Starting phenix.real_space_refine on Thu Mar 21 15:08:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1y_15093/03_2024/8a1y_15093_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1y_15093/03_2024/8a1y_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_15093/03_2024/8a1y_15093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1y_15093/03_2024/8a1y_15093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1y_15093/03_2024/8a1y_15093_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1y_15093/03_2024/8a1y_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 13.00, per 1000 atoms: 0.43 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: 23.76 Conformation dependent library (CDL) restraints added in 2.8 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: 4.43 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: 10.84 Time building geometry restraints manager: 24.56 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: 13930 35.63 - 71.27: 536 71.27 - 106.90: 38 106.90 - 142.53: 13 142.53 - 178.16: 2 Dihedral angle restraints: 14519 sinusoidal: 8024 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 14516 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: 0.500 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: 0.460 Extract box with map and model: 3.420 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 99.430 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.020 ------------------------------------------------------------------------------- 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 : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 THR cc_start: 0.9048 (m) cc_final: 0.8772 (p) REVERT: A 349 ARG cc_start: 0.8252 (mtm-85) cc_final: 0.7447 (mtp85) REVERT: A 445 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8038 (mt-10) REVERT: B 57 MET cc_start: 0.8722 (mmt) cc_final: 0.8426 (mmt) REVERT: B 122 MET cc_start: 0.8742 (ttm) cc_final: 0.8515 (ttp) REVERT: B 382 MET cc_start: 0.8533 (tpt) cc_final: 0.7627 (tpt) REVERT: C 84 VAL cc_start: 0.6120 (t) cc_final: 0.5887 (t) REVERT: C 94 ARG cc_start: 0.7340 (mtt180) cc_final: 0.5932 (tpp80) REVERT: D 32 LEU cc_start: 0.9017 (mt) cc_final: 0.8788 (mt) REVERT: D 207 GLU cc_start: 0.7976 (tp30) cc_final: 0.7744 (tp30) REVERT: F 24 PHE cc_start: 0.6945 (t80) cc_final: 0.6737 (m-80) REVERT: F 210 ARG cc_start: 0.3751 (mmt-90) cc_final: 0.3416 (mmt90) REVERT: F 264 PHE cc_start: 0.5706 (m-80) cc_final: 0.5112 (m-80) REVERT: F 312 ARG cc_start: 0.4690 (ttp-170) cc_final: 0.3482 (mmm160) REVERT: F 375 TYR cc_start: 0.6595 (m-80) cc_final: 0.6265 (m-80) outliers start: 1 outliers final: 0 residues processed: 292 average time/residue: 0.6652 time to fit residues: 282.6374 Evaluate side-chains 212 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.224 ------------------------------------------------------------------------------- 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: 3.9990 chunk 143 optimal weight: 4.9990 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: 3.9990 chunk 90 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 171 optimal weight: 20.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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: 0.7505 moved from start: 0.1677 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= 0.266 Angle : 0.531 7.887 21042 Z= 0.278 Chirality : 0.042 0.162 2371 Planarity : 0.003 0.029 2614 Dihedral : 13.025 172.305 2488 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.89 % Allowed : 16.71 % Favored : 82.40 % 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: 0.76 (0.19), residues: 1908 helix: 1.36 (0.18), residues: 888 sheet: -0.39 (0.38), residues: 189 loop : -0.12 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 308 HIS 0.003 0.001 HIS B 330 PHE 0.023 0.001 PHE F 11 TYR 0.014 0.001 