Starting phenix.real_space_refine on Fri Dec 15 05:41:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1y_15093/12_2023/8a1y_15093_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1y_15093/12_2023/8a1y_15093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1y_15093/12_2023/8a1y_15093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1y_15093/12_2023/8a1y_15093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1y_15093/12_2023/8a1y_15093_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1y_15093/12_2023/8a1y_15093_trim_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.130 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 7 5.49 5 S 91 5.16 5 C 9843 2.51 5 N 2454 2.21 5 O 2782 1.98 5 H 14864 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30045 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 6910 Classifications: {'peptide': 448} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 424} Chain: "B" Number of atoms: 6347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 6347 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 15, 'TRANS': 396} Chain: "C" Number of atoms: 3840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3840 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "D" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3166 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 9, 'TRANS': 192} Chain: "E" Number of atoms: 3078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 3078 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "F" Number of atoms: 6269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 6269 Classifications: {'peptide': 408} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 383} Chain: "B" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 274 Unusual residues: {'3PE': 3, 'FMN': 1, 'HQO': 1, 'LMT': 2, 'RBF': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 25 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18773 SG CYS D 112 67.035 82.568 59.443 1.00121.94 S ATOM 20665 SG CYS E 26 64.349 82.937 62.001 1.00110.64 S ATOM 17447 SG CYS D 29 67.030 84.311 65.651 1.00 92.56 S ATOM 22170 SG CYS E 120 70.308 84.504 63.885 1.00117.42 S ATOM 24391 SG CYS F 70 52.091 66.625 37.855 1.00276.78 S ATOM 24440 SG CYS F 76 50.364 63.329 37.299 1.00271.01 S ATOM 24474 SG CYS F 79 55.179 60.974 38.770 1.00261.99 S ATOM 24959 SG CYS F 111 56.470 64.481 39.250 1.00255.78 S Time building chain proxies: 13.93, per 1000 atoms: 0.46 Number of scatterers: 30045 At special positions: 0 Unit cell: (111.739, 136.849, 131.827, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 91 16.00 P 7 15.00 O 2782 8.00 N 2454 7.00 C 9843 6.00 H 14864 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 25.88 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D1001 " pdb="FE2 FES D1001 " - pdb=" SG CYS D 29 " pdb="FE1 FES D1001 " - pdb=" SG CYS E 26 " pdb="FE1 FES D1001 " - pdb=" SG CYS D 112 " pdb="FE2 FES D1001 " - pdb=" SG CYS E 120 " pdb=" FES F1502 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 79 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 76 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 70 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 111 " Number of angles added : 12 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 12 sheets defined 46.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.87 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 163 through 184 removed outlier: 3.773A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 218 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.780A pdb=" N ARG A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'B' and resid 4 through 14 removed outlier: 4.529A pdb=" N HIS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N HIS B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 34 removed outlier: 4.775A pdb=" N ALA B 25 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 31 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 34 " --> pdb=" O ALA B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 61 removed outlier: 3.543A pdb=" N ILE B 58 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 60 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 86 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.646A pdb=" N LEU B 104 " --> pdb=" O TRP B 100 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 151 Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 160 through 166 removed outlier: 3.560A pdb=" N ILE B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 204 through 215 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 237 through 243 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 278 through 289 removed outlier: 3.758A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 315 Processing helix chain 'B' and resid 321 through 324 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 354 through 373 removed outlier: 3.572A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 409 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'C' and resid 8 through 32 Processing helix chain 'C' and resid 34 through 53 removed outlier: 3.568A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 183 through 189 Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'D' and resid 8 through 15 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 38 through 65 removed outlier: 4.920A pdb=" N ASN D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N HIS