Starting phenix.real_space_refine on Fri Feb 16 11:14:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk6_33245/02_2024/7xk6_33245_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk6_33245/02_2024/7xk6_33245.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk6_33245/02_2024/7xk6_33245.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk6_33245/02_2024/7xk6_33245.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk6_33245/02_2024/7xk6_33245_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk6_33245/02_2024/7xk6_33245_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 6 5.49 5 S 92 5.16 5 C 9778 2.51 5 N 2448 2.21 5 O 2794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B GLU 15": "OE1" <-> "OE2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F GLU 134": "OE1" <-> "OE2" Residue "F TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 206": "OE1" <-> "OE2" Residue "F GLU 220": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15123 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422} Conformer: "B" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 422} bond proxies already assigned to first conformer: 3474 Chain: "B" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3173 Classifications: {'peptide': 412} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 396} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1558 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1507 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 190} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3165 Classifications: {'peptide': 408} Link IDs: {'PTRANS': 24, 'TRANS': 383} Chain: "B" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 221 Unusual residues: {'0NI': 1, 'FMN': 1, 'LMT': 1, 'PEE': 2, 'RBF': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' CA': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8663 SG CYS D 29 45.569 69.551 91.992 1.00 50.25 S ATOM 10264 SG CYS E 26 43.772 72.562 87.829 1.00 51.15 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA A 338 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 338 " occ=0.50 Time building chain proxies: 10.73, per 1000 atoms: 0.71 Number of scatterers: 15123 At special positions: 0 Unit cell: (91.52, 126.72, 155.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 92 16.00 P 6 15.00 O 2794 8.00 N 2448 7.00 C 9778 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.49 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 301 " pdb="FE2 FES E 301 " - pdb=" SG CYS E 26 " pdb="FE2 FES E 301 " - pdb=" SG CYS D 29 " pdb="FE1 FES E 301 " - pdb=" SG CYS E 120 " pdb="FE1 FES E 301 " - pdb=" SG CYS D 112 " pdb=" FES F 501 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 111 " Number of angles added : 7 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3466 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 14 sheets defined 44.0% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 163 through 169 removed outlier: 4.518A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.526A pdb=" N ILE B 10 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N HIS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N HIS B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 34 removed outlier: 3.618A pdb=" N PHE B 24 " --> pdb=" O GLU B 21 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ALA B 25 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 26 " --> pdb=" O TRP B 23 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU B 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 29 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR B 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 33 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 34 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.784A pdb=" N VAL B 60 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 86 removed outlier: 3.513A pdb=" N LEU B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 96 Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.711A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 150 Proline residue: B 131 - end of helix removed outlier: 3.559A pdb=" N TRP B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 168 Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 204 through 215 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 277 through 289 removed outlier: 3.632A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 315 Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 327 through 330 No H-bonds generated for 'chain 'B' and resid 327 through 330' Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 354 through 373 removed outlier: 4.031A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 409 removed outlier: 3.949A pdb=" N LEU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix removed outlier: 3.593A pdb=" N ASP B 397 " --> pdb=" O ALA B 393 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 32 removed outlier: 3.530A pdb=" N VAL C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 