TYR B 360 ARG 0.016 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 234 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 220 time to evaluate : 2.407 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: A 46 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7319 (mtp85) REVERT: A 60 ASP cc_start: 0.7244 (t0) cc_final: 0.7020 (t0) REVERT: A 307 THR cc_start: 0.9101 (m) cc_final: 0.8796 (p) REVERT: A 349 ARG cc_start: 0.8272 (mtm-85) cc_final: 0.7427 (mtp85) REVERT: A 445 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7875 (mt-10) REVERT: B 57 MET cc_start: 0.8979 (mmt) cc_final: 0.8674 (mmt) REVERT: B 382 MET cc_start: 0.8312 (tpt) cc_final: 0.7491 (tpt) REVERT: C 94 ARG cc_start: 0.6489 (mtt180) cc_final: 0.6183 (mtt90) REVERT: D 207 GLU cc_start: 0.8047 (tp30) cc_final: 0.7790 (tp30) REVERT: E 120 CYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6698 (m) REVERT: E 139 SER cc_start: 0.8388 (p) cc_final: 0.8172 (p) REVERT: F 312 ARG cc_start: 0.4545 (ttp-170) cc_final: 0.3427 (mmm160) REVERT: F 375 TYR cc_start: 0.6582 (m-80) cc_final: 0.6283 (m-80) REVERT: F 383 MET cc_start: 0.1906 (ttm) cc_final: 0.1476 (ttm) outliers start: 14 outliers final: 9 residues processed: 231 average time/residue: 0.5885 time to fit residues: 204.2467 Evaluate side-chains 208 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 198 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 336 HIS 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: 0.5980 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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: 0.7562 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15533 Z= 0.314 Angle : 0.529 7.120 21042 Z= 0.270 Chirality : 0.042 0.261 2371 Planarity : 0.003 0.029 2614 Dihedral : 11.388 171.111 2488 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.72 % Allowed : 16.07 % Favored : 82.21 % 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: 0.53 (0.19), residues: 1908 helix: 1.19 (0.18), residues: 887 sheet: -0.42 (0.39), residues: 184 loop : -0.27 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 70 HIS 0.003 0.001 HIS A 215 PHE 0.026 0.001 PHE B 14 TYR 0.016 0.001 TYR F 309 ARG 0.002 0.000 ARG A 115 *********************** 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 218 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7316 (mtp85) REVERT: A 60 ASP cc_start: 0.7347 (t0) cc_final: 0.7115 (t0) REVERT: A 307 THR cc_start: 0.9203 (m) cc_final: 0.8892 (p) REVERT: A 417 ASP cc_start: 0.9008 (OUTLIER) cc_final: 0.8741 (m-30) REVERT: A 445 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7691 (mt-10) REVERT: B 57 MET cc_start: 0.8906 (mmt) cc_final: 0.8655 (mmt) REVERT: B 322 MET cc_start: 0.8986 (tpp) cc_final: 0.8664 (tpp) REVERT: B 382 MET cc_start: 0.8551 (tpt) cc_final: 0.7785 (tpt) REVERT: C 94 ARG cc_start: 0.6415 (mtt180) cc_final: 0.5709 (ttm110) REVERT: D 207 GLU cc_start: 0.8085 (tp30) cc_final: 0.7864 (tp30) REVERT: E 64 LEU cc_start: 0.8859 (mt) cc_final: 0.8629 (mp) REVERT: E 139 SER cc_start: 0.8463 (p) cc_final: 0.8232 (p) REVERT: F 312 ARG cc_start: 0.4706 (ttp-170) cc_final: 0.3509 (mmm160) REVERT: F 318 PHE cc_start: 0.5682 (OUTLIER) cc_final: 0.5256 (p90) REVERT: F 375 TYR cc_start: 0.6397 (m-80) cc_final: 0.6014 (m-80) REVERT: F 377 MET cc_start: 0.5045 (tpt) cc_final: 0.4709 (tpt) REVERT: F 390 MET cc_start: -0.0406 (mtp) cc_final: -0.0621 (mtp) outliers start: 27 outliers final: 20 residues processed: 209 average time/residue: 0.5321 time to fit residues: 166.2612 Evaluate side-chains 203 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 318 PHE Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 336 HIS Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 172 optimal weight: 0.0470 chunk 182 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- 