Starting phenix.real_space_refine on Fri Dec 15 16:50:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wff_32464/12_2023/7wff_32464_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wff_32464/12_2023/7wff_32464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wff_32464/12_2023/7wff_32464.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wff_32464/12_2023/7wff_32464.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wff_32464/12_2023/7wff_32464_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wff_32464/12_2023/7wff_32464_updated.pdb" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 2 5.49 5 S 177 5.16 5 C 21076 2.51 5 N 5105 2.21 5 O 5762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B ARG 282": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "D PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 444": "NH1" <-> "NH2" Residue "D ARG 466": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "F GLU 2": "OE1" <-> "OE2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 255": "OE1" <-> "OE2" Residue "F ARG 317": "NH1" <-> "NH2" Residue "F ARG 340": "NH1" <-> "NH2" Residue "F TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 647": "NH1" <-> "NH2" Residue "F ARG 664": "NH1" <-> "NH2" Residue "F ARG 681": "NH1" <-> "NH2" Residue "F ARG 692": "NH1" <-> "NH2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G ARG 175": "NH1" <-> "NH2" Residue "a ARG 116": "NH1" <-> "NH2" Residue "a ARG 142": "NH1" <-> "NH2" Residue "a ARG 155": "NH1" <-> "NH2" Residue "a GLU 180": "OE1" <-> "OE2" Residue "a ARG 194": "NH1" <-> "NH2" Residue "a ARG 219": "NH1" <-> "NH2" Residue "a ARG 285": "NH1" <-> "NH2" Residue "a ARG 296": "NH1" <-> "NH2" Residue "a ARG 342": "NH1" <-> "NH2" Residue "a GLU 414": "OE1" <-> "OE2" Residue "b GLU 31": "OE1" <-> "OE2" Residue "b GLU 54": "OE1" <-> "OE2" Residue "b GLU 97": "OE1" <-> "OE2" Residue "b GLU 140": "OE1" <-> "OE2" Residue "b TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 244": "OE1" <-> "OE2" Residue "b ARG 285": "NH1" <-> "NH2" Residue "b GLU 335": "OE1" <-> "OE2" Residue "c ARG 90": "NH1" <-> "NH2" Residue "c ARG 99": "NH1" <-> "NH2" Residue "c ARG 143": "NH1" <-> "NH2" Residue "e ARG 177": "NH1" <-> "NH2" Residue "f ARG 107": "NH1" <-> "NH2" Residue "f GLU 147": "OE1" <-> "OE2" Residue "f ARG 188": "NH1" <-> "NH2" Residue "g ARG 92": "NH1" <-> "NH2" Residue "g GLU 98": "OE1" <-> "OE2" Residue "g GLU 105": "OE1" <-> "OE2" Residue "g GLU 154": "OE1" <-> "OE2" Residue "g GLU 170": "OE1" <-> "OE2" Residue "g GLU 176": "OE1" <-> "OE2" Residue "h GLU 97": "OE1" <-> "OE2" Residue "h ARG 102": "NH1" <-> "NH2" Residue "i ARG 150": "NH1" <-> "NH2" Residue "j GLU 119": "OE1" <-> "OE2" Residue "j ARG 122": "NH1" <-> "NH2" Residue "j GLU 153": "OE1" <-> "OE2" Residue "j GLU 222": "OE1" <-> "OE2" Residue "j ARG 239": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 32124 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2372 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3780 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 467} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 776 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3950 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 21, 'TRANS': 475} Chain: "E" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 695 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "F" Number of atoms: 5330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5330 Classifications: {'peptide': 677} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 22, 'TRANS': 654} Chain breaks: 3 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "G" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1281 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Chain: "a" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2655 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain: "b" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 18, 'TRANS': 288} Chain breaks: 2 Chain: "c" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 10, 'TRANS': 117} Chain: "d" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 762 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "e" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1206 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "f" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1277 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 146} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "g" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 965 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "h" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1170 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "i" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1098 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1331 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'LHG': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23629 SG CYS c 120 79.780 48.124 65.698 1.00 66.02 S ATOM 23662 SG CYS c 126 77.013 49.434 63.573 1.00 64.75 S ATOM 23680 SG CYS c 129 75.335 43.501 64.010 1.00 67.34 S ATOM 23955 SG CYS c 162 78.165 43.477 66.375 1.00 73.63 S Time building chain proxies: 16.40, per 1000 atoms: 0.51 Number of scatterers: 32124 At special positions: 0 Unit cell: (124.8, 144.56, 215.