52 removed outlier: 4.163A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 93 through 96 No H-bonds generated for 'chain 'C' and resid 93 through 96' Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 183 through 188 removed outlier: 4.027A pdb=" N GLN C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.835A pdb=" N GLY C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 253 Processing helix chain 'D' and resid 8 through 16 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 38 through 61 Processing helix chain 'D' and resid 71 through 93 removed outlier: 3.522A pdb=" N ALA D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 removed outlier: 3.534A pdb=" N GLN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'D' and resid 122 through 124 No H-bonds generated for 'chain 'D' and resid 122 through 124' Processing helix chain 'D' and resid 127 through 157 removed outlier: 3.762A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 185 through 201 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'E' and resid 3 through 13 removed outlier: 3.679A pdb=" N LEU E 7 " --> pdb=" O HIS E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 35 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 79 through 101 Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 136 through 166 removed outlier: 4.204A pdb=" N LYS E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N TYR E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 176 through 193 removed outlier: 4.732A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N PHE E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 29 removed outlier: 3.927A pdb=" N PHE F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 62 removed outlier: 3.961A pdb=" N ALA F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 97 removed outlier: 3.567A pdb=" N ASP F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 186 through 188 No H-bonds generated for 'chain 'F' and resid 186 through 188' Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 245 through 251 removed outlier: 3.516A pdb=" N TRP F 250 " --> pdb=" O SER F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 296 removed outlier: 3.749A pdb=" N MET F 285 " --> pdb=" O GLY F 282 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA F 286 " --> pdb=" O ALA F 283 " (cutoff:3.500A) Proline residue: F 287 - end of helix removed outlier: 3.640A pdb=" N SER F 290 " --> pdb=" O PRO F 287 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE F 292 " --> pdb=" O ARG F 289 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE F 293 " --> pdb=" O SER F 290 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP F 294 " --> pdb=" O HIS F 291 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN F 295 " --> pdb=" O ILE F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 327 Processing helix chain 'F' and resid 355 through 362 Processing helix chain 'F' and resid 370 through 372 No H-bonds generated for 'chain 'F' and resid 370 through 372' Processing helix chain 'F' and resid 381 through 394 removed outlier: 3.573A pdb=" N ALA F 385 " --> pdb=" O PRO F 381 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN F 389 " --> pdb=" O ALA F 385 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU F 394 " --> pdb=" O MET F 390 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= B, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.620A pdb=" N SER A 89 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 78 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLU A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL A 76 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.181A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 132 through 134 removed outlier: 6.567A pdb=" N ALA A 148 " --> pdb=" O TRP A 237 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE A 239 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE A 150 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS A 188 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL A 151 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TYR A 190 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 306 through 308 removed outlier: 3.526A pdb=" N THR A 307 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N SER A 17 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 10.274A pdb=" N ARG A 276 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 12.669A pdb=" N VAL A 19 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 14.512A pdb=" N VAL A 278 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 14.209A pdb=" N SER A 21 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 71 through 77 removed outlier: 14.717A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.461A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 135 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU C 169 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU C 165 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= H, first