D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 92 Processing helix chain 'D' and resid 95 through 109 removed outlier: 6.008A pdb=" N VAL D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE D 109 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'D' and resid 127 through 156 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 179 through 182 Processing helix chain 'D' and resid 184 through 201 removed outlier: 3.846A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP D 196 " --> pdb=" O GLY D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 35 through 62 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 76 through 101 removed outlier: 4.493A pdb=" N PHE E 80 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE E 83 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE E 84 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE E 93 " --> pdb=" O LEU E 90 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 94 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE E 97 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU E 98 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE E 101 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 116 removed outlier: 3.523A pdb=" N ALA E 108 " --> pdb=" O PRO E 104 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N PHE E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Proline residue: E 114 - end of helix Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.649A pdb=" N VAL E 126 " --> pdb=" O ILE E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 164 Processing helix chain 'E' and resid 176 through 191 Processing helix chain 'F' and resid 3 through 28 Processing helix chain 'F' and resid 55 through 62 Processing helix chain 'F' and resid 92 through 97 removed outlier: 4.136A pdb=" N HIS F 97 " --> pdb=" O THR F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 125 through 129 Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 189 through 195 Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 235 through 237 No H-bonds generated for 'chain 'F' and resid 235 through 237' Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 282 through 296 removed outlier: 3.506A pdb=" N MET F 285 " --> pdb=" O GLY F 282 " (cutoff:3.500A) Proline residue: F 287 - end of helix removed outlier: 3.502A pdb=" N PHE F 293 " --> pdb=" O SER F 290 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP F 294 " --> pdb=" O HIS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 329 removed outlier: 3.500A pdb=" N LEU F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 346 No H-bonds generated for 'chain 'F' and resid 344 through 346' Processing helix chain 'F' and resid 355 through 362 removed outlier: 3.764A pdb=" N TYR F 360 " --> pdb=" O HIS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 372 No H-bonds generated for 'chain 'F' and resid 370 through 372' Processing helix chain 'F' and resid 381 through 394 Processing sheet with id= A, first strand: chain 'A' and resid 1 through 4 removed outlier: 8.473A pdb=" N ILE A 2 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 210 " --> pdb=" O ILE A 2 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE A 4 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASP A 212 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 189 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N HIS A 209 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 191 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE A 211 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS A 193 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N GLY A 213 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TRP A 237 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N THR A 152 " --> pdb=" O TRP A 237 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE A 239 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.812A pdb=" N SER A 89 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 78 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLU A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N VAL A 76 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.138A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 273 through 278 removed outlier: 3.751A pdb=" N VAL A 325 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 73 through 77 removed outlier: 14.041A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.313A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 169 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU C 165 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= G, first strand: chain 'C' and resid 204 through 206 Processing sheet with id= H, first strand: chain 'F' and resid 46 through 49 removed outlier: 7.633A pdb=" N MET F 119 " --> pdb=" O SER F 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 257 through 262 removed outlier: 6.677A pdb=" N LYS F 151 " --> pdb=" O ILE F 138 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 167 through 172 Processing sheet with id= K, first strand: chain 'F' and resid 175 through 178 Processing sheet with id= L, first strand: chain 'F' and resid 374 through 378 removed outlier: 7.212A pdb=" N VAL F 334 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N TYR F 309 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N HIS F 336 " --> pdb=" O TYR F 309 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ALA F 311 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA F 338 " --> pdb=" O ALA F 311 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1662 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: 10.50 Time building geometry restraints manager: 26.