cc_start: 0.9531 (t0) cc_final: 0.9080 (m-30) REVERT: d 98 ASN cc_start: 0.8387 (m-40) cc_final: 0.7544 (t0) REVERT: d 108 MET cc_start: 0.3417 (ppp) cc_final: 0.2719 (pmm) outliers start: 55 outliers final: 49 residues processed: 364 average time/residue: 0.3175 time to fit residues: 180.8742 Evaluate side-chains 366 residues out of total 2924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 314 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 137 GLU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 51 CYS Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain N residue 15 LYS Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 35 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 122 ASP Chi-restraints excluded: chain O residue 183 ASN Chi-restraints excluded: chain O residue 224 THR Chi-restraints excluded: chain O residue 246 PHE Chi-restraints excluded: chain O residue 261 MET Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 130 GLN Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain V residue 153 HIS Chi-restraints excluded: chain V residue 165 ASP Chi-restraints excluded: chain W residue 5 ASP Chi-restraints excluded: chain W residue 126 ARG Chi-restraints excluded: chain X residue 49 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Y residue 65 THR Chi-restraints excluded: chain Y residue 66 ASN Chi-restraints excluded: chain Y residue 69 LYS Chi-restraints excluded: chain Z residue 31 LYS Chi-restraints excluded: chain Z residue 33 LEU Chi-restraints excluded: chain Z residue 35 TYR Chi-restraints excluded: chain Z residue 62 VAL Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain a residue 52 ILE Chi-restraints excluded: chain a residue 66 VAL Chi-restraints excluded: chain a residue 168 PHE Chi-restraints excluded: chain a residue 213 VAL Chi-restraints excluded: chain a residue 239 GLN Chi-restraints excluded: chain a residue 264 TYR Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain d residue 95 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 1.9990 chunk 253 optimal weight: 1.9990 chunk 72 optimal weight: 50.0000 chunk 219 optimal weight: 0.8980 chunk 35 optimal weight: 50.0000 chunk 66 optimal weight: 40.0000 chunk 238 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 244 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 43 optimal weight: 50.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 22 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN ** U 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 45 ASN ** a 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.145105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.098483 restraints weight = 75973.898| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.39 r_work: 0.3440 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 21992 Z= 0.249 Angle : 0.686 12.386 29877 Z= 0.360 Chirality : 0.039 0.292 3629 Planarity : 0.004 0.073 3977 Dihedral : 3.970 48.353 3242 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.51 % Rotamer: Outliers : 3.00 % Allowed : 25.72 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: 4.28 (0.15), residues: 3057 helix: 3.33 (0.10), residues: 2568 sheet: 0.01 (0.83), residues: 42 loop : -0.24 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP a 221 HIS 0.009 0.001 HIS N 38 PHE 0.035 0.002 PHE O 205 TYR 0.023 0.001 TYR a 237 ARG 0.013 0.001 ARG K 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6421.94 seconds wall clock time: 114 minutes 17.31 seconds (6857.31 seconds total)