Starting phenix.real_space_refine on Wed Feb 21 08:53:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1v_15090/02_2024/8a1v_15090_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1v_15090/02_2024/8a1v_15090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1v_15090/02_2024/8a1v_15090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1v_15090/02_2024/8a1v_15090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1v_15090/02_2024/8a1v_15090_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1v_15090/02_2024/8a1v_15090_trim_updated.pdb" } resolution = 2.73 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= 0.000 sd= 0.002 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 P 6 5.49 5 S 90 5.16 5 Na 2 4.78 5 C 9637 2.51 5 N 2413 2.21 5 O 3110 1.98 5 H 14644 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "D TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29906 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6877 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Chain: "B" Number of atoms: 6063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6063 Classifications: {'peptide': 395} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 379} Chain: "C" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3774 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "D" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3154 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "E" Number of atoms: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3058 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 7, 'TRANS': 188} Chain: "F" Number of atoms: 6239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 6239 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 194 Unusual residues: {' NA': 2, '3PE': 2, 'FMN': 1, 'LMT': 1, 'RBF': 1, 'UQ2': 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "E" 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: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 186 Classifications: {'water': 186} Link IDs: {None: 185} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 140 Classifications: {'water': 140} Link IDs: {None: 139} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18378 SG CYS D 112 67.218 81.729 58.586 1.00 17.12 S ATOM 20270 SG CYS E 26 64.479 81.955 61.129 1.00 4.66 S ATOM 17045 SG CYS D 29 67.525 83.498 64.844 1.00 12.46 S ATOM 21775 SG CYS E 120 70.553 83.794 62.634 1.00 26.39 S ATOM 23956 SG CYS F 70 53.270 67.208 37.380 1.00 37.47 S ATOM 24005 SG CYS F 76 51.681 63.791 37.086 1.00 43.20 S ATOM 24039 SG CYS F 79 56.014 61.536 39.069 1.00 39.85 S ATOM 24523 SG CYS F 111 57.653 64.918 39.445 1.00 32.48 S Time building chain proxies: 14.68, per 1000 atoms: 0.49 Number of scatterers: 29906 At special positions: 0 Unit cell: (113.15, 134.137, 131.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 4 26.01 S 90 16.00 P 6 15.00 Na 2 11.00 O 3110 8.00 N 2413 7.00 C 9637 6.00 H 14644 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: 28.11 Conformation dependent library (CDL) restraints added in 3.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 202 " pdb="FE1 FES E 202 " - pdb=" SG CYS E 26 " pdb="FE2 FES E 202 " - pdb=" SG CYS D 29 " pdb="FE1 FES E 202 " - pdb=" SG CYS D 112 " pdb="FE2 FES E 202 " - pdb=" SG CYS E 120 " pdb=" FES F1502 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 76 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 79 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 111 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 70 " Number of angles added : 12 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3420 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 13 sheets defined 46.8% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 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 107 through 112 removed outlier: 4.356A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 163 through 169 removed outlier: 3.920A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 379 through 383 removed outlier: 3.621A pdb=" N VAL A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 379 through 383' Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 415 through 424 removed outlier: 5.190A pdb=" N LEU A 420 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'B' and resid 21 through 34 removed outlier: 3.665A pdb=" N ALA B 25 " --> pdb=" O GLU B 21 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 65 through 86 Processing helix chain 'B' and resid 90 through 98 Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.555A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 151 removed outlier: 3.709A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix removed outlier: 3.552A pdb=" N TRP B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 167 removed outlier: 3.705A pdb=" N SER B 163 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE B 164 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 165 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 190 Processing helix chain 'B' and resid 204 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 277 through 290 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 332 removed outlier: 3.754A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 354 through 374 Processing helix chain 'B' and resid 382 through 409 removed outlier: 3.829A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) 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: 3.578A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 46 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 183 through 189 removed outlier: 3.988A pdb=" N TRP C 189 " --> pdb=" O TRP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'D' and resid 9 through 14 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 38 through 61 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 68 