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: 0.7574 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15533 Z= 0.255 Angle : 0.496 7.446 21042 Z= 0.253 Chirality : 0.041 0.357 2371 Planarity : 0.003 0.031 2614 Dihedral : 10.550 171.869 2488 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.91 % Allowed : 17.03 % Favored : 81.06 % 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: 0.46 (0.19), residues: 1908 helix: 1.15 (0.18), residues: 889 sheet: -0.52 (0.40), residues: 182 loop : -0.32 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 335 HIS 0.003 0.001 HIS A 215 PHE 0.025 0.001 PHE F 11 TYR 0.022 0.001 TYR F 309 ARG 0.002 0.000 ARG F 199 *********************** 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 218 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 2.324 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: A 46 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7297 (mtp85) REVERT: A 207 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7267 (mt-10) REVERT: A 307 THR cc_start: 0.9274 (m) cc_final: 0.8907 (p) REVERT: B 57 MET cc_start: 0.8853 (mmt) cc_final: 0.8520 (mmt) REVERT: B 322 MET cc_start: 0.9037 (tpp) cc_final: 0.8704 (tpp) REVERT: B 382 MET cc_start: 0.8498 (tpt) cc_final: 0.7703 (tpt) REVERT: C 94 ARG cc_start: 0.6256 (mtt180) cc_final: 0.5847 (ttm170) REVERT: D 52 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8631 (t) REVERT: D 207 GLU cc_start: 0.8048 (tp30) cc_final: 0.7832 (tp30) REVERT: E 120 CYS cc_start: 0.7453 (OUTLIER) cc_final: 0.6866 (m) REVERT: E 139 SER cc_start: 0.8479 (p) cc_final: 0.8239 (p) REVERT: F 276 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.7280 (mtt) REVERT: F 312 ARG cc_start: 0.4122 (ttp-170) cc_final: 0.3033 (mmm160) REVERT: F 375 TYR cc_start: 0.6332 (m-80) cc_final: 0.5499 (m-80) outliers start: 30 outliers final: 21 residues processed: 211 average time/residue: 0.5487 time to fit residues: 175.5271 Evaluate side-chains 201 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 336 HIS Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 126 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- 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: 0.7621 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15533 Z= 0.396 Angle : 0.562 7.481 21042 Z= 0.290 Chirality : 0.043 0.276 2371 Planarity : 0.004 0.037 2614 Dihedral : 10.627 174.789 2488 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.42 % Allowed : 17.28 % Favored : 80.29 % 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: 0.12 (0.19), residues: 1908 helix: 0.90 (0.18), residues: 887 sheet: -0.65 (0.39), residues: 182 loop : -0.54 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.003 0.001 HIS E 3 PHE 0.024 0.001 PHE F 11 TYR 0.014 0.002 TYR F 309 ARG 0.003 0.000 ARG F 210 *********************** 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 218 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7235 (mtp85) REVERT: A 60 ASP cc_start: 0.7510 (t0) cc_final: 0.7260 (t0) REVERT: A 307 THR cc_start: 0.9319 (m) cc_final: 0.9017 (p) REVERT: B 57 MET cc_start: 0.8777 (mmt) cc_final: 0.8391 (mmt) REVERT: B 223 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8548 (p0) REVERT: B 382 MET cc_start: 0.8628 (tpt) cc_final: 0.7813 (tpt) REVERT: C 94 ARG cc_start: 0.6427 (mtt180) cc_final: 0.6019 (ttm170) REVERT: D 52 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8637 (t) REVERT: D 126 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7493 (mm-30) REVERT: E 64 LEU cc_start: 0.8852 (mt) cc_final: 0.8617 (mp) REVERT: E 120 CYS cc_start: 0.7521 (OUTLIER) cc_final: 0.6867 (m) REVERT: E 139 SER cc_start: 0.8495 (p) cc_final: 0.8236 (p) REVERT: F 312 ARG cc_start: 0.4030 (ttp-170) cc_final: 0.2936 (mmm160) outliers start: 38 outliers final: 30 residues processed: 