Starting phenix.real_space_refine on Mon Mar 18 21:57:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bto_30180/03_2024/7bto_30180.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bto_30180/03_2024/7bto_30180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bto_30180/03_2024/7bto_30180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bto_30180/03_2024/7bto_30180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bto_30180/03_2024/7bto_30180.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bto_30180/03_2024/7bto_30180.pdb" } resolution = 3.97 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 984 atoms to isotropic. 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 46 5.16 5 C 13618 2.51 5 N 3506 2.21 5 O 4113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 104": "NH1" <-> "NH2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F ARG 131": "NH1" <-> "NH2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F ARG 456": "NH1" <-> "NH2" Residue "G ARG 65": "NH1" <-> "NH2" Residue "G ARG 131": "NH1" <-> "NH2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 352": "NH1" <-> "NH2" Residue "G ARG 456": "NH1" <-> "NH2" Residue "I TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 989": "NH1" <-> "NH2" Residue "C TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 989": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21283 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3693 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 17, 'PTRANS': 13, 'TRANS': 438} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3691 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 17, 'PTRANS': 13, 'TRANS': 438} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1334 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 157} Chain: "E" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1334 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 157} Chain: "F" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3574 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 5, 'PTRANS': 9, 'TRANS': 421} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 3574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3574 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 5, 'PTRANS': 9, 'TRANS': 421} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3099 Classifications: {'peptide': 384} Link IDs: {'CIS': 5, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 359} Chain: "C" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 490 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 10.82, per 1000 atoms: 0.51 Number of scatterers: 21283 At special positions: 0 Unit cell: (163.35, 149.85, 148.5, 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 46 16.00 O 4113 8.00 N 3506 7.00 C 13618 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: 7.86 Conformation dependent library (CDL) restraints added in 3.9 seconds 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5030 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 22 sheets defined 39.7% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 removed outlier: 3.605A pdb=" N GLN A 15 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 54 removed outlier: 3.534A pdb=" N PHE A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLN A 34 " --> pdb=" O TRP A 30 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR A 35 " --> pdb=" O ASP A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.908A pdb=" N GLY A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 163 Processing helix chain 'A' and resid 177 through 186 removed outlier: 4.036A pdb=" N TYR A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 213 Processing helix chain 'A' and resid 256 through 267 removed outlier: 3.724A pdb=" N LEU A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 335 through 346 removed outlier: 3.638A pdb=" N TYR A 346 " --> pdb=" O HIS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 378 removed outlier: 4.037A pdb=" N ILE A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN A 378 " --> pdb=" O TYR A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 444 Processing helix chain 'A' and resid 457 through 464 Processing helix chain 'A' and resid 482 through 507 removed outlier: 3.714A pdb=" N ALA A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.544A pdb=" N VAL B 23 " --> pdb=" O ILE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 54 removed outlier: 3.534A pdb=" N PHE B 32 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN B 34 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR B 35 " --> pdb=" O ASP B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 92 removed outlier: 4.343A pdb=" N TYR B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.910A pdb=" N GLY B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 163 Processing helix chain 'B' and resid 177 through 186 removed outlier: 4.035A pdb=" N TYR B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 213 Processing helix chain 'B' and resid 256 through 267 removed outlier: 3.725A pdb=" N LEU B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 335 through 346 removed outlier: 3.639A pdb=" N TYR B 346 " --> pdb=" O HIS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 378 removed outlier: 4.025A pdb=" N ILE B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN B 378 " --> pdb=" O TYR B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 444 Processing helix chain 'B' and resid 457 through 464 Processing helix chain 'B' and resid 482 through 507 removed outlier: 3.662A pdb=" N ALA B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.786A pdb=" N VAL D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.639A pdb=" N GLU D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 82 Processing helix chain 'D' and resid 83 through 89 Processing helix chain 'D' and resid 93 through 100 Processing helix chain 'D' and resid 112 through 123 Processing helix chain 'D' and resid 131 through 136 removed outlier: 4.159A pdb=" N ASN D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 151 Processing helix chain 'E' and resid 29 through 38 removed outlier: 3.786A pdb=" N VAL E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 76 removed outlier: 3.639A pdb=" N GLU E 71 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET E 72 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU E 76 " --> pdb=" O MET E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 82 Processing helix chain 'E' and resid 83 through 89 Processing helix chain 'E' and resid 93 through 100 Processing helix chain 'E' and resid 112 through 123 Processing helix chain 'E' and resid 131 through 136 removed outlier: 4.159A pdb=" N ASN E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 151 Processing helix chain 'F' and resid 34 through 47 Processing helix chain 'F' and resid 57 through 73 removed outlier: 3.612A pdb=" N LEU F 61 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG F 65 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU F 66 " --> pdb=" O ALA F 62 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLN F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 71 " --> pdb=" O GLN F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 88 removed outlier: 3.584A pdb=" N TRP F 81 " --> pdb=" O ASN F 77 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 172 through 180 removed outlier: 4.029A pdb=" N PHE F 177 " --> pdb=" O ILE F 173 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 197 removed outlier: 3.612A