through 92 removed outlier: 3.660A pdb=" N ARG D 71 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 104 removed outlier: 6.179A pdb=" N VAL D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'D' and resid 127 through 157 Processing helix chain 'D' and resid 179 through 182 Processing helix chain 'D' and resid 184 through 201 removed outlier: 3.671A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (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 removed outlier: 3.528A pdb=" N ILE E 43 " --> pdb=" O PHE E 39 " (cutoff:3.500A) Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 79 through 101 removed outlier: 3.682A pdb=" N ASP E 99 " --> pdb=" O GLU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 113 through 116 No H-bonds generated for 'chain 'E' and resid 113 through 116' Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'E' and resid 136 through 166 removed outlier: 3.591A pdb=" N LYS E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 4.686A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 29 removed outlier: 3.654A pdb=" N LYS F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 94 through 96 No H-bonds generated for 'chain 'F' and resid 94 through 96' Processing helix chain 'F' and resid 100 through 105 removed outlier: 3.692A pdb=" N GLU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 128 No H-bonds generated for 'chain 'F' and resid 125 through 128' Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 186 through 194 removed outlier: 4.638A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS F 194 " --> pdb=" O GLY F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 245 through 251 Processing helix chain 'F' and resid 282 through 296 Proline residue: F 287 - end of helix removed outlier: 3.524A pdb=" N LEU F 296 " --> pdb=" O PHE F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 329 Processing helix chain 'F' and resid 355 through 362 removed outlier: 4.684A pdb=" N TYR F 360 " --> pdb=" O HIS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 393 Processing helix chain 'F' and resid 398 through 400 No H-bonds generated for 'chain 'F' and resid 398 through 400' Processing sheet with id= A, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.420A pdb=" N LEU A 274 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.517A pdb=" N SER A 89 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU A 78 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.621A 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: 7.085A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 132 through 134 removed outlier: 6.664A pdb=" N LYS A 188 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL A 151 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR A 190 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.588A pdb=" N ASP C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.384A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 11.963A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU C 165 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 204 through 206 Processing sheet with id= G, first strand: chain 'F' and resid 47 through 49 removed outlier: 7.249A pdb=" N MET F 119 " --> pdb=" O SER F 38 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 80 through 82 Processing sheet with id= I, first strand: chain 'F' and resid 134 through 136 Processing sheet with id= J, first strand: chain 'F' and resid 147 through 150 Processing sheet with id= K, first strand: chain 'F' and resid 167 through 172 Processing sheet with id= L, first strand: chain 'F' and resid 175 through 178 Processing sheet with id= M, first strand: chain 'F' and resid 333 through 339 removed outlier: 6.767A pdb=" N MET F 305 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N MET F 276 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1689 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: 10.74 Time building geometry restraints manager: 28.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.10: 14631 1.10 - 1.37: 4891 1.37 - 1.65: 10179 1.65 - 1.93: 153 1.93 - 2.20: 8 Bond restraints: 29862 Sorted by residual: bond pdb=" ND2 ASN B 375 " pdb="HD21 ASN B 375 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" ND2 ASN B 375 " pdb="HD22 ASN B 375 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" O3P FAD F1501 " pdb=" P FAD F1501 " ideal model delta sigma weight residual 1.660 1.584 0.076 2.00e-02 2.50e+03 1.46e+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 1.37e+01 bond pdb=" O5' FAD F1501 " pdb=" P FAD F1501 " ideal model delta sigma weight residual 1.637 1.576 0.061 2.00e-02 2.50e+03 9.18e+00 ... (remaining 29857 not shown) Histogram of bond angle deviations from ideal: 75.48 - 87.18: 4 87.18 - 98.89: 0 98.89 - 110.59: 31006 110.59 - 122.29: 18772 122.29 - 133.99: 4182 Bond angle restraints: 53964 Sorted by residual: angle pdb=" C SER B 44 " pdb=" N SER B 45 " pdb=" CA SER B 45 " ideal model delta sigma weight residual 121.70 128.09 -6.39 1.80e+00 3.09e-01 1.26e+01 angle pdb=" C2 LMT D 301 " pdb=" C3 LMT D 301 " pdb=" C4 LMT D 301 " ideal model delta sigma weight residual 117.09 107.69 9.40 3.00e+00 1.11e-01 9.81e+00 angle pdb=" C2 LMT E 201 " pdb=" C3 LMT E 201 " pdb=" C4 LMT E 201 " ideal model delta sigma weight residual 117.09 107.76 9.33 3.00e+00 1.11e-01 9.68e+00 angle pdb=" C2 LMT B 603 " pdb=" C3 LMT B 603 " pdb=" C4 LMT B 603 " ideal model delta sigma weight residual 117.09 107.93 9.16 3.00e+00 1.11e-01 9.32e+00 angle pdb=" C VAL B 373 " pdb=" CA VAL B 373 " pdb=" CB VAL B 373 " ideal model delta sigma weight residual 111.65 107.55 4.10 1.41e+00 5.03e-01 8.47e+00 ... (remaining 53959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 13693 34.93 - 69.85: 470 69.85 - 104.78: 25 104.78 - 139.71: 6 139.71 - 174.64: 3 Dihedral angle restraints: 14197 sinusoidal: 