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.11: 14851 1.11 - 1.39: 6010 1.39 - 1.66: 9375 1.66 - 1.93: 153 1.93 - 2.20: 8 Bond restraints: 30397 Sorted by residual: bond pdb=" N1 HQO B 607 " pdb=" O4 HQO B 607 " ideal model delta sigma weight residual 1.285 1.383 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C1 HQO B 607 " pdb=" O1 HQO B 607 " ideal model delta sigma weight residual 1.335 1.243 0.092 2.00e-02 2.50e+03 2.14e+01 bond pdb=" O3P FAD F1501 " pdb=" P FAD F1501 " ideal model delta sigma weight residual 1.660 1.585 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C4 RBF B 601 " pdb=" C4A RBF B 601 " ideal model delta sigma weight residual 1.481 1.407 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C1 HQO B 607 " pdb=" C2 HQO B 607 " ideal model delta sigma weight residual 1.368 1.436 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 30392 not shown) Histogram of bond angle deviations from ideal: 75.24 - 86.99: 4 86.99 - 98.74: 0 98.74 - 110.48: 30959 110.48 - 122.23: 19605 122.23 - 133.98: 4318 Bond angle restraints: 54886 Sorted by residual: angle pdb=" C2 LMT E 201 " pdb=" C3 LMT E 201 " pdb=" C4 LMT E 201 " ideal model delta sigma weight residual 117.09 107.38 9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C2 LMT B 605 " pdb=" C3 LMT B 605 " pdb=" C4 LMT B 605 " ideal model delta sigma weight residual 117.09 107.61 9.48 3.00e+00 1.11e-01 9.98e+00 angle pdb=" C2 LMT D1002 " pdb=" C3 LMT D1002 " pdb=" C4 LMT D1002 " ideal model delta sigma weight residual 117.09 107.64 9.45 3.00e+00 1.11e-01 9.92e+00 angle pdb=" C2 LMT B 603 " pdb=" C3 LMT B 603 " pdb=" C4 LMT B 603 " ideal model delta sigma weight residual 117.09 107.69 9.40 3.00e+00 1.11e-01 9.81e+00 angle pdb=" C10 LMT B 603 " pdb=" C9 LMT B 603 " pdb=" C8 LMT B 603 " ideal model delta sigma weight residual 116.03 107.29 8.74 3.00e+00 1.11e-01 8.49e+00 ... (remaining 54881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 13691 35.63 - 71.27: 304 71.27 - 106.90: 38 106.90 - 142.53: 13 142.53 - 178.16: 2 Dihedral angle restraints: 14048 sinusoidal: 7553 harmonic: 6495 Sorted by residual: dihedral pdb=" C10 FMN C1000 " pdb=" C1' FMN C1000 " pdb=" N10 FMN C1000 " pdb=" C2' FMN C1000 " ideal model delta sinusoidal sigma weight residual -102.41 75.75 -178.16 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C10 FMN B 600 " pdb=" C1' FMN B 600 " pdb=" N10 FMN B 600 " pdb=" C2' FMN B 600 " ideal model delta sinusoidal sigma weight residual 257.59 87.68 169.91 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' FMN B 600 " pdb=" O5' FMN B 600 " pdb=" P FMN B 600 " pdb=" O1P FMN B 600 " ideal model delta sinusoidal sigma weight residual 75.26 -22.53 97.78 1 2.00e+01 2.50e-03 2.72e+01 ... (remaining 14045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1902 0.044 - 0.088: 319 0.088 - 0.132: 133 0.132 - 0.176: 5 0.176 - 0.221: 12 Chirality restraints: 2371 Sorted by residual: chirality pdb=" C4' LMT B 605 " pdb=" C3' LMT B 605 " pdb=" C5' LMT B 605 " pdb=" O1B LMT B 605 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C3B LMT D1002 " pdb=" C2B LMT D1002 " pdb=" C4B LMT D1002 " pdb=" O3B LMT D1002 " both_signs ideal model delta sigma weight residual False 2.50 2.28 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C5' LMT B 605 " pdb=" C4' LMT B 605 " pdb=" C6' LMT B 605 " pdb=" O5' LMT B 605 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2368 not shown) Planarity restraints: 4443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 213 " 0.016 5.00e-02 4.00e+02 2.42e-02 9.37e-01 pdb=" N PRO A 214 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 214 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 214 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 160 " -0.015 5.00e-02 4.00e+02 2.31e-02 8.50e-01 pdb=" N PRO F 161 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO F 161 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 161 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 102 " -0.014 5.00e-02 4.00e+02 2.11e-02 7.12e-01 pdb=" N PRO E 103 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " -0.012 5.00e-02 4.00e+02 ... (remaining 4440 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1328 2.18 - 2.79: 60253 2.79 - 3.39: 84338 3.39 - 4.00: 110458 4.00 - 4.60: 171522 Nonbonded interactions: 427899 Sorted by model distance: nonbonded pdb=" H LEU D 38 " pdb=" OE1 GLU D 153 " model vdw 1.577 1.850 nonbonded pdb=" O ASN F 140 " pdb=" HZ1 LYS F 148 " model vdw 1.597 1.850 nonbonded pdb=" OE1 GLU C 109 " pdb=" H GLU C 109 " model vdw 1.613 1.850 nonbonded pdb=" H GLY A 301 " pdb=" O GLN A 322 " model vdw 1.623 1.850 nonbonded pdb=" O VAL D 48 " pdb=" HG1 THR D 52 " model vdw 1.635 1.850 ... (remaining 427894 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.460 Extract box with map and model: 3.790 Check model and map are aligned: 0.700 Set scattering table: 0.390 Process input model: 108.110 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 15533 Z= 0.274 Angle : 0.535 9.709 21042 Z= 0.239 Chirality : 0.041 0.221 2371 Planarity : 0.002 0.024 2614 Dihedral : 17.508 178.163 5865 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.06 % Allowed : 14.09 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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 (0.20), residues: 1908 helix: 1.95 (0.19), residues: 871 sheet: -0.26 (0.40), residues: 185 loop : 0.02 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 103 HIS 0.002 0.000 HIS B 328 PHE 0.006 0.001 PHE B 166 TYR 0.005 0.001 TYR B 27 ARG 0.001 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 292 average time/residue: 0.6377 time to fit residues: 271.5557 Evaluate side-chains 208 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.798 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 9.9990 chunk 143 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 171 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN B 84 ASN D 75 GLN E 79 ASN F 295 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15533 Z= 0.254 Angle : 0.526 7.803 21042 Z= 0.276 Chirality : 0.042 0.168 2371 Planarity : 0.003 0.036 2614 Dihedral : 12.974 172.322 2488 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.96 % Allowed : 16.90 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.78 (0.19), residues: 1908 helix: 1.39 (0.18), residues: 889 sheet: -0.26 (0.39), residues: 175 loop : -0.15 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 308 HIS 0.002 0.001 HIS B 330 PHE 0.022 0.001 PHE F 11 TYR 0.014 0.001 TYR B 360 ARG 0.011 0.000 ARG F 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 214 time to evaluate : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 225 average time/residue: 0.5639 time to fit residues: 197.6846 Evaluate side-chains 197 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 2.204 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3239 time to fit residues: 8.6294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 10.0000 chunk 53 optimal weight: 0.0870 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 171 optimal weight: 20.0000 chunk 185 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 HIS D 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15533 Z= 0.310 Angle : 0.541 7.141 21042 Z= 0.275 Chirality : 0.042 0.291 2371 Planarity : 0.004 0.030 2614 Dihedral : 11.103 171.833 2488 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.40 % Allowed : 16.71 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.45 (0.19), residues: 1908 helix: 1.14 (0.18), residues: 887 sheet: -0.51 (0.39), residues: 184 loop : -0.32 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 70 HIS 0.003 0.001 HIS B 330 PHE 0.031 0.001 PHE B 14 TYR 0.019 0.001 TYR F 309 ARG 0.003 0.000 ARG F 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 2.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 209 average time/residue: 0.5822 time to fit residues: 186.6129 Evaluate side-chains 196 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 183 time to evaluate : 2.607 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3725 time to fit residues: 11.7198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 172 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15533 Z= 0.243 Angle : 0.492 6.577 21042 Z= 0.251 Chirality : 0.041 0.346 2371 Planarity : 0.003 0.030 2614 Dihedral : 10.568 170.458 2488 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.77 % Allowed : 16.96 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.48 (0.19), residues: 1908 helix: 1.16 (0.18), residues: 886 sheet: -0.55 (0.39), residues: 184 loop : -0.29 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 70 HIS 0.003 0.001 HIS A 215 PHE 0.022 0.001 PHE F 11 TYR 0.013 0.001 TYR B 360 ARG 0.004 0.000 ARG F 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 189 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 199 average time/residue: 0.5718 time to fit residues: 173.9893 Evaluate side-chains 184 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 2.423 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3400 time to fit residues: 7.8159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 0.1980 chunk 103 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 chunk 155 optimal weight: 30.0000 chunk 126 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15533 Z= 0.145 Angle : 0.456 6.878 21042 Z= 0.230 Chirality : 0.040 0.345 2371 Planarity : 0.003 0.030 2614 Dihedral : 10.078 167.627 2488 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.45 % Allowed : 16.96 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.70 (0.20), residues: 1908 helix: 1.38 (0.18), residues: 879 sheet: -0.32 (0.40), residues: 168 loop : -0.25 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 70 HIS 0.012 0.001 HIS B 20 PHE 0.020 0.001 PHE F 11 TYR 0.026 0.001 TYR F 309 ARG 0.003 0.000 ARG F 298 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 188 average time/residue: 0.5820 time to fit residues: 168.6553 Evaluate side-chains 180 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 176 time to evaluate : 2.442 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3524 time to fit residues: 5.4591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 3.9990 chunk 164 optimal weight: 0.0070 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15533 Z= 0.281 Angle : 0.504 7.006 21042 Z= 0.258 Chirality : 0.041 0.302 2371 Planarity : 0.003 0.032 2614 Dihedral : 10.085 171.401 2488 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.83 % Allowed : 16.84 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.50 (0.19), residues: 1908 helix: 1.21 (0.18), residues: 887 sheet: -0.49 (0.39), residues: 182 loop : -0.33 