pdb=" N TYR F 197 " --> pdb=" O LEU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 248 removed outlier: 3.538A pdb=" N PHE F 248 " --> pdb=" O THR F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 273 through 292 removed outlier: 3.532A pdb=" N THR F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 326 removed outlier: 3.508A pdb=" N GLU F 326 " --> pdb=" O ARG F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 353 Processing helix chain 'F' and resid 366 through 373 Processing helix chain 'F' and resid 383 through 391 Processing helix chain 'F' and resid 416 through 426 Processing helix chain 'G' and resid 34 through 47 Processing helix chain 'G' and resid 57 through 73 removed outlier: 3.624A pdb=" N LEU G 61 " --> pdb=" O GLN G 57 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLN G 69 " --> pdb=" O ARG G 65 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN G 70 " --> pdb=" O GLU G 66 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU G 71 " --> pdb=" O GLN G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 88 removed outlier: 3.581A pdb=" N TRP G 81 " --> pdb=" O ASN G 77 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG G 83 " --> pdb=" O SER G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 105 Processing helix chain 'G' and resid 172 through 180 removed outlier: 4.043A pdb=" N PHE G 177 " --> pdb=" O ILE G 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN G 178 " --> pdb=" O ARG G 174 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE G 180 " --> pdb=" O ALA G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 197 removed outlier: 3.615A pdb=" N TYR G 197 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 248 removed outlier: 3.539A pdb=" N PHE G 248 " --> pdb=" O THR G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 258 Processing helix chain 'G' and resid 273 through 292 removed outlier: 3.541A pdb=" N THR G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 326 removed outlier: 3.507A pdb=" N GLU G 326 " --> pdb=" O ARG G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 353 Processing helix chain 'G' and resid 366 through 373 Processing helix chain 'G' and resid 383 through 391 Processing helix chain 'G' and resid 416 through 426 Processing helix chain 'I' and resid 20 through 24 removed outlier: 3.601A pdb=" N GLU I 23 " --> pdb=" O PRO I 20 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE I 24 " --> pdb=" O LEU I 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 20 through 24' Processing helix chain 'I' and resid 111 through 117 Processing helix chain 'I' and resid 134 through 141 removed outlier: 3.621A pdb=" N TYR I 138 " --> pdb=" O TRP I 134 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS I 141 " --> pdb=" O ASN I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 158 Processing helix chain 'I' and resid 158 through 193 removed outlier: 3.673A pdb=" N ASP I 191 " --> pdb=" O ASN I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 259 removed outlier: 3.936A pdb=" N VAL I 256 " --> pdb=" O GLU I 253 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER I 259 " --> pdb=" O VAL I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 307 through 318 Processing helix chain 'I' and resid 318 through 326 removed outlier: 4.698A pdb=" N ARG I 324 " --> pdb=" O SER I 320 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA I 326 " --> pdb=" O ILE I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 343 removed outlier: 3.830A pdb=" N LEU I 341 " --> pdb=" O ASP I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 356 removed outlier: 4.053A pdb=" N GLN I 355 " --> pdb=" O ILE I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 356 through 369 removed outlier: 3.530A pdb=" N LEU I 367 " --> pdb=" O LYS I 363 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN I 369 " --> pdb=" O ASP I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 391 Processing helix chain 'C' and resid 975 through 990 Processing helix chain 'C' and resid 998 through 1003 removed outlier: 3.654A pdb=" N LEU C1003 " --> pdb=" O LEU C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1031 Processing helix chain 'H' and resid 975 through 990 Processing helix chain 'H' and resid 1016 through 1031 Processing sheet with id=AA1, first strand: chain 'A' and resid 253 through 254 Processing sheet with id=AA2, first strand: chain 'A' and resid 296 through 300 removed outlier: 6.685A pdb=" N PHE A 296 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LYS A 350 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ALA A 298 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG A 352 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 300 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA A 354 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL A 399 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 387 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER A 405 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N VAL A 381 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 253 through 254 Processing sheet with id=AA4, first strand: chain 'B' and resid 296 through 300 removed outlier: 6.686A pdb=" N PHE B 296 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS B 350 " --> pdb=" O PHE B 296 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ALA B 298 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG B 352 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL B 300 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA B 354 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B 399 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 387 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N SER B 405 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL B 381 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 5 through 8 removed outlier: 3.887A pdb=" N ASP D 50 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 104 through 107 Processing sheet with id=AA7, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.888A pdb=" N ASP E 50 " --> pdb=" O TYR E 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 104 through 107 Processing sheet with id=AA9, first strand: chain 'F' and resid 108 through 112 Processing sheet with id=AB1, first strand: chain 'F' and resid 134 through 138 removed outlier: 6.026A pdb=" N VAL F 156 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU F 200 " --> pdb=" O LEU F 161 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN F 163 " --> pdb=" O LEU F 200 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 261 through 264 Processing sheet with id=AB3, first strand: chain 'F' and resid 358 through 359 removed outlier: 6.233A pdb=" N VAL F 333 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR F 381 " --> pdb=" O VAL F 333 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHE F 335 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LYS F 332 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE F 406 " --> pdb=" O LYS F 332 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE F 334 " --> pdb=" O ILE F 406 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL F 403 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N PHE F 432 " --> pdb=" O VAL F 403 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N PHE F 405 " --> pdb=" O PHE F 432 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N PHE F 434 " --> pdb=" O PHE F 405 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE F 407 " --> pdb=" O PHE