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 177 16.00 P 2 15.00 O 5762 8.00 N 5105 7.00 C 21076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.40 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES c 301 " pdb="FE2 FES c 301 " - pdb=" SG CYS c 129 " pdb="FE1 FES c 301 " - pdb=" SG CYS c 120 " pdb="FE1 FES c 301 " - pdb=" SG CYS c 126 " pdb="FE2 FES c 301 " - pdb=" SG CYS c 162 " Number of angles added : 6 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7504 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 153 helices and 13 sheets defined 51.7% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.30 Creating SS restraints... Processing helix chain 'A' and resid 27 through 59 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 71 through 83 removed outlier: 3.758A pdb=" N ALA A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 113 Proline residue: A 102 - end of helix removed outlier: 3.864A pdb=" N ILE A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N SER A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TYR A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 151 removed outlier: 3.912A pdb=" N TRP A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Proline residue: A 142 - end of helix Processing helix chain 'A' and resid 155 through 170 removed outlier: 3.606A pdb=" N LEU A 159 " --> pdb=" O LYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 251 through 274 Processing helix chain 'A' and resid 298 through 324 removed outlier: 3.788A pdb=" N PHE A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 337 Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'B' and resid 30 through 48 Proline residue: B 34 - end of helix removed outlier: 4.262A pdb=" N ILE B 37 " --> pdb=" O PRO B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 77 Processing helix chain 'B' and resid 95 through 111 Processing helix chain 'B' and resid 118 through 121 No H-bonds generated for 'chain 'B' and resid 118 through 121' Processing helix chain 'B' and resid 126 through 145 removed outlier: 6.058A pdb=" N LEU B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 145 " --> pdb=" O MET B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 167 Proline residue: B 156 - end of helix Processing helix chain 'B' and resid 175 through 204 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.706A pdb=" N VAL B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 244 Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 251 through 259 removed outlier: 4.149A pdb=" N ASP B 255 " --> pdb=" O GLN B 251 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 285 removed outlier: 4.363A pdb=" N PHE B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 316 removed outlier: 4.155A pdb=" N GLY B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N THR B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 340 removed outlier: 3.917A pdb=" N ILE B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY B 338 " --> pdb=" O TYR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 374 removed outlier: 3.927A pdb=" N GLY B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 384 Processing helix chain 'B' and resid 387 through 390 No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 392 through 406 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 430 through 453 removed outlier: 3.615A pdb=" N ILE B 435 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 453 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 496 Proline residue: B 494 - end of helix Processing helix chain 'B' and resid 499 through 506 Processing helix chain 'B' and resid 509 through 511 No H-bonds generated for 'chain 'B' and resid 509 through 511' Processing helix chain 'C' and resid 8 through 30 removed outlier: 3.823A pdb=" N ALA C 12 " --> pdb=" O ASP C 8 " (cutoff:3.500A) Proline residue: C 21 - end of helix Processing helix chain 'C' and resid 61 through 84 removed outlier: 4.379A pdb=" N VAL C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Proline residue: C 81 - end of helix Processing helix chain 'C' and resid 91 through 113 Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 35 through 58 Processing helix chain 'D' and resid 93 through 112 removed outlier: 3.750A pdb=" N PHE D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) Proline residue: D 112 - end of helix Processing helix chain 'D' and resid 117 through 136 removed outlier: 3.899A pdb=" N ILE D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 159 removed outlier: 3.931A pdb=" N GLU D 150 " --> pdb=" O MET D 146 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU D 151 " --> pdb=" O TRP D 147 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Proline residue: D 153 - end of helix Processing helix chain 'D' and resid 166 through 193 removed outlier: 4.213A pdb=" N PHE D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 206 No H-bonds generated for 'chain 'D' and resid 203 through 206' Processing helix chain 'D' and resid 213 through 230 removed outlier: 4.192A pdb=" N LEU D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 243 removed outlier: 4.240A pdb=" N ASP D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 255 removed outlier: 4.103A pdb=" N LEU D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 269 No H-bonds generated for 'chain 'D' and resid 266 through 269' Processing helix chain 'D' and resid 276 through 303 removed outlier: 3.688A pdb=" N MET D 281 " --> pdb=" O HIS D 277 " (cutoff:3.500A) Proline residue: D 284 - end of helix removed outlier: 3.614A pdb=" N VAL D 288 " --> pdb=" O PRO D 284 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 302 - end of helix Processing helix chain 'D' and resid 308 through 327 removed outlier: 3.731A pdb=" N GLY D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE D 322 " --> pdb=" O HIS D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 362 Processing helix chain 'D' and resid 378 through 391 Processing helix chain 'D' and resid 398 through 411 removed outlier: 4.493A pdb=" N PHE D 407 " --> pdb=" O GLU D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 429 removed outlier: 4.020A pdb=" N PHE D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 Proline residue: D 436 - end of helix Processing helix chain 'D' and resid 465 through 483 Proline residue: D 477 - end of helix Processing helix chain 'D' and resid 485 through 487 No H-bonds generated for 'chain 'D' and resid 485 through 487' Processing helix chain 'D' and resid 493 through 504 removed outlier: 4.549A pdb=" N ASN D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR D 503 " --> pdb=" O ILE D 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 22 removed outlier: 3.808A pdb=" N VAL E 6 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 7 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLY E 17 " --> pdb=" O PHE E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 52 Processing helix chain 'E' and resid 58 through 87 Processing helix chain 'F' and resid 15 through 23 Proline residue: F 19 - end of helix Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 39 through 64 Processing helix chain 'F' and resid 91 through 114 removed outlier: 3.699A pdb=" N VAL F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN F 113 " --> pdb=" O ILE F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 139 Processing helix chain 'F' and resid 144 through 162 Processing helix chain 'F' and resid 169 through 199 removed outlier: 3.792A pdb=" N GLY F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY F 195 " --> pdb=" O LEU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 211 removed outlier: 3.715A pdb=" N GLU F 210 " --> pdb=" O GLN F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 223 through 240 removed outlier: 3.912A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Proline residue: F 237 - end of helix Processing helix chain 'F' and resid 248 through 251 No H-bonds generated for 'chain 'F' and resid 248 through 251' Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 268 through 283 removed outlier: 3.644A pdb=" N GLY F 273 " --> pdb=" O MET F 269 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE F 274 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL F 277 " --> pdb=" O GLY F 273 " (cutoff:3.500A) Proline residue: F 282 - end of helix Processing helix chain 'F' and resid 288 through 301 removed outlier: 4.677A pdb=" N TYR F 292 " --> pdb=" O PRO F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 335 Processing helix chain 'F' and resid 339 through 371 removed outlier: 4.048A pdb=" N LEU F 343 " --> pdb=" O TYR F 339 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA F 354 " --> pdb=" O ALA F 350 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU F 355 " --> pdb=" O TYR F 351 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA F 369 " --> pdb=" O HIS F 365 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE F 370 " --> pdb=" O SER F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 378 No H-bonds generated for 'chain 'F' and resid 375 through 378' Processing helix chain 'F' and resid 381 through 384 No H-bonds generated for 'chain 'F' and resid 381 through 384' Processing helix chain 'F' and resid 392 through 406 Processing helix chain 'F' and resid 415 through 424 Processing helix chain 'F' and resid 430 through 453 removed outlier: 4.018A pdb=" N ILE F 434 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA F 435 " --> pdb=" O PHE F 431 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR F 453 " --> pdb=" O ILE F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 467 through 473 Processing helix chain 'F' and resid 545 through 563 Proline residue: F 550 - end of helix removed outlier: 3.743A pdb=" N GLY F 562 " --> pdb=" O THR F 558 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA F 563 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 575 No H-bonds generated for 'chain 'F' and resid 572 through 575' Processing helix chain 'F' and resid 603 through 624 removed outlier: 3.801A pdb=" N LEU F 623 " --> pdb=" O ILE F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 643 removed outlier: 3.742A pdb=" N SER F 639 " --> pdb=" O THR F 635 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN F 641 " --> pdb=" O LEU F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 674 removed outlier: 4.198A pdb=" N ASN F 655 " --> pdb=" O GLU F 651 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLY F 665 " --> pdb=" O SER F 661 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N TYR F 666 " --> pdb=" O TYR F 662 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE F 667 " --> pdb=" O ASN F 663 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP F 668 " --> pdb=" O ARG F 664 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER F 669 " --> pdb=" O GLY F 665 " (cutoff:3.500A) Processing helix chain 'F' and resid 676 through 693 removed outlier: 3.539A pdb=" N ILE F 693 " --> pdb=" O PHE F 689 " (cutoff:3.500A) Processing helix chain 'F' and resid 695 through 713 removed outlier: 4.011A pdb=" N GLY F 702 " --> pdb=" O THR F 698 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 27 Processing helix chain 'G' and resid 32 through 52 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 70 through 79 Processing helix chain 'G' and resid 100 through 115 Processing helix chain 'G' and resid 120 through 124 Processing helix chain 'G' and resid 140 through 149 Processing helix chain 'G' and resid 153 through 174 removed outlier: 4.090A pdb=" N SER G 160 " --> pdb=" O PHE G 156 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE G 161 " --> pdb=" O GLU G 157 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 130 Processing helix chain 'a' and resid 133 through 142 Processing helix chain 'a' and resid 158 through 161 Processing helix chain 'a' and resid 174 through 176 No H-bonds generated for 'chain 'a' and resid 174 through 176' Processing helix chain 'a' and resid 181 through 194 Processing helix chain 'a' and resid 209 through 215 Processing helix chain 'a' and resid 234 through 236 No H-bonds generated for 'chain 'a' and resid 234 through 236' Processing helix chain 'a' and resid 249 through 252 Processing helix chain 'a' and resid 258 through 263 Processing helix chain 'a' and resid 285 through 297 Processing helix chain 'a' and resid 316 through 318 No H-bonds generated for 'chain 'a' and resid 316 through 318' Processing helix chain 'a' and resid 332 through 340 Processing helix