209 average time/residue: 0.5962 time to fit residues: 187.8103 Evaluate side-chains 205 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 172 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 51 GLN Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 336 HIS Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.7608 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15533 Z= 0.279 Angle : 0.504 8.203 21042 Z= 0.258 Chirality : 0.041 0.226 2371 Planarity : 0.003 0.035 2614 Dihedral : 10.216 174.919 2488 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.04 % Allowed : 17.98 % Favored : 79.97 % 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: 0.21 (0.19), residues: 1908 helix: 0.99 (0.18), residues: 886 sheet: -0.66 (0.40), residues: 182 loop : -0.51 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 70 HIS 0.004 0.001 HIS B 330 PHE 0.023 0.001 PHE F 11 TYR 0.014 0.001 TYR F 375 ARG 0.002 0.000 ARG F 303 *********************** 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 217 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7238 (mtp85) REVERT: A 307 THR cc_start: 0.9322 (m) cc_final: 0.9017 (p) REVERT: B 57 MET cc_start: 0.8773 (mmt) cc_final: 0.8379 (mmt) REVERT: B 223 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8522 (p0) REVERT: B 382 MET cc_start: 0.8600 (tpt) cc_final: 0.7854 (tpt) REVERT: C 94 ARG cc_start: 0.6409 (mtt180) cc_final: 0.5945 (ttm170) REVERT: D 44 MET cc_start: 0.8443 (tpt) cc_final: 0.7973 (tpt) REVERT: D 52 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8631 (t) REVERT: D 126 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7446 (mm-30) REVERT: E 120 CYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6838 (m) REVERT: E 139 SER cc_start: 0.8495 (p) cc_final: 0.8222 (p) REVERT: F 276 MET cc_start: 0.7633 (mtt) cc_final: 0.7219 (mtt) REVERT: F 312 ARG cc_start: 0.4062 (ttp-170) cc_final: 0.2886 (mmm160) REVERT: F 317 MET cc_start: 0.5396 (ttp) cc_final: 0.5144 (mtp) REVERT: F 377 MET cc_start: 0.5269 (tpt) cc_final: 0.4768 (tpt) outliers start: 32 outliers final: 25 residues processed: 208 average time/residue: 0.5601 time to fit residues: 176.5021 Evaluate side-chains 207 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 336 HIS Chi-restraints excluded: chain F residue 352 THR 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: 0.6980 chunk 104 optimal weight: 0.0570 chunk 133 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- 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: 0.7601 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15533 Z= 0.231 Angle : 0.484 7.038 21042 Z= 0.247 Chirality : 0.040 0.148 2371 Planarity : 0.003 0.035 2614 Dihedral : 9.899 174.576 2488 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.79 % Allowed : 18.05 % Favored : 80.17 % 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: 0.37 (0.19), residues: 1908 helix: 1.15 (0.18), residues: 878 sheet: -0.63 (0.39), residues: 182 loop : -0.44 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 103 HIS 0.004 0.001 HIS B 330 PHE 0.024 0.001 PHE F 333 TYR 0.013 0.001 TYR B 360 ARG 0.002 0.000 ARG A 395 *********************** 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 220 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 2.329 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: A 46 ARG cc_start: 0.7654 (mtm-85) cc_final: 0.7201 (mtp85) REVERT: A 307 THR cc_start: 0.9327 (m) cc_final: 0.9021 (p) REVERT: B 57 MET cc_start: 0.8805 (mmt) cc_final: 0.8440 (mmt) REVERT: B 223 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8538 (p0) REVERT: B 382 MET cc_start: 0.8539 (tpt) cc_final: 0.7768 (tpt) REVERT: C 94 ARG cc_start: 0.6401 (mtt180) cc_final: 0.5915 (ttm170) REVERT: D 44 MET cc_start: 0.8413 (tpt) cc_final: 0.7938 (tpt) REVERT: D 52 