strand: chain 'C' and resid 204 through 206 Processing sheet with id= I, first strand: chain 'F' and resid 34 through 37 removed outlier: 3.574A pdb=" N ILE F 35 " --> pdb=" O THR F 49 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 107 through 109 removed outlier: 3.644A pdb=" N LYS F 82 " --> pdb=" O GLU F 122 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP F 120 " --> pdb=" O LYS F 84 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 257 through 260 removed outlier: 3.706A pdb=" N ILE F 260 " --> pdb=" O TRP F 133 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR F 136 " --> pdb=" O ALA F 153 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN F 140 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU F 149 " --> pdb=" O ASN F 140 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN F 142 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE F 147 " --> pdb=" O ASN F 142 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 167 through 172 removed outlier: 3.506A pdb=" N ILE F 208 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 175 through 178 Processing sheet with id= N, first strand: chain 'F' and resid 335 through 339 removed outlier: 6.131A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU F 374 " --> pdb=" O VAL F 277 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE F 279 " --> pdb=" O GLU F 374 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR F 376 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY F 281 " --> pdb=" O TYR F 376 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N CYS F 378 " --> pdb=" O GLY F 281 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 6.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.37: 4890 1.37 - 1.58: 10363 1.58 - 1.78: 14 1.78 - 1.99: 148 1.99 - 2.20: 8 Bond restraints: 15423 Sorted by residual: bond pdb=" C4A RBF B 601 " pdb=" N5 RBF B 601 " ideal model delta sigma weight residual 1.288 1.447 -0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" C10 RBF B 601 " pdb=" N1 RBF B 601 " ideal model delta sigma weight residual 1.304 1.460 -0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" C5A RBF B 601 " pdb=" N5 RBF B 601 " ideal model delta sigma weight residual 1.350 1.488 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" CA SER B 239 " pdb=" CB SER B 239 " ideal model delta sigma weight residual 1.528 1.436 0.092 1.34e-02 5.57e+03 4.73e+01 bond pdb=" C PRO B 217 " pdb=" O PRO B 217 " ideal model delta sigma weight residual 1.235 1.163 0.071 1.11e-02 8.12e+03 4.11e+01 ... (remaining 15418 not shown) Histogram of bond angle deviations from ideal: 88.37 - 97.56: 12 97.56 - 106.75: 523 106.75 - 115.94: 9573 115.94 - 125.13: 10520 125.13 - 134.32: 274 Bond angle restraints: 20902 Sorted by residual: angle pdb=" S1 FES F 501 " pdb="FE2 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 90.64 13.69 1.14e+00 7.69e-01 1.44e+02 angle pdb=" S1 FES F 501 " pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 90.63 13.70 1.20e+00 6.94e-01 1.30e+02 angle pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " pdb="FE2 FES F 501 " ideal model delta sigma weight residual 75.66 88.59 -12.93 1.14e+00 7.69e-01 1.29e+02 angle pdb=" S1 FES E 301 " pdb="FE2 FES E 301 " pdb=" S2 FES E 301 " ideal model delta sigma weight residual 104.33 91.46 12.87 1.14e+00 7.69e-01 1.27e+02 angle pdb="FE1 FES E 301 " pdb=" S2 FES E 301 " pdb="FE2 FES E 301 " ideal model delta sigma weight residual 75.66 88.37 -12.71 1.14e+00 7.69e-01 1.24e+02 ... (remaining 20897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 8937 35.47 - 70.94: 219 70.94 - 106.41: 16 106.41 - 141.87: 8 141.87 - 177.34: 7 Dihedral angle restraints: 9187 sinusoidal: 3752 harmonic: 5435 Sorted by residual: dihedral pdb=" CA HIS A 215 " pdb=" C HIS A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta harmonic sigma weight residual 180.00 121.90 58.10 0 5.00e+00 4.00e-02 1.35e+02 dihedral pdb=" CA SER F 99 " pdb=" C SER F 99 " pdb=" N LYS F 100 " pdb=" CA LYS F 100 " ideal model delta harmonic sigma weight residual 180.00 -127.22 -52.78 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA GLN D 24 " pdb=" C GLN D 24 " pdb=" N VAL D 25 " pdb=" CA VAL D 25 " ideal model delta harmonic sigma weight residual -180.00 -142.93 -37.07 0 5.00e+00 4.00e-02 5.50e+01 ... (remaining 9184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2217 0.104 - 0.208: 111 0.208 - 0.312: 14 0.312 - 0.415: 3 0.415 - 0.519: 4 Chirality restraints: 2349 Sorted by residual: chirality pdb=" CA PRO C 174 " pdb=" N PRO C 174 " pdb=" C PRO C 174 " pdb=" CB PRO C 174 " both_signs ideal model delta sigma weight residual False 2.72 2.20 0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" CB ILE B 220 " pdb=" CA ILE B 220 " pdb=" CG1 ILE B 220 " pdb=" CG2 ILE B 220 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.51 2.00e-01 2.50e+01 6.56e+00 chirality pdb=" CA PRO B 379 " pdb=" N PRO B 379 " pdb=" C PRO B 379 " pdb=" CB PRO B 379 