chain 'a' and resid 353 through 362 removed outlier: 4.148A pdb=" N GLU a 357 " --> pdb=" O LYS a 354 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU a 360 " --> pdb=" O GLU a 357 " (cutoff:3.500A) Processing helix chain 'a' and resid 375 through 384 removed outlier: 3.590A pdb=" N ASP a 384 " --> pdb=" O ALA a 380 " (cutoff:3.500A) Processing helix chain 'a' and resid 394 through 403 removed outlier: 4.828A pdb=" N ARG a 402 " --> pdb=" O LEU a 398 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP a 403 " --> pdb=" O ALA a 399 " (cutoff:3.500A) Processing helix chain 'a' and resid 413 through 419 Processing helix chain 'a' and resid 423 through 426 No H-bonds generated for 'chain 'a' and resid 423 through 426' Processing helix chain 'a' and resid 445 through 453 Processing helix chain 'b' and resid 29 through 37 Processing helix chain 'b' and resid 218 through 221 No H-bonds generated for 'chain 'b' and resid 218 through 221' Processing helix chain 'b' and resid 262 through 267 removed outlier: 3.870A pdb=" N LEU b 267 " --> pdb=" O PRO b 263 " (cutoff:3.500A) Processing helix chain 'b' and resid 305 through 310 removed outlier: 3.829A pdb=" N TRP b 308 " --> pdb=" O GLY b 305 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP b 309 " --> pdb=" O SER b 306 " (cutoff:3.500A) Processing helix chain 'c' and resid 98 through 104 Processing helix chain 'c' and resid 112 through 114 No H-bonds generated for 'chain 'c' and resid 112 through 114' Processing helix chain 'c' and resid 116 through 118 No H-bonds generated for 'chain 'c' and resid 116 through 118' Processing helix chain 'c' and resid 147 through 150 No H-bonds generated for 'chain 'c' and resid 147 through 150' Processing helix chain 'd' and resid 88 through 108 Processing helix chain 'd' and resid 116 through 118 No H-bonds generated for 'chain 'd' and resid 116 through 118' Processing helix chain 'd' and resid 122 through 125 No H-bonds generated for 'chain 'd' and resid 122 through 125' Processing helix chain 'd' and resid 133 through 155 Proline residue: d 142 - end of helix removed outlier: 3.515A pdb=" N GLU d 155 " --> pdb=" O GLU d 151 " (cutoff:3.500A) Processing helix chain 'e' and resid 102 through 108 Processing helix chain 'e' and resid 115 through 128 removed outlier: 6.090A pdb=" N SER e 120 " --> pdb=" O GLN e 116 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU e 124 " --> pdb=" O SER e 120 " (cutoff:3.500A) Proline residue: e 125 - end of helix Processing helix chain 'e' and resid 138 through 154 Processing helix chain 'e' and resid 162 through 164 No H-bonds generated for 'chain 'e' and resid 162 through 164' Processing helix chain 'e' and resid 167 through 169 No H-bonds generated for 'chain 'e' and resid 167 through 169' Processing helix chain 'f' and resid 140 through 143 No H-bonds generated for 'chain 'f' and resid 140 through 143' Processing helix chain 'f' and resid 146 through 154 removed outlier: 4.090A pdb=" N TYR f 151 " --> pdb=" O GLU f 147 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP f 152 " --> pdb=" O GLU f 148 " (cutoff:3.500A) Processing helix chain 'f' and resid 216 through 218 No H-bonds generated for 'chain 'f' and resid 216 through 218' Processing helix chain 'f' and resid 223 through 232 removed outlier: 3.777A pdb=" N SER f 232 " --> pdb=" O VAL f 228 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 78 No H-bonds generated for 'chain 'g' and resid 75 through 78' Processing helix chain 'g' and resid 86 through 107 removed outlier: 3.841A pdb=" N LYS g 94 " --> pdb=" O ALA g 90 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP g 102 " --> pdb=" O GLU g 98 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET g 103 " --> pdb=" O GLY g 99 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ARG g 104 " --> pdb=" O LEU g 100 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLU g 105 " --> pdb=" O ARG g 101 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N MET g 106 " --> pdb=" O ASP g 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 112 through 136 removed outlier: 3.794A pdb=" N GLN g 128 " --> pdb=" O ALA g 124 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR g 131 " --> pdb=" O SER g 127 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN g 132 " --> pdb=" O GLN g 128 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASN g 135 " --> pdb=" O THR g 131 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE g 136 " --> pdb=" O ASN g 132 " (cutoff:3.500A) Processing helix chain 'g' and resid 139 through 164 removed outlier: 4.144A pdb=" N ASN g 143 " --> pdb=" O GLU g 139 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP g 144 " --> pdb=" O SER g 140 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 182 Processing helix chain 'h' and resid 116 through 134 removed outlier: 3.669A pdb=" N LYS h 124 " --> pdb=" O MET h 120 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU h 134 " --> pdb=" O LEU h 130 " (cutoff:3.500A) Processing helix chain 'h' and resid 142 through 165 Processing helix chain 'h' and resid 172 through 194 removed outlier: 3.930A pdb=" N ASN h 185 " --> pdb=" O ARG h 181 " (cutoff:3.500A) Processing helix chain 'h' and resid 198 through 219 removed outlier: 4.320A pdb=" N ASP h 207 " --> pdb=" O SER h 203 " (cutoff:3.500A) Processing helix chain 'i' and resid 132 through 135 No H-bonds generated for 'chain 'i' and resid 132 through 135' Processing helix chain 'i' and resid 150 through 156 Processing helix chain 'j' and resid 115 through 125 removed outlier: 3.716A pdb=" N CYS j 125 " --> pdb=" O PHE j 121 " (cutoff:3.500A) Processing helix chain 'j' and resid 221 through 228 Processing sheet with id= A, first strand: chain 'a' and resid 348 through 350 Processing sheet with id= B, first strand: chain 'b' and resid 42 through 47 removed outlier: 3.505A pdb=" N SER b 47 " --> pdb=" O ILE b 50 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER b 66 " --> pdb=" O VAL b 72 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL b 72 " --> pdb=" O SER b 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'b' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'b' and resid 137 through 142 Processing sheet with id= E, first strand: chain 'b' and resid 183 through 186 Processing sheet with id= F, first strand: chain 'c' and resid 158 through 160 Processing sheet with id= G, first strand: chain 'f' and resid 164 through 167 Processing sheet with id= H, first strand: chain 'f' and resid 170 through 174 Processing sheet with id= I, first strand: chain 'f' and resid 194 through 196 Processing sheet with id= J, first strand: chain 'i' and resid 139 through 142 removed outlier: 6.305A pdb=" N HIS i 118 " --> pdb=" O PHE i 207 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE i 207 " --> pdb=" O HIS i 118 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR i 120 " --> pdb=" O ILE i 205 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE i 205 " --> pdb=" O THR i 120 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ARG i 122 " --> pdb=" O TYR i 203 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TYR i 203 " --> pdb=" O ARG i 122 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LYS i 172 " --> pdb=" O ASP i 100 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP i 100 " --> pdb=" O LYS i 172 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN i 174 " --> pdb=" O PHE i 98 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE i 98 " --> pdb=" O GLN i 174 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'i' and resid 120 through 122 removed outlier: 3.712A pdb=" N ASP i 130 " --> pdb=" O ALA i 121 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'j' and resid 243 through 249 removed outlier: 6.801A pdb=" N ASP j 91 " --> pdb=" O ALA j 245 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS j 247 " --> pdb=" O TYR j 89 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N TYR j 89 " --> pdb=" O CYS j 247 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLN j 249 " --> pdb=" O LYS j 87 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N LYS j 87 " --> pdb=" O GLN j 249 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLY j 108 " --> pdb=" O VAL j 217 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL j 217 " --> pdb=" O GLY j 108 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'j' and resid 146 through 149 removed outlier: 3.770A pdb=" N SER j 184 " --> pdb=" O PHE j 198 " (cutoff:3.500A) 1448 hydrogen bonds defined for protein. 4179 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: 9.54 Time building geometry restraints manager: 13.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 13514 1.40 - 1.60: 19095 1.60 - 1.79: 150 1.79 - 1.99: 147 1.99 - 2.19: 4 Bond restraints: 32910 Sorted by residual: bond pdb=" C1 SQD F 802 " pdb=" O5 SQD F 802 " ideal model delta sigma weight residual 1.500 1.404 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C5 SQD F 802 " pdb=" O5 SQD F 802 " ideal model delta sigma weight residual 1.483 1.408 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C3 SQD F 802 " pdb=" O3 SQD F 802 " ideal model delta sigma weight residual 1.451 1.378 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C23 SQD F 802 " pdb=" C24 SQD F 802 " ideal model delta sigma weight residual 1.592 1.520 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" O9 SQD F 802 " pdb=" S SQD F 802 " ideal model delta sigma weight residual 1.511 1.442 0.069 2.00e-02 2.50e+03 1.17e+01 ... (remaining 32905 not shown) Histogram of bond angle deviations from ideal: 88.62 - 97.75: 6 97.75 - 106.89: 948 106.89 - 116.03: 20152 116.03 - 125.16: 22932 125.16 - 134.30: 591 Bond angle restraints: 44629 Sorted by residual: angle pdb=" S1 FES c 301 " pdb="FE2 FES c 301 " pdb=" S2 FES c 301 " ideal model delta sigma weight residual 104.33 88.72 15.61 1.14e+00 7.69e-01 1.87e+02 angle pdb=" S1 FES c 301 " pdb="FE1 FES c 301 " pdb=" S2 FES c 301 " ideal model delta sigma weight residual 104.33 88.62 15.71 1.20e+00 6.94e-01 1.71e+02 angle pdb="FE1 FES c 301 " pdb=" S2 FES c 301 " pdb="FE2 FES c 301 " ideal model delta sigma weight residual 75.66 89.90 -14.24 1.14e+00 7.69e-01 1.56e+02 angle pdb="FE1 FES c 301 " pdb=" S1 FES c 301 " pdb="FE2 FES c 301 " ideal model delta sigma weight residual 75.66 89.74 -14.08 1.20e+00 6.94e-01 1.38e+02 angle pdb=" N PRO F 409 " pdb=" CA PRO F 409 " pdb=" C PRO F 409 " ideal model delta sigma weight residual 110.70 120.94 -10.24 1.22e+00 6.72e-01 7.05e+01 ... (remaining 44624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 17196 17.55 - 35.10: 1723 35.10 - 52.64: 287 52.64 - 70.19: 41 70.19 - 87.74: 19 Dihedral angle restraints: 19266 sinusoidal: 7536 harmonic: 11730 Sorted by residual: dihedral pdb=" CA LEU B 246 " pdb=" C LEU B 246 " pdb=" N ALA B 247 " pdb=" CA ALA B 247 " ideal model delta harmonic sigma weight residual -180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA TYR a 160 " pdb=" C TYR a 160 " pdb=" N GLU a 161 " pdb=" CA GLU a 161 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ALA f 117 " pdb=" C ALA f 117 " pdb=" N PHE f 118 " pdb=" CA PHE f 118 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 19263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.901: 5061 0.901 - 1.802: 0 1.802 - 2.703: 0 2.703 - 3.604: 0 3.604 - 4.505: 1 Chirality restraints: 5062 Sorted by residual: chirality pdb=" C1 SQD F 802 " pdb=" C2 SQD F 802 " pdb=" O5 SQD F 802 " pdb=" O6 SQD F 802 " both_signs ideal model delta sigma weight residual False -2.39 2.12 -4.51 2.00e-01 2.50e+01 5.07e+02 chirality pdb=" CA PRO F 409 " pdb=" N PRO F 409 " pdb=" C PRO F 409 " pdb=" CB PRO F 409 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA LYS a 164 " pdb=" N LYS a 164 " pdb=" C LYS a 164 " pdb=" CB LYS a 164 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 