F 434 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY F 303 " --> pdb=" O GLN F 431 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY F 433 " --> pdb=" O GLY F 303 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS F 307 " --> pdb=" O THR F 435 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N TYR F 304 " --> pdb=" O LEU F 458 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N SER F 460 " --> pdb=" O TYR F 304 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP F 306 " --> pdb=" O SER F 460 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 108 through 112 Processing sheet with id=AB5, first strand: chain 'G' and resid 134 through 138 removed outlier: 6.024A pdb=" N VAL G 156 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU G 200 " --> pdb=" O LEU G 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN G 163 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 261 through 264 Processing sheet with id=AB7, first strand: chain 'G' and resid 358 through 359 removed outlier: 6.232A pdb=" N VAL G 333 " --> pdb=" O ILE G 379 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR G 381 " --> pdb=" O VAL G 333 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE G 335 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS G 332 " --> pdb=" O VAL G 404 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE G 406 " --> pdb=" O LYS G 332 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE G 334 " --> pdb=" O ILE G 406 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL G 403 " --> pdb=" O TYR G 430 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N PHE G 432 " --> pdb=" O VAL G 403 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE G 405 " --> pdb=" O PHE G 432 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE G 434 " --> pdb=" O PHE G 405 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE G 407 " --> pdb=" O PHE G 434 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY G 303 " --> pdb=" O GLN G 431 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY G 433 " --> pdb=" O GLY G 303 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS G 307 " --> pdb=" O THR G 435 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TYR G 304 " --> pdb=" O LEU G 458 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N SER G 460 " --> pdb=" O TYR G 304 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP G 306 " --> pdb=" O SER G 460 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 17 through 19 Processing sheet with id=AB9, first strand: chain 'I' and resid 26 through 28 removed outlier: 3.888A pdb=" N LYS I 99 " --> pdb=" O ILE I 76 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 46 through 48 removed outlier: 6.234A pdb=" N ILE I 46 " --> pdb=" O GLY I 58 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY I 58 " --> pdb=" O ILE I 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 202 through 205 Processing sheet with id=AC3, first strand: chain 'I' and resid 249 through 251 removed outlier: 4.275A pdb=" N ASP I 249 " --> pdb=" O TRP I 233 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 285 through 287 730 hydrogen bonds defined for protein. 2115 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: 5.57 Time building geometry restraints manager: 8.58 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: 5962 1.33 - 1.46: 4385 1.46 - 1.58: 11300 1.58 - 1.70: 1 1.70 - 1.82: 78 Bond restraints: 21726 Sorted by residual: bond pdb=" C ASN C1010 " pdb=" N PRO C1011 " ideal model delta sigma weight residual 1.334 1.420 -0.086 2.34e-02 1.83e+03 1.36e+01 bond pdb=" C ASN H1010 " pdb=" N PRO H1011 " ideal model delta sigma weight residual 1.334 1.419 -0.085 2.34e-02 1.83e+03 1.33e+01 bond pdb=" CA ILE B 430 " pdb=" CB ILE B 430 " ideal model delta sigma weight residual 1.540 1.605 -0.065 2.70e-02 1.37e+03 5.84e+00 bond pdb=" C SER C1007 " pdb=" N PRO C1008 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.51e+00 bond pdb=" C SER H1007 " pdb=" N PRO H1008 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.62e+00 ... (remaining 21721 not shown) Histogram of bond angle deviations from ideal: 96.25 - 104.24: 223 104.24 - 112.22: 10101 112.22 - 120.21: 9966 120.21 - 128.19: 8938 128.19 - 136.18: 174 Bond angle restraints: 29402 Sorted by residual: angle pdb=" N LYS A 98 " pdb=" CA LYS A 98 " pdb=" C LYS A 98 " ideal model delta sigma weight residual 110.80 96.25 14.55 2.13e+00 2.20e-01 4.66e+01 angle pdb=" C SER G 266 " pdb=" N GLN G 267 " pdb=" CA GLN G 267 " ideal model delta sigma weight residual 121.70 133.63 -11.93 1.80e+00 3.09e-01 4.39e+01 angle pdb=" C SER F 266 " pdb=" N GLN F 267 " pdb=" CA GLN F 267 " ideal model delta sigma weight residual 121.70 133.62 -11.92 1.80e+00 3.09e-01 4.38e+01 angle pdb=" C THR B 409 " pdb=" N ASP B 410 " pdb=" CA ASP B 410 " ideal model delta sigma weight residual 121.70 132.42 -10.72 1.80e+00 3.09e-01 3.55e+01 angle pdb=" C ALA A 97 " pdb=" N LYS A 98 " pdb=" CA LYS A 98 " ideal model delta sigma weight residual 121.54 132.87 -11.33 1.91e+00 2.74e-01 3.52e+01 ... (remaining 29397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.17: 11924 15.17 - 30.34: 814 30.34 - 45.51: 216 45.51 - 60.68: 11 60.68 - 75.85: 22 Dihedral angle restraints: 12987 sinusoidal: 5206 harmonic: 7781 Sorted by residual: dihedral pdb=" CA LYS A 80 " pdb=" C LYS A 80 " pdb=" N THR A 81 " pdb=" CA THR A 81 " ideal model delta harmonic sigma weight residual 180.00 125.45 54.55 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA LYS B 80 " pdb=" C LYS B 80 " pdb=" N THR B 81 " pdb=" CA THR B 81 " ideal model delta harmonic sigma weight residual 180.00 125.62 54.38 0 5.00e+00 4.00e-02 1.18e+02 dihedral pdb=" CA VAL A 474 " pdb=" C VAL A 474 " pdb=" N GLU A 475 " pdb=" CA GLU A 475 " ideal model delta harmonic sigma weight residual 180.00 135.81 44.19 0 5.00e+00 4.00e-02 7.81e+01 ... (remaining 12984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2619 0.075 - 0.150: 549 0.150 - 0.225: 67 0.225 - 0.300: 14 0.300 - 0.375: 6 Chirality restraints: 3255 Sorted by residual: chirality pdb=" CB ILE A 310 " pdb=" CA ILE A 310 " pdb=" CG1 ILE A 310 " pdb=" CG2 ILE A 310 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE B 310 " pdb=" CA ILE B 310 " pdb=" CG1 ILE B 310 " pdb=" CG2 ILE B 310 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CB ILE A 361 " pdb=" CA ILE A 361 " pdb=" CG1 ILE A 361 " pdb=" CG2 ILE A 361 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 3252 not shown) Planarity restraints: 3796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C1007 " -0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO C1008 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO C1008 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C1008 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 72 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.41e+00 pdb=" N PRO I 73 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO I 73 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO I 73 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 46 " -0.050 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO I 47 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO I 47 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 47 " -0.042 5.00e-02 4.00e+02 ... (remaining 3793 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 5 2.08 - 2.78: 4781 2.78 - 3.49: 28842 3.49 - 4.19: 48711 4.19 - 4.90: 82048 Nonbonded interactions: 164387 Sorted by model distance: nonbonded