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.92e+00 ... (remaining 2346 not shown) Planarity restraints: 2612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 0NI B 602 " 0.280 2.00e-02 2.50e+03 2.36e-01 6.98e+02 pdb=" C16 0NI B 602 " -0.398 2.00e-02 2.50e+03 pdb=" C17 0NI B 602 " -0.089 2.00e-02 2.50e+03 pdb=" C18 0NI B 602 " 0.022 2.00e-02 2.50e+03 pdb=" C19 0NI B 602 " 0.185 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 0NI B 602 " -0.073 2.00e-02 2.50e+03 6.13e-02 4.70e+01 pdb=" C11 0NI B 602 " 0.097 2.00e-02 2.50e+03 pdb=" C12 0NI B 602 " 0.025 2.00e-02 2.50e+03 pdb=" C13 0NI B 602 " 0.010 2.00e-02 2.50e+03 pdb=" C14 0NI B 602 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " -0.069 2.00e-02 2.50e+03 2.83e-02 3.82e+01 pdb=" C10 FMN C 301 " -0.009 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " 0.027 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " -0.016 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " -0.021 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " -0.015 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " -0.019 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " 0.017 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " 0.033 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " 0.026 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " 0.025 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " -0.012 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " -0.014 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " 0.004 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " 0.002 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " 0.011 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " -0.021 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " 0.067 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " -0.017 2.00e-02 2.50e+03 ... (remaining 2609 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 271 2.68 - 3.24: 14135 3.24 - 3.79: 22231 3.79 - 4.35: 32394 4.35 - 4.90: 53677 Nonbonded interactions: 122708 Sorted by model distance: nonbonded pdb=" OE2 GLU F 275 " pdb=" OH TYR F 363 " model vdw 2.129 2.440 nonbonded pdb=" NH1 ARG F 80 " pdb=" OE1 GLU F 107 " model vdw 2.205 2.520 nonbonded pdb=" OH TYR B 87 " pdb=" O ASP B 230 " model vdw 2.207 2.440 nonbonded pdb=" O LEU F 95 " pdb=" OG SER F 99 " model vdw 2.221 2.440 nonbonded pdb=" O4' FMN B 600 " pdb=" O5' FMN B 600 " model vdw 2.225 2.432 ... (remaining 122703 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.700 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 48.300 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.159 15423 Z= 0.491 Angle : 1.014 16.787 20902 Z= 0.607 Chirality : 0.057 0.519 2349 Planarity : 0.008 0.236 2612 Dihedral : 16.488 177.342 5721 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.36 % Favored : 96.33 % Rotamer: Outliers : 0.70 % Allowed : 2.94 % Favored : 96.35 % Cbeta Deviations : 0.58 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 2.35 % Twisted General : 0.16 % 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: -2.57 (0.16), residues: 1910 helix: -1.08 (0.16), residues: 835 sheet: -1.38 (0.37), residues: 168 loop : -2.36 (0.17), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 146 HIS 0.004 0.001 HIS A 215 PHE 0.034 0.002 PHE B 213 TYR 0.041 0.002 TYR B 412 ARG 0.004 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 203 time to evaluate : 1.712 Fit side-chains REVERT: A 75 LYS cc_start: 0.7757 (ttmm) cc_final: 0.7158 (tttt) REVERT: A 396 ASP cc_start: 0.8098 (m-30) cc_final: 0.7774 (m-30) REVERT: A 404 SER cc_start: 0.8884 (t) cc_final: 0.8581 (m) REVERT: B 9 ASP cc_start: 0.7221 (m-30) cc_final: 0.7003 (m-30) REVERT: B 151 ARG cc_start: 0.7889 (mmm160) cc_final: 0.6415 (mpt180) REVERT: C 110 GLN cc_start: 0.8493 (mt0) cc_final: 0.8035 (mt0) REVERT: C 116 GLN cc_start: 0.7774 (mt0) cc_final: 0.7556 (mt0) REVERT: C 129 ASP cc_start: 0.7253 (t0) cc_final: 0.6302 (p0) REVERT: D 68 ASN cc_start: 0.7504 (m110) cc_final: 0.6989 (t0) REVERT: D 96 ASP cc_start: 0.7205 (m-30) cc_final: 0.6949 (m-30) REVERT: D 210 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.5798 (tp30) REVERT: E 10 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7836 (ttmm) REVERT: E 15 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7677 (pt0) REVERT: E 101 PHE cc_start: 0.7390 (m-80) cc_final: 0.7039 (m-80) REVERT: F 126 GLU cc_start: 0.6407 (mp0) cc_final: 0.6166 (mp0) REVERT: F 200 TYR cc_start: 0.6778 (m-80) cc_final: 0.6500 (m-80) REVERT: F 383 MET cc_start: 0.7800 (ttp) cc_final: 0.7591 (ttp) outliers start: 11 outliers final: 5 residues processed: 212 average time/residue: 1.3712 time to fit residues: 318.2443 Evaluate side-chains 146 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 174 PRO Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 34 ASP Chi-restraints excluded: chain F residue 366 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 88 GLN A 109 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN B 78 GLN B 156 ASN B 178 GLN B 219 GLN B 243 GLN B 251 ASN B 313 ASN B 354 ASN B 404 ASN C 37 GLN C 46 GLN C 120 ASN C 160 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN D 88 GLN D 100 GLN D 205 GLN E 79 ASN E 107 ASN F 78 GLN F 176 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15423 Z= 0.282 Angle : 0.587 9.009 20902 Z= 0.305 Chirality : 0.045 0.190 2349 Planarity : 0.005 0.119 2612 Dihedral : 14.295 177.372 2371 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.05 % Allowed : 9.28 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 1910 helix: 0.07 (0.18), residues: 847 sheet: -0.93 (0.37), residues: 176 loop : -1.84 (0.18), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 103 HIS 0.006 0.001 HIS B 46 PHE 0.018 0.002 PHE C 235 TYR 0.019 0.002 TYR D 141 ARG 0.005 0.001 ARG F 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 149 time to evaluate : 1.679 Fit side-chains REVERT: A 22 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7536 (m-30) REVERT: A 75 LYS cc_start: 0.7832 (ttmm) cc_final: 0.7226 (tttt) REVERT: A 396 ASP cc_start: 0.8101 (m-30) cc_final: 0.7799 (m-30) REVERT: A 404 SER cc_start: 0.8790 (t) cc_final: 0.8559 (m) REVERT: B 9 ASP cc_start: 0.7109 (m-30) cc_final: 0.6835 (m-30) REVERT: B 107 MET cc_start: 0.8549 (ttm) cc_final: 0.8286 (ttm) REVERT: B 151 ARG cc_start: 0.8194 (mmm160) cc_final: 0.6708 (mpt180) REVERT: C 110 GLN cc_start: 0.8535 (mt0) cc_final: 0.8111 (mt0) REVERT: C 116 GLN cc_start: 0.7760 (mt0) cc_final: 0.7500 (mt0) REVERT: C 129 ASP cc_start: 0.7330 (t0) cc_final: 0.6552 (p0) REVERT: D 68 ASN cc_start: 0.7423 (m110) cc_final: 0.6853 (t0) REVERT: D 210 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.5795 (tp30) REVERT: F 126 GLU cc_start: 0.6440 (mp0) cc_final: 0.6221 (mp0) REVERT: F 200 TYR cc_start: 0.6957 (m-80) cc_final: 0.6682 (m-80) REVERT: F 382 MET cc_start: 0.6825 (ttm) cc_final: 0.6588 (mtp) outliers start: 32 outliers final: 14 residues processed: 168 average time/residue: 1.3457 time to fit residues: 248.3708 Evaluate side-chains 152 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 137 optimal weight: 0.0670 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15423 Z= 0.287 Angle : 0.572 8.627 20902 Z= 0.297 Chirality : 0.045 0.181 2349 Planarity : 0.005 0.109 2612 Dihedral : 12.667 179.776 2363 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.82 % Allowed : 10.50 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.18), residues: 1910 helix: 0.55 (0.18), residues: 844 sheet: -0.70 (0.39), residues: 172 loop : -1.64 (0.18), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 103 HIS 0.006 0.001 HIS B 330 PHE 0.020 0.001 PHE B 213 TYR 0.018 0.001 TYR D 141 ARG 0.006 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 146 time to evaluate : 1.671 Fit side-chains REVERT: A 75 LYS cc_start: 0.7777 (ttmm) cc_final: 0.7204 (tttt) REVERT: A 171 SER cc_start: 0.7416 (OUTLIER) cc_final: 0.7076 (m) REVERT: A 396 ASP cc_start: 0.8127 (m-30) cc_final: 0.7836 (m-30) REVERT: A 404 SER cc_start: 0.8797 (t) cc_final: 0.8539 (m) REVERT: B 9 ASP cc_start: 0.7087 (m-30) cc_final: 0.6814 (m-30) REVERT: B 107 MET cc_start: 0.8579 (ttm) cc_final: 0.8298 (ttm) REVERT: B 151 ARG cc_start: 0.8137 (mmm160) cc_final: 0.6687 (mpt180) REVERT: B 409 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8901 (mt) REVERT: C 129 ASP cc_start: 0.7341 (t0) cc_final: 0.6425 (p0) REVERT: C 242 MET cc_start: 0.8296 (mmm) cc_final: 0.8073 (tpp) REVERT: D 68 ASN cc_start: 0.7367 (m110) cc_final: 0.6812 (t0) REVERT: D 119 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6892 (tm-30) REVERT: D 210 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.5726 (tp30) REVERT: E 33 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8218 (mttm) REVERT: E 101 PHE cc_start: 0.7126 (m-80) cc_final: 0.6890 (m-80) REVERT: F 126 GLU cc_start: 0.6449 (mp0) cc_final: 0.6209 (mp0) REVERT: F 200 TYR cc_start: 0.6955 (m-80) cc_final: 0.6704 (m-80) outliers start: 44 outliers final: 19 residues processed: 175 average time/residue: 1.3226 time to fit residues: 255.3552 Evaluate side-chains 162 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 138 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 337 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 172 optimal weight: 0.5980 chunk 182 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 ASN F 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15423 Z= 0.220 Angle : 0.520 7.958 20902 Z= 0.270 Chirality : 0.043 0.177 2349 Planarity : 0.005 0.102 2612 Dihedral : 11.639 176.821 2363 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.50 % Allowed : 12.16 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.19), residues: 1910 helix: 0.87 (0.19), residues: 842 sheet: -0.52 (0.40), residues: 172 loop : -1.42 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.004 0.001 HIS B 330 PHE 0.017 0.001 PHE B 213 TYR 0.016 0.001 TYR D 141 ARG 0.006 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 