5059 not shown) Planarity restraints: 5538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C23 LHG D 601 " 0.161 2.00e-02 2.50e+03 9.29e-02 8.62e+01 pdb=" C24 LHG D 601 " -0.048 2.00e-02 2.50e+03 pdb=" O10 LHG D 601 " -0.059 2.00e-02 2.50e+03 pdb=" O8 LHG D 601 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 LHG F 801 " -0.099 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" C24 LHG F 801 " 0.029 2.00e-02 2.50e+03 pdb=" O10 LHG F 801 " 0.037 2.00e-02 2.50e+03 pdb=" O8 LHG F 801 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 LHG F 801 " 0.095 2.00e-02 2.50e+03 5.48e-02 3.00e+01 pdb=" C8 LHG F 801 " -0.027 2.00e-02 2.50e+03 pdb=" O7 LHG F 801 " -0.029 2.00e-02 2.50e+03 pdb=" O9 LHG F 801 " -0.038 2.00e-02 2.50e+03 ... (remaining 5535 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3584 2.74 - 3.28: 34417 3.28 - 3.82: 55753 3.82 - 4.36: 69509 4.36 - 4.90: 115225 Nonbonded interactions: 278488 Sorted by model distance: nonbonded pdb=" OG SER i 132 " pdb=" O ARG i 137 " model vdw 2.203 2.440 nonbonded pdb=" OG1 THR A 176 " pdb=" OH TYR C 80 " model vdw 2.204 2.440 nonbonded pdb=" O SER D 473 " pdb=" OH TYR d 98 " model vdw 2.216 2.440 nonbonded pdb=" O ILE D 132 " pdb=" OG SER D 136 " model vdw 2.217 2.440 nonbonded pdb=" O LEU b 251 " pdb=" OH TYR b 316 " model vdw 2.218 2.440 ... (remaining 278483 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.960 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: 0.030 Extract box with map and model: 15.710 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 90.010 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.006 0.096 32910 Z= 0.408 Angle : 0.941 15.712 44629 Z= 0.520 Chirality : 0.081 4.505 5062 Planarity : 0.006 0.093 5538 Dihedral : 14.275 87.738 11762 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.03 % Favored : 90.88 % Rotamer: Outliers : 0.26 % Allowed : 4.34 % Favored : 95.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.11), residues: 4011 helix: -2.00 (0.09), residues: 2146 sheet: -3.36 (0.24), residues: 305 loop : -3.35 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP h 80 HIS 0.013 0.002 HIS F 265 PHE 0.027 0.002 PHE F 149 TYR 0.038 0.002 TYR G 66 ARG 0.007 0.001 ARG G 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1067 time to evaluate : 3.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 1073 average time/residue: 0.4465 time to fit residues: 768.6987 Evaluate side-chains 750 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 748 time to evaluate : 3.731 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3751 time to fit residues: 6.3117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 336 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 311 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 361 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN F 35 ASN F 62 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 GLN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS F 459 ASN F 644 ASN G 56 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 177 HIS ** b 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 347 ASN c 106 ASN c 157 ASN c 163 GLN c 189 ASN d 70 GLN e 54 GLN e 111 GLN e 116 GLN ** e 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 126 GLN f 215 ASN ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 126 ASN ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 194 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32910 Z= 0.218 Angle : 0.662 10.484 44629 Z= 0.339 Chirality : 0.045 0.325 5062 Planarity : 0.005 0.074 5538 Dihedral : 6.657 59.839 4439 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.65 % Favored : 92.30 % Rotamer: Outliers : 2.40 % Allowed : 14.22 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.12), residues: 4011 helix: -0.68 (0.10), residues: 2141 sheet: -3.00 (0.25), residues: 318 loop : -2.94 (0.14), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP h 80 HIS 0.012 0.001 HIS a 309 PHE 0.031 0.002 PHE f 118 TYR 0.021 0.002 TYR a 160 ARG 0.006 0.001 ARG b 257 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 839 time to evaluate : 3.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 51 residues processed: 878 average time/residue: 0.4251 time to fit residues: 610.5831 Evaluate side-chains 780 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 729 time to evaluate : 3.725 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.2931 time to fit residues: 33.1203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 200 optimal weight: 20.0000 chunk 112 optimal weight: 0.9990 chunk 300 optimal weight: 0.0980 chunk 246 optimal weight: 0.0570 chunk 99 optimal weight: 0.5980 chunk 362 optimal weight: 0.2980 chunk 391 optimal weight: 0.0040 chunk 322 optimal weight: 0.9990 chunk 359 optimal weight: 0.1980 chunk 123 optimal weight: 5.9990 chunk 290 optimal weight: 0.7980 overall best weight: 0.1310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 ASN F 206 GLN ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 170 ASN ** b 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 169 ASN ** c 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 106 ASN ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32910 Z= 0.177 Angle : 0.640 9.908 44629 Z= 0.324 Chirality : 0.044 0.251 5062 Planarity : 0.005 0.069 5538 Dihedral : 6.207 58.308 4439 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.68 % Favored : 92.30 % Rotamer: Outliers : 2.02 % Allowed : 17.40 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.13), residues: 4011 helix: -0.13 (0.11), residues: 2146 sheet: -2.83 (0.27), residues: 306 loop : -2.81 (0.14), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP h 80 HIS 0.008 0.001 HIS G 56 PHE 0.023 0.001 PHE C 58 TYR 0.024 0.002 TYR B 446 ARG 0.006 0.000 ARG b 257 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 856 time to evaluate : 3.