pdb=" N PHE B 200 " pdb=" CE2 PHE B 393 " model vdw 1.372 3.420 nonbonded pdb=" N PHE A 200 " pdb=" CD2 PHE A 393 " model vdw 1.757 3.420 nonbonded pdb=" N PHE B 200 " pdb=" CD2 PHE B 393 " model vdw 1.785 3.420 nonbonded pdb=" N PHE A 200 " pdb=" CE2 PHE A 393 " model vdw 1.816 3.420 nonbonded pdb=" ND2 ASN B 390 " pdb=" O THR B 395 " model vdw 1.943 2.520 ... (remaining 164382 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 97 or (resid 98 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 through 423 or (resid 424 and \ (name N or name CA or name C or name O or name CB )) or resid 425 through 510)) selection = (chain 'B' and (resid 11 through 84 or (resid 85 and (name N or name CA or name \ C or name O or name CB )) or resid 86 through 510)) } ncs_group { reference = (chain 'C' and (resid 974 through 1016 or (resid 1017 and (name N or name CA or \ name C or name O or name CB )) or resid 1018 through 1035)) selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 4.670 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 52.330 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 21726 Z= 0.332 Angle : 1.122 15.301 29402 Z= 0.590 Chirality : 0.063 0.375 3255 Planarity : 0.007 0.080 3796 Dihedral : 11.728 75.848 7957 Min Nonbonded Distance : 1.372 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 0.35 % Allowed : 6.21 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 3.90 % Twisted General : 0.59 % 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: -4.82 (0.13), residues: 2606 helix: -2.69 (0.12), residues: 978 sheet: -2.70 (0.31), residues: 245 loop : -3.81 (0.14), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 23 HIS 0.007 0.002 HIS A 270 PHE 0.034 0.003 PHE G 415 TYR 0.034 0.003 TYR B 260 ARG 0.011 0.001 ARG I 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 518 time to evaluate : 2.588 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: symmetry clash revert: symmetry clash REVERT: A 86 ILE cc_start: 0.8031 (tt) cc_final: 0.7800 (tp) REVERT: A 98 LYS cc_start: 0.7684 (mtmm) cc_final: 0.7309 (mtpp) REVERT: A 136 PHE cc_start: 0.8409 (t80) cc_final: 0.7949 (t80) REVERT: A 392 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7318 (m-10) REVERT: A 429 ASN cc_start: 0.7283 (m-40) cc_final: 0.6591 (p0) REVERT: A 484 ASP cc_start: 0.7962 (p0) cc_final: 0.7619 (p0) REVERT: B 139 THR cc_start: 0.8473 (p) cc_final: 0.8261 (p) REVERT: B 358 PHE cc_start: 0.7297 (p90) cc_final: 0.7052 (p90) REVERT: B 484 ASP cc_start: 0.7891 (p0) cc_final: 0.7569 (p0) REVERT: D 8 ILE cc_start: 0.8858 (pt) cc_final: 0.8623 (mm) REVERT: D 96 GLU cc_start: 0.8553 (tt0) cc_final: 0.8327 (tp30) REVERT: D 118 ARG cc_start: 0.8690 (ttt90) cc_final: 0.8224 (tpp80) REVERT: D 123 GLU cc_start: 0.8567 (mm-30) cc_final: 0.7028 (mp0) REVERT: D 135 GLN cc_start: 0.8472 (tt0) cc_final: 0.8043 (tp40) REVERT: D 137 TYR cc_start: 0.7536 (m-80) cc_final: 0.7069 (m-80) REVERT: D 164 VAL cc_start: 0.9014 (p) cc_final: 0.8712 (p) REVERT: E 8 ILE cc_start: 0.8924 (pt) cc_final: 0.8697 (mm) REVERT: E 118 ARG cc_start: 0.8705 (ttt90) cc_final: 0.8262 (tpp80) REVERT: E 123 GLU cc_start: 0.8960 (mm-30) cc_final: 0.7847 (mp0) REVERT: E 135 GLN cc_start: 0.8503 (tt0) cc_final: 0.8036 (tp40) REVERT: E 164 VAL cc_start: 0.9083 (p) cc_final: 0.8820 (p) REVERT: F 118 LEU cc_start: 0.9052 (tm) cc_final: 0.8739 (tp) REVERT: F 174 ARG cc_start: 0.7732 (ttt-90) cc_final: 0.7295 (ttt-90) REVERT: F 244 THR cc_start: 0.9435 (m) cc_final: 0.9198 (p) REVERT: F 343 ASP cc_start: 0.7651 (t70) cc_final: 0.7372 (t0) REVERT: G 118 LEU cc_start: 0.8989 (tm) cc_final: 0.8754 (tp) REVERT: G 244 THR cc_start: 0.9410 (m) cc_final: 0.9196 (p) REVERT: G 343 ASP cc_start: 0.7664 (t70) cc_final: 0.7404 (t0) REVERT: I 100 MET cc_start: 0.8125 (mmm) cc_final: 0.7772 (mmt) REVERT: I 168 PHE cc_start: 0.8076 (m-10) cc_final: 0.7869 (m-10) REVERT: I 178 GLU cc_start: 0.8953 (pp20) cc_final: 0.8581 (pp20) outliers start: 8 outliers final: 2 residues processed: 525 average time/residue: 0.3573 time to fit residues: 275.7022 Evaluate side-chains 262 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 259 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 430 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 9.9990 chunk 197 optimal weight: 0.0030 chunk 109 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 151 optimal weight: 0.2980 chunk 236 optimal weight: 3.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 240 GLN A 243 ASN A 428 ASN ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN B 240 GLN B 243 ASN B 428 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 HIS F 221 ASN ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 HIS G 221 ASN G 387 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 GLN I 258 HIS I 313 HIS C1000 ASN C1022 GLN H1000 ASN H1012 GLN H1018 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21726 Z= 0.206 Angle : 0.762 10.508 29402 Z= 0.395 Chirality : 0.048 0.264 3255 Planarity : 0.005 0.070 3796 Dihedral : 7.478 48.117 2851 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 3.24 % Allowed : 11.30 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 3.90 % Twisted General : 0.31 % 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: -3.89 (0.14), residues: 2606 helix: -1.19 (0.15), residues: 1029 sheet: -2.76 (0.31), residues: 247 loop : -3.84 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP I 134 HIS 0.005 0.001 HIS B 219 PHE 0.026 0.002 PHE I 225 TYR 0.015 0.001 TYR A 260 ARG 0.008 0.001 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 310 time to evaluate : 2.690 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: A 136 PHE cc_start: 0.7972 (t80) cc_final: 0.6963 (t80) REVERT: A 391 LEU cc_start: 0.8280 (tp) cc_final: 0.7843 (tp) REVERT: A 484 ASP cc_start: 0.8205 (p0) cc_final: 0.7826 (p0) REVERT: B 184 LEU cc_start: 0.7735 (tt) cc_final: 0.7430 (tt) REVERT: B 391 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8072 (tp) REVERT: B 392 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7519 (m-10) REVERT: B 425 GLU cc_start: 0.6373 (tt0) cc_final: 0.6154 (tm-30) REVERT: B 484 ASP cc_start: 0.8073 (p0) cc_final: 0.7739 (p0) REVERT: D 118 ARG cc_start: 0.8647 (ttt90) cc_final: 0.8283 (tpp80) REVERT: D 123 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7315 (mp0) REVERT: D 136 ASN cc_start: 0.7464 (p0) cc_final: 0.7143 (p0) REVERT: D 137 TYR cc_start: 0.7400 (m-80) cc_final: 0.6894 (m-80) REVERT: E 118 ARG cc_start: 0.8684 (ttt90) cc_final: 0.8316 (tpp80) REVERT: E 123 GLU cc_start: 0.8606 (mm-30) cc_final: 0.7921 (mp0) REVERT: F 118 LEU cc_start: 0.9014 (tm) cc_final: 0.8675 (tp) REVERT: F 343 ASP cc_start: 0.7853 (t70) cc_final: 0.7387 (t0) REVERT: G 118 LEU cc_start: 0.8999 (tm) cc_final: 0.8726 (tp) REVERT: G 343 ASP cc_start: 0.7902 (t70) cc_final: 0.7410 (t0) REVERT: I 66 ILE cc_start: -0.3438 (OUTLIER) cc_final: -0.3713 (tt) REVERT: I 100 MET cc_start: 0.7730 (mmm) cc_final: 0.7018 (tpp) REVERT: I 134 TRP cc_start: 0.6842 (m-90) cc_final: 0.6558 (m-90) REVERT: I 178 GLU cc_start: 0.9046 (pp20) cc_final: 0.8683 (pp20) REVERT: I 189 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.7352 (t80) REVERT: I 193 LEU cc_start: 0.9317 (tt) cc_final: 0.9091 (tt) REVERT: I 263 LEU cc_start: 0.3849 (OUTLIER) cc_final: 0.3525 (pp) REVERT: I 378 GLU cc_start: 0.8699 (tt0) cc_final: 0.8448 (tm-30) REVERT: I 379 ILE cc_start: 0.9685 (mt) cc_final: 0.9139 (mm) REVERT: H 1018 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8046 (pm20) outliers start: 75 outliers final: 34 residues processed: 365 average time/residue: 0.3647 time to fit residues: 195.8109 Evaluate side-chains 272 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 232 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 362 PHE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 277 ILE Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain H residue 1018 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 196 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 236 optimal weight: 0.7980 chunk 255 optimal weight: 0.3980 chunk 210 optimal weight: 5.9990 chunk 234 optimal weight: 0.0020 chunk 80 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN F 351 GLN ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21726 Z= 0.199 Angle : 0.737 10.228 29402 Z= 0.376 Chirality : 0.047 0.278 3255 Planarity : 0.005 0.075 3796 Dihedral : 6.833 37.260 2847 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 3.49 % Allowed : 13.59 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.35 (0.15), residues: 2606 helix: -0.47 (0.16), residues: 1019 sheet: -2.69 (0.31), residues: 249 loop : -3.72 (0.14), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 17 HIS 0.004 0.001 HIS A 13 PHE 0.021 0.001 PHE H1021 TYR 0.021 0.001 TYR B 188 ARG 0.006 0.000 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 256 time to evaluate : 2.550 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: A 13 HIS cc_start: 0.8200 (m170) cc_final: 0.7853 (m170) REVERT: A 17 TRP cc_start: 0.8076 (m100) cc_final: 0.7759 (m100) REVERT: A 136 PHE cc_start: 0.8018 (t80) cc_final: 0.6825 (t80) REVERT: A 184 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6489 (tt) REVERT: A 265 MET cc_start: 0.8113 (ptp) cc_final: 0.7586 (mtp) REVERT: A 484 ASP cc_start: 0.8185 (p0) cc_final: 0.7727 (p0) REVERT: A 503 ARG cc_start: 0.8815 (ptp-170) cc_final: 0.8567 (ptp90) REVERT: B 153 ARG cc_start: 0.5430 (ttp-170) cc_final: 0.5226 (ttp-170) REVERT: B 392 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7476 (m-10) REVERT: B 425 GLU cc_start: 0.6409 (tt0) cc_final: 0.6099 (tm-30) REVERT: D 118 ARG cc_start: 0.8675 (ttt90) cc_final: 0.8299 (tpp80) REVERT: D 123 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7345 (mp0) REVERT: D 136 ASN cc_start: 0.7440 (p0) cc_final: 0.7129 (p0) REVERT: D 137 TYR cc_start: 0.7180 (m-80) cc_final: 0.6861 (m-80) REVERT: D 146 ASP cc_start: 0.8328 (m-30) cc_final: 0.7743 (t0) REVERT: E 118 ARG cc_start: 0.8700 (ttt90) cc_final: 0.8346 (tpp80) REVERT: E 123 GLU cc_start: 0.8629 (mm-30) cc_final: 0.7909 (mp0) REVERT: F 343 ASP cc_start: 0.7852 (t70) cc_final: 0.7414 (t0) REVERT: G 283 ILE cc_start: 0.9523 (mt) cc_final: 0.9321 (tp) REVERT: G 343 ASP cc_start: 0.7860 (t70) cc_final: 0.7445 (t0) REVERT: I 66 ILE cc_start: -0.3401 (OUTLIER) cc_final: -0.3665 (tt) REVERT: I 73 PRO cc_start: 0.6874 (Cg_exo) cc_final: 0.6630 (Cg_endo) REVERT: I 100 MET cc_start: 0.7757 (mmm) cc_final: 0.7164 (tmm) REVERT: I 134 TRP cc_start: 0.6986 (m-90) cc_final: 0.6593 (m-90) REVERT: I 178 GLU cc_start: 0.8978 (pp20) cc_final: 0.8635 (pp20) REVERT: I 189 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7358 (t80) REVERT: I 193 LEU cc_start: 0.9323 (tt) cc_final: 0.9090 (tt) REVERT: I 263 LEU cc_start: 0.3760 (OUTLIER) cc_final: 0.3444 (pp) REVERT: H 1018 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8102 (pm20) outliers start: 81 outliers final: 36 residues processed: 310 average time/residue: 0.3512 time to fit residues: 163.5738 Evaluate side-chains 270 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 228 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain H residue 1018 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 9.9990 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 158 optimal weight: 0.9980 chunk 237 optimal weight: 10.0000 chunk 251 optimal weight: 0.4980 chunk 124 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN ** F 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 ASN ** G 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 975 ASN H1018 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 21726 Z= 0.366 Angle : 0.830 12.545 29402 Z= 0.428 Chirality : 0.050 0.296 3255 Planarity : 0.005 0.071 3796 Dihedral : 6.958 37.735 2845 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.24 % Favored : 85.76 % Rotamer: Outliers : 4.31 % Allowed : 14.45 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -3.32 (0.15), residues: 2606 helix: -0.38 (0.16), residues: 1048 sheet: -2.80 (0.30), residues: 245 loop : -3.80 (0.14), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B 17 HIS 0.009 0.002 HIS I 303 PHE 0.030 0.002 PHE B 85 TYR 0.024 0.002 TYR A 35 ARG 0.006 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 223 time to evaluate : 2.625 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: A 13 HIS cc_start: 0.8492 (m170) cc_final: 0.8101 (m170) REVERT: A 17 TRP cc_start: 0.8013 (m100) cc_final: 0.7670 (m100) REVERT: A 30 TRP cc_start: 0.7471 (m100) cc_final: 0.7218 (m100) REVERT: A 130 LYS cc_start: 0.8178 (pptt) cc_final: 0.7654 (pttt) REVERT: A 136 PHE cc_start: 0.8167 (t80) cc_final: 0.7593 (t80) REVERT: A 429 ASN cc_start: 0.6968 (m-40) cc_final: 0.6063 (p0) REVERT: B 85 PHE cc_start: 0.8259 (t80) cc_final: 0.7998 (t80) REVERT: B 204 HIS cc_start: 0.8340 (OUTLIER) cc_final: 0.8107 (p-80) REVERT: B 392 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7504 (m-10) REVERT: B 425 GLU cc_start: 0.6968 (tt0) cc_final: 0.6745 (tm-30) REVERT: D 123 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7764 (mp0) REVERT: D 136 ASN cc_start: 0.7360 (p0) cc_final: 0.6928 (p0) REVERT: D 137 TYR cc_start: 0.7599 (m-80) cc_final: 0.7392 (m-80) REVERT: E 123 GLU cc_start: 0.8729 (mm-30) cc_final: 0.7960 (mp0) REVERT: F 118 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8923 (tp) REVERT: F 343 ASP cc_start: 0.8228 (t70) cc_final: 0.7571 (t0) REVERT: G 343 ASP cc_start: 0.8227 (t70) cc_final: 0.7586 (t0) REVERT: I 66 ILE cc_start: -0.3643 (OUTLIER) cc_final: -0.3882 (tt) REVERT: I 73 PRO cc_start: 0.6936 (Cg_exo) cc_final: 0.6727 (Cg_endo) REVERT: I 98 MET cc_start: 0.5440 (OUTLIER) cc_final: 0.5114 (mtt) REVERT: I 100 MET cc_start: 0.7804 (mmm) cc_final: 0.7218 (tmm) REVERT: I 134 TRP cc_start: 0.7252 (m-90) cc_final: 0.6849 (m-90) REVERT: I 168 PHE cc_start: 0.8497 (m-80) cc_final: 0.8260 (m-80) REVERT: I 178 GLU cc_start: 0.8927 (pp20) cc_final: 0.8559 (pp20) REVERT: I 189 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7310 (t80) REVERT: I 263 LEU cc_start: 0.3707 (OUTLIER) cc_final: 0.3258 (pp) REVERT: H 995 ASN cc_start: 0.5110 (m110) cc_final: 0.4798 (t0) outliers start: 100 outliers final: 64 residues processed: 301 average time/residue: 0.3577 time to fit residues: 161.4475 Evaluate side-chains 265 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 194 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 415 PHE Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 60 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 403 VAL Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain I residue 367 LEU Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain H residue 1018 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 0.0970 chunk 142 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 187 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 214 optimal weight: 8.9990 chunk 173 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 225 