149 time to evaluate : 1.840 Fit side-chains REVERT: A 75 LYS cc_start: 0.7751 (ttmm) cc_final: 0.7191 (tttt) REVERT: A 171 SER cc_start: 0.7384 (OUTLIER) cc_final: 0.7055 (m) REVERT: A 396 ASP cc_start: 0.8080 (m-30) cc_final: 0.7739 (m-30) REVERT: A 404 SER cc_start: 0.8765 (t) cc_final: 0.8510 (m) REVERT: B 107 MET cc_start: 0.8543 (ttm) cc_final: 0.8310 (ttm) REVERT: B 151 ARG cc_start: 0.8129 (mmm160) cc_final: 0.6643 (mpt180) REVERT: C 129 ASP cc_start: 0.7364 (t0) cc_final: 0.6486 (p0) REVERT: D 68 ASN cc_start: 0.7312 (m110) cc_final: 0.6736 (t0) REVERT: D 210 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5687 (tp30) REVERT: E 33 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8228 (mttm) REVERT: F 126 GLU cc_start: 0.6366 (mp0) cc_final: 0.6133 (mp0) REVERT: F 200 TYR cc_start: 0.6988 (m-80) cc_final: 0.6735 (m-80) REVERT: F 382 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6662 (mtp) outliers start: 39 outliers final: 17 residues processed: 174 average time/residue: 1.2733 time to fit residues: 244.4581 Evaluate side-chains 162 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 141 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 337 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 2 optimal weight: 0.2980 chunk 136 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 0.0040 chunk 163 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 overall best weight: 2.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15423 Z= 0.276 Angle : 0.554 8.887 20902 Z= 0.286 Chirality : 0.044 0.178 2349 Planarity : 0.005 0.126 2612 Dihedral : 11.312 178.006 2360 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.01 % Allowed : 12.68 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.19), residues: 1910 helix: 0.91 (0.19), residues: 840 sheet: -0.53 (0.40), residues: 172 loop : -1.38 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.005 0.001 HIS B 330 PHE 0.018 0.001 PHE B 213 TYR 0.019 0.001 TYR D 141 ARG 0.006 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 140 time to evaluate : 1.726 Fit side-chains REVERT: A 39 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7384 (tmm) REVERT: A 75 LYS cc_start: 0.7765 (ttmm) cc_final: 0.7195 (tttt) REVERT: A 171 SER cc_start: 0.7480 (OUTLIER) cc_final: 0.7221 (m) REVERT: A 404 SER cc_start: 0.8798 (t) cc_final: 0.8480 (m) REVERT: B 107 MET cc_start: 0.8569 (ttm) cc_final: 0.8296 (ttm) REVERT: B 151 ARG cc_start: 0.8140 (mmm160) cc_final: 0.6656 (mpt180) REVERT: B 380 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.7597 (tt0) REVERT: B 409 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8869 (mt) REVERT: C 129 ASP cc_start: 0.7385 (t0) cc_final: 0.6594 (p0) REVERT: D 68 ASN cc_start: 0.7313 (m110) cc_final: 0.6722 (t0) REVERT: D 119 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6871 (tm-30) REVERT: D 210 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.5721 (tp30) REVERT: E 33 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8295 (mttm) REVERT: F 126 GLU cc_start: 0.6304 (mp0) cc_final: 0.6102 (mp0) REVERT: F 200 TYR cc_start: 0.7065 (m-80) cc_final: 0.6823 (m-80) REVERT: F 382 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6723 (mtp) outliers start: 47 outliers final: 26 residues processed: 173 average time/residue: 1.3265 time to fit residues: 255.4390 Evaluate side-chains 172 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 331 ASP Chi-restraints excluded: chain F residue 337 CYS Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 45 optimal weight: 0.0060 chunk 182 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15423 Z= 0.288 Angle : 0.560 7.880 20902 Z= 0.289 Chirality : 0.044 0.176 2349 Planarity : 0.005 0.119 2612 Dihedral : 11.226 178.143 2360 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.94 % Allowed : 13.76 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 1910 helix: 0.93 (0.19), residues: 840 sheet: -0.49 (0.40), residues: 172 loop : -1.35 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.005 0.001 HIS B 330 PHE 0.019 0.001 PHE B 213 TYR 0.019 0.001 TYR D 141 ARG 0.007 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 141 time to evaluate : 1.828 Fit side-chains REVERT: A 39 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7380 (tmm) REVERT: A 75 LYS cc_start: 0.7751 (ttmm) cc_final: 0.7164 (tttt) REVERT: A 171 SER cc_start: 0.7499 (OUTLIER) cc_final: 0.7250 (m) REVERT: A 404 SER cc_start: 0.8753 (t) cc_final: 0.8549 (p) REVERT: B 5 LYS cc_start: 0.7317 (tmmt) cc_final: 0.6786 (tttp) REVERT: B 107 MET cc_start: 0.8581 (ttm) cc_final: 0.8311 (ttm) REVERT: B 151 ARG cc_start: 0.8143 (mmm160) cc_final: 0.6640 (mpt180) REVERT: B 380 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: B 409 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8882 (mt) REVERT: C 129 ASP cc_start: 0.7408 (t0) cc_final: 0.6672 (p0) REVERT: D 68 ASN cc_start: 0.7473 (m110) cc_final: 0.6820 (t0) REVERT: D 96 