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 30 residues processed: 895 average time/residue: 0.4124 time to fit residues: 607.8956 Evaluate side-chains 769 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 739 time to evaluate : 4.062 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3183 time to fit residues: 22.7842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 357 optimal weight: 0.9990 chunk 272 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 243 optimal weight: 0.9990 chunk 363 optimal weight: 0.7980 chunk 384 optimal weight: 9.9990 chunk 189 optimal weight: 0.0870 chunk 344 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 GLN a 170 ASN ** b 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 169 ASN ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32910 Z= 0.194 Angle : 0.640 10.370 44629 Z= 0.322 Chirality : 0.044 0.259 5062 Planarity : 0.004 0.067 5538 Dihedral : 6.077 58.636 4439 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.20 % Allowed : 19.72 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.13), residues: 4011 helix: 0.14 (0.11), residues: 2160 sheet: -2.68 (0.28), residues: 290 loop : -2.67 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP h 80 HIS 0.007 0.001 HIS D 344 PHE 0.024 0.001 PHE j 198 TYR 0.028 0.002 TYR a 226 ARG 0.004 0.000 ARG G 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 808 time to evaluate : 4.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 47 residues processed: 841 average time/residue: 0.4315 time to fit residues: 594.6239 Evaluate side-chains 777 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 730 time to evaluate : 3.790 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.2893 time to fit residues: 30.9676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 320 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 286 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 328 optimal weight: 0.0070 chunk 265 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 345 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 54 GLN e 161 GLN ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32910 Z= 0.200 Angle : 0.640 8.674 44629 Z= 0.321 Chirality : 0.044 0.264 5062 Planarity : 0.004 0.067 5538 Dihedral : 5.931 59.146 4439 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 1.99 % Allowed : 22.00 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 4011 helix: 0.31 (0.11), residues: 2155 sheet: -2.54 (0.28), residues: 295 loop : -2.56 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP h 80 HIS 0.007 0.001 HIS D 344 PHE 0.028 0.001 PHE D 82 TYR 0.032 0.001 TYR G 66 ARG 0.008 0.000 ARG b 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 793 time to evaluate : 3.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 31 residues processed: 833 average time/residue: 0.4341 time to fit residues: 593.2224 Evaluate side-chains 757 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 726 time to evaluate : 3.949 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3082 time to fit residues: 23.0850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 129 optimal weight: 0.7980 chunk 346 optimal weight: 2.9990 chunk 76 optimal weight: 0.0870 chunk 225 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 385 optimal weight: 0.0970 chunk 319 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 127 optimal weight: 5.9990 chunk 202 optimal weight: 0.2980 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN F 35 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 129 ASN e 70 ASN e 161 GLN ** f 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32910 Z= 0.179 Angle : 0.637 10.842 44629 Z= 0.319 Chirality : 0.044 0.266 5062 Planarity : 0.004 0.065 5538 Dihedral : 5.809 58.656 4439 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.02 % Allowed : 22.84 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 4011 helix: 0.43 (0.11), residues: 2146 sheet: -2.36 (0.28), residues: 301 loop : -2.52 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 9 HIS 0.008 0.001 HIS D 344 PHE 0.041 0.001 PHE G 80 TYR 0.022 0.001 TYR a 226 ARG 0.007 0.000 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 829 time to evaluate : 3.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 29 residues processed: 864 average time/residue: 0.4185 time to fit residues: 594.4504 Evaluate side-chains 766 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 737 time to evaluate : 3.825 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2905 time to fit residues: 21.0920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 371 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 281 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 324 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 383 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 233 optimal weight: 0.0770 chunk 177 optimal weight: 2.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 ASN ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 663 ASN G 71 ASN ** c 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32910 Z= 0.282 Angle : 0.693 9.637 44629 Z= 0.347 Chirality : 0.046 0.276 5062 Planarity : 0.004 0.068 5538 Dihedral : 5.986 59.234 4439 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 1.97 % Allowed : 24.17 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.13), residues: 4011 helix: 0.42 (0.11), residues: 2159 sheet: -2.55 (0.27), residues: 317 loop : -2.46 (0.15), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 125 HIS 0.009 0.001 HIS B 250 PHE 0.035 0.002 PHE e 147 TYR 0.026 0.002 TYR f 102 ARG 0.006 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 782 time to evaluate : 4.