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 GLN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1018 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21726 Z= 0.181 Angle : 0.705 10.691 29402 Z= 0.361 Chirality : 0.047 0.246 3255 Planarity : 0.004 0.060 3796 Dihedral : 6.443 35.925 2845 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 3.24 % Allowed : 15.62 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.16), residues: 2606 helix: -0.03 (0.16), residues: 1056 sheet: -2.54 (0.30), residues: 250 loop : -3.61 (0.14), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 17 HIS 0.006 0.001 HIS B 219 PHE 0.032 0.002 PHE B 358 TYR 0.013 0.001 TYR B 188 ARG 0.004 0.000 ARG H 981 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 249 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: A 13 HIS cc_start: 0.8211 (m170) cc_final: 0.7817 (m170) REVERT: A 17 TRP cc_start: 0.8017 (m100) cc_final: 0.7710 (m100) REVERT: A 130 LYS cc_start: 0.8065 (pptt) cc_final: 0.7582 (pttt) REVERT: A 136 PHE cc_start: 0.7790 (t80) cc_final: 0.6816 (t80) REVERT: A 184 LEU cc_start: 0.7132 (tt) cc_final: 0.6925 (tt) REVERT: A 265 MET cc_start: 0.8361 (ptp) cc_final: 0.7750 (mtp) REVERT: A 503 ARG cc_start: 0.8797 (ptp-170) cc_final: 0.8577 (ptp90) REVERT: B 85 PHE cc_start: 0.8255 (t80) cc_final: 0.7956 (t80) REVERT: B 392 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7794 (m-10) REVERT: D 123 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7664 (mp0) REVERT: D 136 ASN cc_start: 0.7436 (p0) cc_final: 0.6970 (p0) REVERT: D 137 TYR cc_start: 0.7251 (m-80) cc_final: 0.6955 (m-80) REVERT: E 123 GLU cc_start: 0.8698 (mm-30) cc_final: 0.7868 (mp0) REVERT: F 118 LEU cc_start: 0.9051 (tm) cc_final: 0.8833 (tp) REVERT: F 267 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7142 (mm-40) REVERT: F 343 ASP cc_start: 0.8046 (t70) cc_final: 0.7638 (t0) REVERT: G 343 ASP cc_start: 0.8058 (t70) cc_final: 0.7724 (t0) REVERT: I 66 ILE cc_start: -0.3715 (OUTLIER) cc_final: -0.4111 (tp) REVERT: I 100 MET cc_start: 0.7576 (mmm) cc_final: 0.6802 (tmm) REVERT: I 134 TRP cc_start: 0.7124 (m-90) cc_final: 0.6845 (m-90) REVERT: I 168 PHE cc_start: 0.8420 (m-80) cc_final: 0.8144 (m-80) REVERT: I 178 GLU cc_start: 0.8893 (pp20) cc_final: 0.8497 (pp20) REVERT: I 189 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7206 (t80) REVERT: I 263 LEU cc_start: 0.4033 (OUTLIER) cc_final: 0.3693 (pp) REVERT: I 373 GLU cc_start: 0.5234 (tp30) cc_final: 0.4865 (tp30) REVERT: H 1013 TYR cc_start: 0.7008 (m-10) cc_final: 0.6705 (p90) outliers start: 75 outliers final: 41 residues processed: 302 average time/residue: 0.3529 time to fit residues: 159.8068 Evaluate side-chains 255 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 209 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 268 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 0.9990 chunk 226 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 251 optimal weight: 0.6980 chunk 208 optimal weight: 10.0000 chunk 116 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN B 489 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 ASN H1018 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21726 Z= 0.178 Angle : 0.694 10.553 29402 Z= 0.350 Chirality : 0.046 0.230 3255 Planarity : 0.004 0.059 3796 Dihedral : 6.114 35.325 2845 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 3.80 % Allowed : 16.09 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.16), residues: 2606 helix: 0.25 (0.17), residues: 1029 sheet: -2.47 (0.30), residues: 260 loop : -3.48 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP B 17 HIS 0.007 0.001 HIS I 64 PHE 0.034 0.001 PHE B 358 TYR 0.015 0.001 TYR I 59 ARG 0.005 0.000 ARG I 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 246 time to evaluate : 2.488 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: A 17 TRP cc_start: 0.8080 (m100) cc_final: 0.7792 (m100) REVERT: A 33 LYS cc_start: 0.8895 (tmmm) cc_final: 0.8640 (mptt) REVERT: A 130 LYS cc_start: 0.8003 (pptt) cc_final: 0.7517 (pttt) REVERT: A 136 PHE cc_start: 0.7732 (t80) cc_final: 0.6863 (t80) REVERT: A 260 TYR cc_start: 0.8444 (t80) cc_final: 0.8232 (t80) REVERT: A 265 MET cc_start: 0.8393 (ptp) cc_final: 0.7710 (mtp) REVERT: A 503 ARG cc_start: 0.8783 (ptp-170) cc_final: 0.8542 (ptp90) REVERT: B 85 PHE cc_start: 0.8242 (t80) cc_final: 0.7955 (t80) REVERT: B 392 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7807 (m-10) REVERT: D 113 MET cc_start: 0.8015 (mmm) cc_final: 0.7711 (mmm) REVERT: D 123 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7683 (mp0) REVERT: D 136 ASN cc_start: 0.7366 (p0) cc_final: 0.6874 (p0) REVERT: E 46 TYR cc_start: 0.8167 (p90) cc_final: 0.7833 (p90) REVERT: E 123 GLU cc_start: 0.8721 (mm-30) cc_final: 0.7890 (mp0) REVERT: F 118 LEU cc_start: 0.9073 (tm) cc_final: 0.8843 (tp) REVERT: F 267 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7122 (mm-40) REVERT: F 343 ASP cc_start: 0.7987 (t70) cc_final: 0.7563 (t0) REVERT: F 362 GLU cc_start: 0.7822 (pm20) cc_final: 0.7538 (pm20) REVERT: F 385 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8953 (tppp) REVERT: G 343 ASP cc_start: 0.7983 (t70) cc_final: 0.7582 (t0) REVERT: G 362 GLU cc_start: 0.7658 (pm20) cc_final: 0.7384 (pm20) REVERT: I 100 MET cc_start: 0.7732 (mmm) cc_final: 0.6944 (tmm) REVERT: I 134 TRP cc_start: 0.7150 (m-90) cc_final: 0.6880 (m-90) REVERT: I 168 PHE cc_start: 0.8462 (m-80) cc_final: 0.8223 (m-80) REVERT: I 178 GLU cc_start: 0.8904 (pp20) cc_final: 0.8532 (pp20) REVERT: I 189 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7201 (t80) REVERT: I 278 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.6121 (tt) REVERT: I 279 ASP cc_start: 0.5739 (m-30) cc_final: 0.5413 (p0) REVERT: I 373 GLU cc_start: 0.5651 (tp30) cc_final: 0.5279 (tp30) REVERT: H 1013 TYR cc_start: 0.7071 (m-10) cc_final: 0.6750 (p90) REVERT: H 1018 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8073 (pm20) outliers start: 88 outliers final: 50 residues processed: 312 average time/residue: 0.3528 time to fit residues: 164.1969 Evaluate side-chains 268 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 212 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 135 ASP Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 267 GLN Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 385 LYS Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 225 PHE Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 278 LEU Chi-restraints excluded: chain H residue 1018 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 143 optimal weight: 0.3980 chunk 183 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 211 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 250 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 152 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN B 489 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 ASN ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21726 Z= 0.224 Angle : 0.712 10.845 29402 Z= 0.362 Chirality : 0.046 0.218 3255 Planarity : 0.004 0.054 3796 Dihedral : 6.111 35.118 2845 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.32 % Favored : 87.68 % Rotamer: Outliers : 3.84 % Allowed : 17.21 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.16), residues: 2606 helix: 0.33 (0.17), residues: 1041 sheet: -2.43 (0.31), residues: 248 loop : -3.47 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP B 17 HIS 0.007 0.001 HIS A 219 PHE 0.033 0.002 PHE B 358 TYR 0.023 0.001 TYR D 46 ARG 0.004 0.000 