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7181 (p0) REVERT: D 119 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.6869 (tm-30) REVERT: E 33 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8290 (mttm) REVERT: F 200 TYR cc_start: 0.6992 (m-80) cc_final: 0.6749 (m-80) REVERT: F 382 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6711 (mtp) outliers start: 46 outliers final: 26 residues processed: 172 average time/residue: 1.3726 time to fit residues: 259.8815 Evaluate side-chains 171 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 137 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 210 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 331 ASP Chi-restraints excluded: chain F residue 337 CYS Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 104 optimal weight: 0.0060 chunk 133 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN F 356 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15423 Z= 0.189 Angle : 0.500 7.882 20902 Z= 0.260 Chirality : 0.042 0.172 2349 Planarity : 0.005 0.110 2612 Dihedral : 10.782 175.959 2360 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.24 % Allowed : 14.85 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 1910 helix: 1.17 (0.19), residues: 840 sheet: -0.45 (0.40), residues: 173 loop : -1.20 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.004 0.001 HIS C 199 PHE 0.015 0.001 PHE B 213 TYR 0.015 0.001 TYR D 141 ARG 0.007 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 1.681 Fit side-chains REVERT: A 75 LYS cc_start: 0.7695 (ttmm) cc_final: 0.7131 (tttt) REVERT: A 171 SER cc_start: 0.7416 (OUTLIER) cc_final: 0.7167 (m) REVERT: A 396 ASP cc_start: 0.7735 (m-30) cc_final: 0.7495 (m-30) REVERT: B 5 LYS cc_start: 0.7146 (tmmt) cc_final: 0.6828 (tttp) REVERT: B 107 MET cc_start: 0.8542 (ttm) cc_final: 0.8254 (ttm) REVERT: B 151 ARG cc_start: 0.8153 (mmm160) cc_final: 0.6602 (mpt180) REVERT: C 129 ASP cc_start: 0.7361 (t0) cc_final: 0.6687 (p0) REVERT: D 68 ASN cc_start: 0.7373 (m110) cc_final: 0.6734 (t0) REVERT: D 96 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7188 (p0) REVERT: D 119 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: F 200 TYR cc_start: 0.6988 (m-80) cc_final: 0.6744 (m-80) REVERT: F 317 MET cc_start: 0.7501 (mtm) cc_final: 0.7226 (mtp) REVERT: F 382 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6627 (mtp) outliers start: 35 outliers final: 18 residues processed: 171 average time/residue: 1.2880 time to fit residues: 242.5175 Evaluate side-chains 157 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 331 ASP Chi-restraints excluded: chain F residue 337 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 165 optimal weight: 0.0370 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15423 Z= 0.332 Angle : 0.582 7.925 20902 Z= 0.300 Chirality : 0.045 0.172 2349 Planarity : 0.005 0.110 2612 Dihedral : 11.076 178.371 2357 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.37 % Allowed : 15.62 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1910 helix: 0.96 (0.19), residues: 839 sheet: -0.43 (0.38), residues: 185 loop : -1.28 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.006 0.001 HIS F 356 PHE 0.020 0.002 PHE B 213 TYR 0.019 0.002 TYR D 141 ARG 0.007 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 1.689 Fit side-chains REVERT: A 39 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7363 (tmm) REVERT: A 75 LYS cc_start: 0.7770 (ttmm) cc_final: 0.7188 (tttt) REVERT: A 171 SER cc_start: 0.7527 (OUTLIER) cc_final: 0.7305 (m) REVERT: A 396 ASP cc_start: 0.7873 (m-30) cc_final: 0.7651 (m-30) REVERT: B 5 LYS cc_start: 0.7169 (tmmt) cc_final: 0.6734 (tttp) REVERT: B 151 ARG cc_start: 0.8149 (mmm160) cc_final: 0.6643 (mpt180) REVERT: D 49 MET cc_start: 0.8268 (mtp) cc_final: 0.7927 (mtm) REVERT: D 68 ASN cc_start: 0.7352 (m110) cc_final: 0.6803 (t0) REVERT: D 96 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7188 (p0) REVERT: D 119 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6828 (tm-30) REVERT: E 15 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7705 (pt0) REVERT: E 33 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8291 (mttm) REVERT: F 119 MET cc_start: 0.6664 (mmm) cc_final: 0.6273 (mmt) REVERT: F 200 TYR cc_start: 0.7073 (m-80) cc_final: 0.6868 (m-80) REVERT: F 317 MET cc_start: 0.7581 (mtm) cc_final: 0.7292 (mtp) REVERT: F 382 MET cc_start: 0.7028 (OUTLIER) cc_final: 0.6726 (mtp) outliers start: 37 outliers final: 26 residues processed: 165 average time/residue: 1.3043 time to fit residues: 237.3732 Evaluate side-chains 166 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain D residue 69 SER Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 331 ASP Chi-restraints excluded: chain F residue 337 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 9.9990 chunk 159 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 111 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS F 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15423 