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 38 residues processed: 814 average time/residue: 0.4250 time to fit residues: 569.0088 Evaluate side-chains 762 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 724 time to evaluate : 3.440 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.2846 time to fit residues: 25.4427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 237 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 243 optimal weight: 0.0980 chunk 261 optimal weight: 7.9990 chunk 189 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 301 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 158 GLN e 66 GLN f 114 HIS ** f 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32910 Z= 0.212 Angle : 0.673 10.333 44629 Z= 0.337 Chirality : 0.045 0.279 5062 Planarity : 0.004 0.067 5538 Dihedral : 5.922 58.742 4439 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 1.21 % Allowed : 24.66 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 4011 helix: 0.50 (0.11), residues: 2124 sheet: -2.51 (0.27), residues: 310 loop : -2.40 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP F 9 HIS 0.010 0.001 HIS D 344 PHE 0.049 0.001 PHE j 145 TYR 0.031 0.002 TYR D 41 ARG 0.008 0.000 ARG i 217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 789 time to evaluate : 4.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 20 residues processed: 804 average time/residue: 0.4673 time to fit residues: 625.5174 Evaluate side-chains 743 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 723 time to evaluate : 4.977 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3249 time to fit residues: 18.1794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 348 optimal weight: 0.3980 chunk 367 optimal weight: 4.9990 chunk 335 optimal weight: 5.9990 chunk 357 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 280 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 323 optimal weight: 2.9990 chunk 338 optimal weight: 9.9990 chunk 356 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 445 GLN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 ASN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 320 GLN ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 32910 Z= 0.333 Angle : 0.744 12.356 44629 Z= 0.373 Chirality : 0.048 0.283 5062 Planarity : 0.005 0.070 5538 Dihedral : 6.144 59.623 4439 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 1.19 % Allowed : 25.61 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 4011 helix: 0.39 (0.11), residues: 2137 sheet: -2.45 (0.28), residues: 320 loop : -2.43 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP F 9 HIS 0.010 0.001 HIS F 247 PHE 0.035 0.002 PHE j 145 TYR 0.036 0.002 TYR D 359 ARG 0.011 0.001 ARG b 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 739 time to evaluate : 3.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 29 residues processed: 758 average time/residue: 0.4298 time to fit residues: 538.1192 Evaluate side-chains 728 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 699 time to evaluate : 3.815 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3172 time to fit residues: 22.4247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 234 optimal weight: 0.5980 chunk 378 optimal weight: 0.0060 chunk 230 optimal weight: 0.8980 chunk 179 optimal weight: 0.9990 chunk 262 optimal weight: 5.9990 chunk 396 optimal weight: 9.9990 chunk 364 optimal weight: 3.9990 chunk 315 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN a 158 GLN ** a 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 320 GLN e 66 GLN ** f 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32910 Z= 0.224 Angle : 0.705 11.462 44629 Z= 0.352 Chirality : 0.046 0.281 5062 Planarity : 0.005 0.070 5538 Dihedral : 6.004 57.831 4439 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.43 % Allowed : 26.37 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 4011 helix: 0.43 (0.11), residues: 2145 sheet: -2.48 (0.27), residues: 323 loop : -2.38 (0.16), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP F 9 HIS 0.010 0.001 HIS D 344 PHE 0.042 0.001 PHE j 145 TYR 0.026 0.002 TYR D 359 ARG 0.011 0.000 ARG b 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 765 time to evaluate : 3.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 769 average time/residue: 0.4363 time to fit residues: 554.0031 Evaluate side-chains 730 residues out of total 3508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 722 time to evaluate : 3.903 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3174 time to fit residues: 9.6699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 250 optimal weight: 0.4980 chunk 336 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 291 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 chunk 87 optimal weight: 0.0980 chunk 316 optimal weight: 0.0980 chunk 132 optimal weight: 0.8980 chunk 324 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN B 222 GLN ** B 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN a 158 GLN a 320 GLN e 111 GLN e 161 GLN ** f 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 185 ASN i 194 ASN ** j 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.127407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.106856 restraints weight = 67360.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.109474 restraints weight = 32694.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111069 restraints weight = 20359.874| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32910 Z= 0.201 Angle : 0.700 11.818 44629 Z= 0.349 Chirality : 0.046 0.360 5062 Planarity : 0.004 0.071 5538 Dihedral : 5.884 59.076 4439 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.69 % Allowed : 26.97 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 4011 helix: 0.52 (0.11), residues: 2124 sheet: -2.62 (0.26), residues: 329 loop : -2.36 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP F 9 HIS 0.009 0.001 HIS B 250 PHE 0.028 0.001 PHE E 45 TYR 0.040 0.002 TYR B 164 ARG 0.016 0.000 ARG G 175 =============================================================================== Job complete usr+sys time: 9799.18 seconds wall clock time: 177 minutes 8.52 seconds (10628.52 seconds total)