ARG I 324 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 220 time to evaluate : 2.490 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: A 17 TRP cc_start: 0.7980 (m100) cc_final: 0.7715 (m100) REVERT: A 33 LYS cc_start: 0.8874 (tmmm) cc_final: 0.8567 (mptt) REVERT: A 130 LYS cc_start: 0.8116 (pptt) cc_final: 0.7698 (pttt) REVERT: A 136 PHE cc_start: 0.7880 (t80) cc_final: 0.7039 (t80) REVERT: A 260 TYR cc_start: 0.8542 (t80) cc_final: 0.8217 (t80) REVERT: A 265 MET cc_start: 0.8417 (ptp) cc_final: 0.7980 (mtp) REVERT: A 308 LYS cc_start: 0.8386 (tptt) cc_final: 0.8159 (tptt) REVERT: B 85 PHE cc_start: 0.8270 (t80) cc_final: 0.7996 (t80) REVERT: B 392 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7842 (m-10) REVERT: D 6 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8949 (p) REVERT: D 123 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7676 (mp0) REVERT: E 46 TYR cc_start: 0.8116 (p90) cc_final: 0.7784 (p90) REVERT: E 123 GLU cc_start: 0.8748 (mm-30) cc_final: 0.7894 (mp0) REVERT: F 118 LEU cc_start: 0.9073 (tm) cc_final: 0.8869 (tp) REVERT: F 343 ASP cc_start: 0.8016 (t70) cc_final: 0.7586 (t0) REVERT: F 385 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9013 (tppp) REVERT: G 343 ASP cc_start: 0.8000 (t70) cc_final: 0.7613 (t0) REVERT: I 100 MET cc_start: 0.7779 (mmm) cc_final: 0.6946 (tmm) REVERT: I 134 TRP cc_start: 0.7208 (m-90) cc_final: 0.6585 (m-90) REVERT: I 168 PHE cc_start: 0.8528 (m-80) cc_final: 0.8282 (m-80) REVERT: I 178 GLU cc_start: 0.8938 (pp20) cc_final: 0.8550 (pp20) REVERT: I 189 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7260 (t80) REVERT: I 346 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7932 (mp) REVERT: I 373 GLU cc_start: 0.4855 (tp30) cc_final: 0.4634 (tp30) REVERT: C 1014 LYS cc_start: 0.5627 (mmmm) cc_final: 0.5263 (tppt) outliers start: 89 outliers final: 63 residues processed: 287 average time/residue: 0.3485 time to fit residues: 150.0127 Evaluate side-chains 271 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 203 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 385 LYS Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 60 MET Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 225 PHE Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain C residue 1029 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 123 optimal weight: 0.0670 chunk 23 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN A 243 ASN A 489 ASN ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 459 HIS H1018 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21726 Z= 0.172 Angle : 0.708 13.599 29402 Z= 0.354 Chirality : 0.046 0.224 3255 Planarity : 0.004 0.058 3796 Dihedral : 5.921 34.248 2845 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 3.32 % Allowed : 17.56 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.16), residues: 2606 helix: 0.43 (0.17), residues: 1037 sheet: -2.37 (0.32), residues: 248 loop : -3.40 (0.15), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 17 HIS 0.005 0.001 HIS A 219 PHE 0.034 0.001 PHE B 136 TYR 0.021 0.001 TYR D 46 ARG 0.006 0.000 ARG H 981 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 231 time to evaluate : 2.250 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: A 17 TRP cc_start: 0.8008 (m100) cc_final: 0.7751 (m100) REVERT: A 33 LYS cc_start: 0.8831 (tmmm) cc_final: 0.8529 (mmtt) REVERT: A 130 LYS cc_start: 0.8074 (pptt) cc_final: 0.7635 (pttt) REVERT: A 136 PHE cc_start: 0.7650 (t80) cc_final: 0.6443 (t80) REVERT: A 260 TYR cc_start: 0.8404 (t80) cc_final: 0.8148 (t80) REVERT: A 265 MET cc_start: 0.8220 (ptp) cc_final: 0.7848 (mtp) REVERT: B 17 TRP cc_start: 0.8083 (OUTLIER) cc_final: 0.7693 (m100) REVERT: B 85 PHE cc_start: 0.8316 (t80) cc_final: 0.7960 (t80) REVERT: B 359 PRO cc_start: 0.8830 (Cg_exo) cc_final: 0.8562 (Cg_endo) REVERT: B 392 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7817 (m-10) REVERT: D 6 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8946 (p) REVERT: D 123 GLU cc_start: 0.8557 (mm-30) cc_final: 0.7674 (mp0) REVERT: E 46 TYR cc_start: 0.8037 (p90) cc_final: 0.7730 (p90) REVERT: E 146 ASP cc_start: 0.8136 (m-30) cc_final: 0.7627 (t70) REVERT: F 343 ASP cc_start: 0.7934 (t70) cc_final: 0.7543 (t0) REVERT: F 385 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9010 (tppp) REVERT: G 343 ASP cc_start: 0.7916 (t70) cc_final: 0.7527 (t0) REVERT: I 100 MET cc_start: 0.7777 (mmm) cc_final: 0.6888 (tmm) REVERT: I 134 TRP cc_start: 0.7185 (m-90) cc_final: 0.6578 (m-90) REVERT: I 168 PHE cc_start: 0.8502 (m-80) cc_final: 0.8253 (m-80) REVERT: I 178 GLU cc_start: 0.8944 (pp20) cc_final: 0.8527 (pp20) REVERT: I 189 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7202 (t80) REVERT: I 324 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7728 (mpt180) REVERT: I 346 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8098 (mp) REVERT: I 373 GLU cc_start: 0.5699 (tp30) cc_final: 0.5365 (tp30) REVERT: C 1014 LYS cc_start: 0.5188 (mmmm) cc_final: 0.4948 (tppt) REVERT: H 1013 TYR cc_start: 0.7149 (m-10) cc_final: 0.6734 (p90) REVERT: H 1018 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8019 (pm20) outliers start: 77 outliers final: 54 residues processed: 291 average time/residue: 0.3673 time to fit residues: 159.5867 Evaluate side-chains 275 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 214 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 385 LYS Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 225 PHE Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain H residue 1018 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 183 optimal weight: 0.4980 chunk 71 optimal weight: 0.4980 chunk 211 optimal weight: 0.0070 chunk 220 optimal weight: 4.9990 chunk 232 optimal weight: 3.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1018 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21726 Z= 0.174 Angle : 0.701 13.145 29402 Z= 0.352 Chirality : 0.046 0.220 3255 Planarity : 0.004 0.058 3796 Dihedral : 5.767 33.675 2845 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 3.19 % Allowed : 17.99 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.16), residues: 2606 helix: 0.44 (0.17), residues: 1037 sheet: -2.27 (0.32), residues: 248 loop : -3.32 (0.15), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 17 HIS 0.003 0.001 HIS D 90 PHE 0.038 0.001 PHE B 136 TYR 0.022 0.001 TYR D 46 ARG 0.005 0.000 ARG C 981 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 225 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 TRP cc_start: 0.8008 (m100) cc_final: 0.7739 (m100) REVERT: A 33 LYS cc_start: 0.8846 (tmmm) cc_final: 0.8527 (mmtt) REVERT: A 130 LYS cc_start: 0.8035 (pptt) cc_final: 0.7615 (pttt) REVERT: A 136 PHE cc_start: 0.7723 (t80) cc_final: 0.6528 (t80) REVERT: A 260 TYR cc_start: 0.8445 (t80) cc_final: 0.8213 (t80) REVERT: A 265 MET cc_start: 0.8186 (ptp) cc_final: 0.7872 (mtp) REVERT: B 17 TRP cc_start: 0.8097 (OUTLIER) cc_final: 0.7732 (m100) REVERT: B 138 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8452 (t) REVERT: B 184 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7981 (mt) REVERT: B 359 PRO cc_start: 0.8606 (Cg_exo) cc_final: 0.8305 (Cg_endo) REVERT: B 392 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7694 (m-10) REVERT: D 123 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7668 (mp0) REVERT: E 46 TYR cc_start: 0.8006 (p90) cc_final: 0.7766 (p90) REVERT: E 146 ASP cc_start: 0.8122 (m-30) cc_final: 0.7669 (t70) REVERT: F 343 