Z= 0.198 Angle : 0.503 7.575 20902 Z= 0.262 Chirality : 0.042 0.171 2349 Planarity : 0.005 0.105 2612 Dihedral : 10.669 175.923 2357 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.86 % Allowed : 16.33 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.19), residues: 1910 helix: 1.20 (0.19), residues: 839 sheet: -0.40 (0.40), residues: 173 loop : -1.14 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.005 0.001 HIS C 199 PHE 0.015 0.001 PHE B 213 TYR 0.015 0.001 TYR D 141 ARG 0.010 0.000 ARG D 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.653 Fit side-chains REVERT: A 39 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7364 (tmm) REVERT: A 75 LYS cc_start: 0.7696 (ttmm) cc_final: 0.7136 (tttt) REVERT: A 396 ASP cc_start: 0.7856 (m-30) cc_final: 0.7638 (m-30) REVERT: B 5 LYS cc_start: 0.7128 (tmmt) cc_final: 0.6801 (tttp) REVERT: B 151 ARG cc_start: 0.8135 (mmm160) cc_final: 0.6617 (mpt180) REVERT: D 49 MET cc_start: 0.8262 (mtp) cc_final: 0.7902 (mtm) REVERT: D 68 ASN cc_start: 0.7259 (m110) cc_final: 0.6755 (t0) REVERT: D 96 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.7188 (p0) REVERT: E 15 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7697 (pt0) REVERT: F 119 MET cc_start: 0.6633 (mmm) cc_final: 0.6159 (mmt) REVERT: F 200 TYR cc_start: 0.7048 (m-80) cc_final: 0.6829 (m-80) REVERT: F 317 MET cc_start: 0.7485 (mtm) cc_final: 0.7213 (mtp) REVERT: F 382 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6654 (mtp) outliers start: 29 outliers final: 19 residues processed: 159 average time/residue: 1.3887 time to fit residues: 243.3552 Evaluate side-chains 155 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 331 ASP Chi-restraints excluded: chain F residue 337 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 173 optimal weight: 0.0020 chunk 149 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 159 optimal weight: 0.5980 overall best weight: 1.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15423 Z= 0.234 Angle : 0.523 7.461 20902 Z= 0.272 Chirality : 0.043 0.173 2349 Planarity : 0.005 0.106 2612 Dihedral : 10.665 176.541 2357 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.66 % Allowed : 16.65 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.19), residues: 1910 helix: 1.20 (0.19), residues: 837 sheet: -0.33 (0.39), residues: 183 loop : -1.16 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.005 0.001 HIS C 199 PHE 0.016 0.001 PHE B 213 TYR 0.018 0.001 TYR D 141 ARG 0.010 0.000 ARG D 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 1.786 Fit side-chains REVERT: A 39 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7371 (tmm) REVERT: A 75 LYS cc_start: 0.7702 (ttmm) cc_final: 0.7138 (tttt) REVERT: B 5 LYS cc_start: 0.7119 (tmmt) cc_final: 0.6781 (tttp) REVERT: B 151 ARG cc_start: 0.8137 (mmm160) cc_final: 0.6619 (mpt180) REVERT: D 49 MET cc_start: 0.8263 (mtp) cc_final: 0.7906 (mtm) REVERT: D 68 ASN cc_start: 0.7255 (m110) cc_final: 0.6739 (t0) REVERT: D 96 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7194 (p0) REVERT: E 15 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7723 (pt0) REVERT: F 119 MET cc_start: 0.6699 (mmm) cc_final: 0.6311 (mmt) REVERT: F 200 TYR cc_start: 0.7064 (m-80) cc_final: 0.6844 (m-80) REVERT: F 382 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6664 (mtp) outliers start: 26 outliers final: 19 residues processed: 156 average time/residue: 1.3677 time to fit residues: 234.7428 Evaluate side-chains 153 residues out of total 1566 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ASP Chi-restraints excluded: chain A residue 39 MET Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 246 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 270 LYS Chi-restraints excluded: chain F residue 331 ASP Chi-restraints excluded: chain F residue 337 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 8 optimal weight: 0.0770 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS C 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.128949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.101717 restraints weight = 35976.600| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.98 r_work: 0.3046 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15423 Z= 0.157 Angle : 0.472 7.404 20902 Z= 0.247 Chirality : 0.041 0.167 2349 Planarity : 0.005 0.103 2612 Dihedral : 10.238 175.147 2357 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.41 % Allowed : 16.90 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % Cis-general : 0.00 % Twisted Proline : 1.18 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 1910 helix: 1.41 (0.19), residues: 838 sheet: -0.42 (0.39), residues: 183 loop : -1.01 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.005 0.001 HIS C 199 PHE 0.013 0.001 PHE B 213 TYR 0.014 0.001 TYR D 141 ARG 0.010 0.000 ARG D 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5004.43 seconds wall clock time: 89 minutes 51.12 seconds (5391.12 seconds total)