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8631 (t) REVERT: D 99 LYS cc_start: 0.8483 (mttt) cc_final: 0.8266 (mttt) REVERT: D 126 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7426 (mm-30) REVERT: E 64 LEU cc_start: 0.8739 (mt) cc_final: 0.8474 (mp) REVERT: E 120 CYS cc_start: 0.7489 (OUTLIER) cc_final: 0.6931 (m) REVERT: E 139 SER cc_start: 0.8510 (p) cc_final: 0.8232 (p) REVERT: F 285 MET cc_start: 0.7790 (mmm) cc_final: 0.7563 (mmm) REVERT: F 312 ARG cc_start: 0.3924 (ttp-170) cc_final: 0.2835 (mmm160) REVERT: F 317 MET cc_start: 0.5378 (ttp) cc_final: 0.5156 (mtp) REVERT: F 397 GLU cc_start: 0.7257 (mm-30) cc_final: 0.5750 (pm20) outliers start: 28 outliers final: 22 residues processed: 213 average time/residue: 0.5700 time to fit residues: 182.7828 Evaluate side-chains 207 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 182 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 120 CYS Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 336 HIS Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3511 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= 0.251 Angle : 0.488 5.058 21042 Z= 0.249 Chirality : 0.040 0.147 2371 Planarity : 0.003 0.035 2614 Dihedral : 9.753 174.729 2488 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.49 % Allowed : 17.60 % Favored : 79.91 % 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: 0.33 (0.19), residues: 1908 helix: 1.14 (0.18), residues: 880 sheet: -0.54 (0.41), residues: 168 loop : -0.52 (0.21), residues: 860 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 0.021 0.001 PHE F 11 TYR 0.012 0.001 TYR B 360 ARG 0.003 0.000 ARG A 395 *********************** 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 226 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 187 time to evaluate : 2.157 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: A 46 ARG cc_start: 0.7667 (mtm-85) cc_final: 0.7212 (mtp85) REVERT: A 307 THR cc_start: 0.9340 (m) cc_final: 0.9035 (p) REVERT: B 57 MET cc_start: 0.8808 (mmt) cc_final: 0.8446 (mmt) REVERT: B 223 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8564 (p0) REVERT: B 382 MET cc_start: 0.8564 (tpt) cc_final: 0.7787 (tpt) REVERT: C 94 ARG cc_start: 0.6416 (mtt180) cc_final: 0.5930 (ttm170) REVERT: D 44 MET cc_start: 0.8415 (tpt) cc_final: 0.7939 (tpt) REVERT: D 126 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7427 (mm-30) REVERT: E 64 LEU cc_start: 0.8692 (mt) cc_final: 0.8438 (mp) REVERT: F 285 MET cc_start: 0.7906 (mmm) cc_final: 0.7681 (mmm) REVERT: F 312 ARG cc_start: 0.3928 (ttp-170) cc_final: 0.2841 (mmm160) REVERT: F 397 GLU cc_start: 0.6815 (mm-30) cc_final: 0.5362 (pm20) outliers start: 39 outliers final: 31 residues processed: 217 average time/residue: 0.5622 time to fit residues: 184.8274 Evaluate side-chains 215 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 336 HIS Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 chunk 169 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3589 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= 0.191 Angle : 0.467 5.204 21042 Z= 0.238 Chirality : 0.039 0.148 2371 Planarity : 0.003 0.034 2614 Dihedral : 9.520 172.255 2488 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.47 % Allowed : 18.43 % Favored : 80.10 % 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: 0.47 (0.19), residues: 1908 helix: 1.24 (0.18), residues: 876 sheet: -0.53 (0.41), residues: 168 loop : -0.41 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 103 HIS 0.002 0.001 HIS A 354 PHE 0.020 0.001 PHE F 11 TYR 0.017 0.001 TYR D 95 ARG 0.001 0.000 ARG F 303 *********************** 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 208 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 2.903 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: A 46 ARG cc_start: 0.7625 (mtm-85) cc_final: 0.7161 (mtp85) REVERT: A 307 THR cc_start: 0.9341 (m) cc_final: 0.9034 (p) REVERT: B 57 MET cc_start: 0.8804 (mmt) cc_final: 0.8439 (mmt) REVERT: B 223 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8564 (p0) REVERT: B 382 MET cc_start: 0.8462 (tpt) cc_final: 0.7696 (tpt) REVERT: C 94 ARG cc_start: 0.6345 (mtt180) cc_final: 0.5834 (ttm170) REVERT: D 44 MET cc_start: 0.8399 (tpt) cc_final: 0.7966 (tpt) REVERT: D 99 LYS cc_start: 0.8384 (mttt) cc_final: 0.8141 (mttt) REVERT: F 285 MET cc_start: 0.7864 (mmm) cc_final: 0.7628 (mmm) REVERT: F 312 ARG cc_start: 0.3930 (ttp-170) cc_final: 0.3043 (mmm160) REVERT: F 397 GLU cc_start: 0.6866 (mm-30) cc_final: 0.5419 (pm20) outliers start: 23 outliers final: 21 residues processed: 203 average time/residue: 0.5851 time to fit residues: 179.0337 Evaluate side-chains 203 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 336 HIS Chi-restraints excluded: chain F residue 352 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15533 Z= 0.303 Angle : 0.512 8.432 21042 Z= 0.263 Chirality : 0.040 0.145 2371 Planarity : 0.004 0.034 2614 Dihedral : 9.558 170.736 2488 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.98 % Allowed : 18.24 % Favored : 79.78 % 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: 0.29 (0.19), residues: 1908 helix: 1.10 (0.18), residues: 885 sheet: -0.74 (0.38), residues: 182 loop : -0.49 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS E 3 PHE 0.019 0.001 PHE F 11 TYR 0.013 0.001 TYR B 360 ARG 0.002 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 216 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 185 time to evaluate : 2.344 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: A 46 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7144 (mtp85) REVERT: A 307 THR cc_start: 0.9354 (m) cc_final: 0.9044 (p) REVERT: B 57 MET cc_start: 0.8811 (mmt) cc_final: 0.8444 (mmt) REVERT: B 223 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8590 (p0) REVERT: B 382 MET cc_start: 0.8587 (tpt) cc_final: 0.7804 (tpt) REVERT: C 94 ARG cc_start: 0.6292 (mtt180) cc_final: 0.5968 (ttm170) REVERT: D 44 MET cc_start: 0.8404 (tpt) cc_final: 0.7947 (tpt) REVERT: D 90 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7034 (mp) REVERT: F 285 MET cc_start: 0.7911 (mmm) cc_final: 0.7682 (mmm) REVERT: F 312 ARG cc_start: 0.3937 (ttp-170) cc_final: 0.3029 (mmm160) REVERT: F 397 GLU cc_start: 0.6939 (mm-30) cc_final: 0.5540 (pm20) outliers start: 31 outliers final: 27 residues processed: 210 average time/residue: 0.6064 time to fit residues: 194.1132 Evaluate side-chains 209 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 93 TYR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 258 CYS Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 326 LEU Chi-restraints excluded: chain F residue 336 HIS Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 377 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.149799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.105034 restraints weight = 67707.115| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.44 r_work: 0.3270 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15533 Z= 0.212 Angle : 0.474 5.569 21042 Z= 0.243 Chirality : 0.040 0.148 2371 Planarity : 0.003 0.035 2614 Dihedral : 9.387 166.264 2488 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.59 % Allowed : 18.75 % Favored : 79.66 % 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 (0.20), residues: 1908 helix: 1.24 (0.18), residues: 878 sheet: -0.57 (0.40), residues: 168 loop : -0.45 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 103 HIS 0.002 0.001 HIS A 215 PHE 0.019 0.001 PHE F 11 TYR 0.012 0.001 TYR B 360 ARG 0.001 0.000 ARG A 318 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6316.05 seconds wall clock time: 112 minutes 11.29 seconds (6731.29 seconds total)