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.004 0.001 HIS B 330 PHE 0.022 0.001 PHE F 11 TYR 0.015 0.001 TYR F 309 ARG 0.002 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 176 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 183 average time/residue: 0.5696 time to fit residues: 160.4923 Evaluate side-chains 181 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 2.560 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3731 time to fit residues: 8.4247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15533 Z= 0.344 Angle : 0.529 7.754 21042 Z= 0.273 Chirality : 0.042 0.234 2371 Planarity : 0.004 0.034 2614 Dihedral : 10.127 169.943 2488 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.51 % Allowed : 17.73 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.22 (0.19), residues: 1908 helix: 1.04 (0.18), residues: 883 sheet: -0.71 (0.39), residues: 182 loop : -0.54 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.005 0.001 HIS B 20 PHE 0.024 0.001 PHE F 11 TYR 0.014 0.001 TYR B 360 ARG 0.002 0.000 ARG F 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 182 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 185 average time/residue: 0.5933 time to fit residues: 168.3837 Evaluate side-chains 179 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 174 time to evaluate : 2.415 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3971 time to fit residues: 6.4289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15533 Z= 0.185 Angle : 0.471 7.547 21042 Z= 0.239 Chirality : 0.040 0.223 2371 Planarity : 0.003 0.034 2614 Dihedral : 9.678 168.999 2488 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.26 % Allowed : 18.05 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.51 (0.19), residues: 1908 helix: 1.30 (0.18), residues: 875 sheet: -0.45 (0.41), residues: 168 loop : -0.43 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 335 HIS 0.004 0.001 HIS B 20 PHE 0.020 0.001 PHE F 11 TYR 0.012 0.001 TYR B 360 ARG 0.002 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 183 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 184 average time/residue: 0.5731 time to fit residues: 163.3238 Evaluate side-chains 181 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 2.385 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4037 time to fit residues: 5.8881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15533 Z= 0.395 Angle : 0.557 6.803 21042 Z= 0.287 Chirality : 0.042 0.152 2371 Planarity : 0.004 0.035 2614 Dihedral : 9.974 167.847 2488 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.45 % Allowed : 18.18 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.13 (0.19), residues: 1908 helix: 1.00 (0.18), residues: 881 sheet: -0.72 (0.39), residues: 182 loop : -0.63 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.004 0.001 HIS B 330 PHE 0.022 0.001 PHE F 11 TYR 0.015 0.002 TYR B 360 ARG 0.003 0.000 ARG F 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 185 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 188 average time/residue: 0.5585 time to fit residues: 161.6449 Evaluate side-chains 183 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 2.248 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3594 time to fit residues: 5.9107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 188 optimal weight: 0.4980 chunk 173 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15533 Z= 0.184 Angle : 0.475 4.932 21042 Z= 0.242 Chirality : 0.040 0.149 2371 Planarity : 0.003 0.035 2614 Dihedral : 9.533 167.922 2488 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.06 % Allowed : 18.75 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.44 (0.19), residues: 1908 helix: 1.27 (0.18), residues: 873 sheet: -0.64 (0.39), residues: 182 loop : -0.46 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 335 HIS 0.004 0.001 HIS B 20 PHE 0.020 0.001 PHE F 11 TYR 0.014 0.001 TYR D 95 ARG 0.003 0.000 ARG A 395 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3816 Ramachandran restraints generated. 1908 Oldfield, 0 Emsley, 1908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Residue SER 69 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.5674 time to fit residues: 162.3618 Evaluate side-chains 177 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 2.610 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4180 time to fit residues: 3.9198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 154 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.150231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.105417 restraints weight = 67602.689| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.46 r_work: 0.3268 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 56 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15533 Z= 0.231 Angle : 0.486 6.363 21042 Z= 0.247 Chirality : 0.040 0.147 2371 Planarity : 0.003 0.036 2614 Dihedral : 9.406 167.281 2488 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.19 % Allowed : 19.13 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.18 % 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: 0.45 (0.19), residues: 1908 helix: 1.28 (0.18), residues: 874 sheet: -0.45 (0.40), residues: 168 loop : -0.51 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.020 0.001 PHE F 11 TYR 0.013 0.001 TYR D 95 ARG 0.002 0.000 ARG F 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6277.07 seconds wall clock time: 121 minutes 31.96 seconds (7291.96 seconds total)