ASP cc_start: 0.7891 (t70) cc_final: 0.7508 (t0) REVERT: G 343 ASP cc_start: 0.7873 (t70) cc_final: 0.7497 (t0) REVERT: G 362 GLU cc_start: 0.7566 (pm20) cc_final: 0.7336 (pm20) REVERT: I 100 MET cc_start: 0.7791 (mmm) cc_final: 0.6873 (tmm) REVERT: I 134 TRP cc_start: 0.7183 (m-90) cc_final: 0.6484 (m-90) REVERT: I 178 GLU cc_start: 0.8925 (pp20) cc_final: 0.8489 (pp20) REVERT: I 189 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7190 (t80) REVERT: I 239 MET cc_start: 0.6799 (mtt) cc_final: 0.6259 (mmm) REVERT: I 324 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7653 (mpt180) REVERT: I 346 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8110 (mp) REVERT: I 373 GLU cc_start: 0.5700 (tp30) cc_final: 0.5370 (tp30) REVERT: C 981 ARG cc_start: 0.6169 (mtt-85) cc_final: 0.5959 (mtt-85) REVERT: C 1014 LYS cc_start: 0.5278 (mmmm) cc_final: 0.5044 (tppt) REVERT: H 1013 TYR cc_start: 0.7127 (m-10) cc_final: 0.6741 (p90) REVERT: H 1018 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8156 (mp10) outliers start: 74 outliers final: 50 residues processed: 282 average time/residue: 0.3596 time to fit residues: 151.6030 Evaluate side-chains 266 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 209 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 504 LYS Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 17 TRP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 14 TYR Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 225 PHE Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain H residue 1018 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.6980 chunk 246 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 206 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 459 HIS H1018 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21726 Z= 0.205 Angle : 0.719 14.204 29402 Z= 0.363 Chirality : 0.046 0.220 3255 Planarity : 0.004 0.059 3796 Dihedral : 5.790 33.591 2845 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.09 % Favored : 88.91 % Rotamer: Outliers : 2.76 % Allowed : 18.51 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.16), residues: 2606 helix: 0.46 (0.17), residues: 1043 sheet: -2.28 (0.33), residues: 248 loop : -3.34 (0.15), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 17 HIS 0.006 0.001 HIS A 219 PHE 0.037 0.001 PHE B 136 TYR 0.022 0.001 TYR D 46 ARG 0.006 0.000 ARG H 981 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5212 Ramachandran restraints generated. 2606 Oldfield, 0 Emsley, 2606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 215 time to evaluate : 2.647 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: A 17 TRP cc_start: 0.7982 (m100) cc_final: 0.7693 (m100) REVERT: A 33 LYS cc_start: 0.8886 (tmmm) cc_final: 0.8537 (mmtm) REVERT: A 109 LEU cc_start: 0.8766 (tp) cc_final: 0.8564 (tp) REVERT: A 130 LYS cc_start: 0.8076 (pptt) cc_final: 0.7664 (pttt) REVERT: A 136 PHE cc_start: 0.7788 (t80) cc_final: 0.6698 (t80) REVERT: A 220 VAL cc_start: 0.7653 (t) cc_final: 0.7293 (m) REVERT: A 260 TYR cc_start: 0.8537 (t80) cc_final: 0.8299 (t80) REVERT: A 308 LYS cc_start: 0.8277 (tptt) cc_final: 0.7923 (tptt) REVERT: A 505 ASP cc_start: 0.8655 (m-30) cc_final: 0.8009 (t0) REVERT: B 17 TRP cc_start: 0.8104 (m-90) cc_final: 0.7753 (m100) REVERT: B 181 TYR cc_start: 0.7708 (t80) cc_final: 0.7456 (t80) REVERT: B 220 VAL cc_start: 0.7537 (t) cc_final: 0.7245 (m) REVERT: B 262 LEU cc_start: 0.9012 (pp) cc_final: 0.8693 (pp) REVERT: B 359 PRO cc_start: 0.8736 (Cg_exo) cc_final: 0.8469 (Cg_endo) REVERT: B 392 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7689 (m-10) REVERT: D 123 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7675 (mp0) REVERT: E 46 TYR cc_start: 0.8034 (p90) cc_final: 0.7786 (p90) REVERT: E 146 ASP cc_start: 0.8175 (m-30) cc_final: 0.7720 (t70) REVERT: F 343 ASP cc_start: 0.7927 (t70) cc_final: 0.7562 (t0) REVERT: F 385 LYS cc_start: 0.9468 (OUTLIER) cc_final: 0.8928 (tppp) REVERT: G 343 ASP cc_start: 0.7917 (t70) cc_final: 0.7548 (t0) REVERT: I 100 MET cc_start: 0.7813 (mmm) cc_final: 0.6887 (tmm) REVERT: I 134 TRP cc_start: 0.7252 (m-90) cc_final: 0.6549 (m-90) REVERT: I 178 GLU cc_start: 0.8936 (pp20) cc_final: 0.8503 (pp20) REVERT: I 189 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7185 (t80) REVERT: I 239 MET cc_start: 0.6670 (mtt) cc_final: 0.6094 (mmm) REVERT: I 324 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7665 (mpt180) REVERT: C 981 ARG cc_start: 0.6198 (mtt-85) cc_final: 0.5997 (mtt-85) REVERT: H 981 ARG cc_start: 0.6177 (mtt-85) cc_final: 0.5890 (mtt-85) REVERT: H 1013 TYR cc_start: 0.7166 (m-10) cc_final: 0.6718 (p90) REVERT: H 1018 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7929 (pm20) outliers start: 64 outliers final: 53 residues processed: 263 average time/residue: 0.3714 time to fit residues: 145.2489 Evaluate side-chains 267 residues out of total 2338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 210 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 13 HIS Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 412 ASN Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain B residue 477 LYS Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain D residue 14 TYR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 225 PHE Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 385 LYS Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain G residue 21 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 225 PHE Chi-restraints excluded: chain G residue 315 LEU Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 404 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 67 TYR Chi-restraints excluded: chain I residue 98 MET Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 252 THR Chi-restraints excluded: chain I residue 268 SER Chi-restraints excluded: chain I residue 301 ILE Chi-restraints excluded: chain C residue 1029 GLU Chi-restraints excluded: chain H residue 1018 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 206 optimal weight: 0.9980 chunk 86 optimal weight: 0.3980 chunk 212 optimal weight: 0.9990 chunk 26 optimal weight: 0.0040 chunk 38 optimal weight: 5.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 GLN B 243 ASN ** F 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 459 HIS ** C1012 GLN ** 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 = 0.3935 r_free = 0.3935 target = 0.108978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.085603 restraints weight = 73056.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.086570 restraints weight = 52879.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.087287 restraints weight = 42507.050| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21726 Z= 0.177 Angle : 0.710 15.853 29402 Z= 0.355 Chirality : 0.046 0.258 3255 Planarity : 0.004 0.060 3796 Dihedral : 5.724 33.192 2845 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 2.46 % Allowed : 18.85 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.19 % Cis-general : 2.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.16), residues: 2606 helix: 0.57 (0.17), residues: 1029 sheet: -2.24 (0.32), residues: 248 loop : -3.30 (0.15), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 17 HIS 0.007 0.001 HIS B 219 PHE 0.040 0.001 PHE B 358 TYR 0.022 0.001 TYR D 46 ARG 0.008 0.000 ARG A 503 =============================================================================== Job complete usr+sys time: 4198.75 seconds wall clock time: 77 minutes 8.85 seconds (4628.85 seconds total)