7803 harmonic: 6394 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 72.23 -174.64 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C10 FMN B 606 " pdb=" C1' FMN B 606 " pdb=" N10 FMN B 606 " pdb=" C2' FMN B 606 " ideal model delta sinusoidal sigma weight residual 257.59 89.88 167.71 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' FMN C1000 " pdb=" O5' FMN C1000 " pdb=" P FMN C1000 " pdb=" O1P FMN C1000 " ideal model delta sinusoidal sigma weight residual 75.26 -141.85 -142.89 1 2.00e+01 2.50e-03 4.31e+01 ... (remaining 14194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1919 0.048 - 0.095: 294 0.095 - 0.143: 107 0.143 - 0.191: 2 0.191 - 0.238: 8 Chirality restraints: 2330 Sorted by residual: chirality pdb=" C4' LMT B 603 " pdb=" C3' LMT B 603 " pdb=" C5' LMT B 603 " pdb=" O1B LMT B 603 " both_signs ideal model delta sigma weight residual False -2.55 -2.79 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C4' LMT D 301 " pdb=" C3' LMT D 301 " pdb=" C5' LMT D 301 " pdb=" O1B LMT D 301 " both_signs ideal model delta sigma weight residual False -2.55 -2.77 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C5' LMT B 603 " pdb=" C4' LMT B 603 " pdb=" C6' LMT B 603 " pdb=" O5' LMT B 603 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 2327 not shown) Planarity restraints: 4373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 375 " -0.031 2.00e-02 2.50e+03 2.99e-02 1.34e+01 pdb=" CG ASN B 375 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN B 375 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN B 375 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 375 " -0.044 2.00e-02 2.50e+03 pdb="HD22 ASN B 375 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 375 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.42e+00 pdb=" N PRO B 376 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 376 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 376 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 70 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.45e+00 pdb=" N PRO A 71 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " 0.022 5.00e-02 4.00e+02 ... (remaining 4370 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1407 2.18 - 2.79: 60651 2.79 - 3.39: 87493 3.39 - 4.00: 117521 4.00 - 4.60: 179004 Nonbonded interactions: 446076 Sorted by model distance: nonbonded pdb=" H TYR F 167 " pdb=" O PHE F 264 " model vdw 1.578 1.850 nonbonded pdb="HH21 ARG B 372 " pdb=" OE1 GLU B 380 " model vdw 1.604 1.850 nonbonded pdb=" O GLY E 175 " pdb=" HG1 THR E 179 " model vdw 1.609 1.850 nonbonded pdb=" O PRO E 114 " pdb=" HG1 THR E 117 " model vdw 1.613 1.850 nonbonded pdb="HH22 ARG A 273 " pdb=" OE2 GLU A 290 " model vdw 1.633 1.850 ... (remaining 446071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.020 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: 0.560 Extract box with map and model: 8.800 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 109.350 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 : 0.003 0.076 15218 Z= 0.222 Angle : 0.538 9.397 20634 Z= 0.250 Chirality : 0.041 0.238 2330 Planarity : 0.003 0.046 2572 Dihedral : 15.901 174.636 5669 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.78 % Allowed : 8.35 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 1.02 (0.20), residues: 1880 helix: 1.48 (0.18), residues: 858 sheet: -0.34 (0.42), residues: 162 loop : 0.17 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS F 356 PHE 0.012 0.001 PHE B 213 TYR 0.009 0.001 TYR E 134 ARG 0.002 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 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. Evaluate side-chains 302 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 290 time to evaluate : 2.810 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 395 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7785 (mtt-85) REVERT: B 28 GLU cc_start: 0.5007 (tp30) cc_final: 0.4578 (mt-10) REVERT: B 261 MET cc_start: 0.8197 (tpp) cc_final: 0.7926 (tpp) REVERT: F 126 GLU cc_start: 0.3264 (tp30) cc_final: 0.2814 (mt-10) REVERT: F 200 TYR cc_start: 0.3025 (m-80) cc_final: 0.2771 (m-80) outliers start: 12 outliers final: 9 residues processed: 301 average time/residue: 2.4665 time to fit residues: 828.3569 Evaluate side-chains 168 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 401 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 9.9990 chunk 140 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 ASN B 324 ASN D 64 ASN D 75 GLN E 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15218 Z= 0.283 Angle : 0.583 7.640 20634 Z= 0.306 Chirality : 0.044 0.292 2330 Planarity : 0.005 0.066 2572 Dihedral : 12.730 176.128 2370 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.07 % Allowed : 13.92 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.42 (0.19), residues: 1880 helix: 1.00 (0.17), residues: 879 sheet: -0.82 (0.38), residues: 173 loop : -0.12 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 103 HIS 0.006 0.001 HIS F 356 PHE 0.022 0.002 PHE D 50 TYR 0.018 0.002 TYR D 141 ARG 0.008 0.001 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 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. Evaluate side-chains 199 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 167 time to evaluate : 2.611 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: A 39 MET cc_start: 0.7980 (tmm) cc_final: 0.7770 (tmm) REVERT: A 395 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8084 (mtt-85) REVERT: B 34 PHE cc_start: 0.6747 (m-10) cc_final: 0.6350 (m-80) REVERT: B 261 MET cc_start: 0.8188 (tpp) cc_final: 0.7960 (tpp) REVERT: C 253 ASP cc_start: 0.6203 (OUTLIER) cc_final: 0.5710 (p0) REVERT: E 71 GLU cc_start: 0.6215 (mp0) cc_final: 0.5968 (mp0) REVERT: F 126 GLU cc_start: 0.3389 (tp30) cc_final: 0.2906 (mt-10) REVERT: F 200 TYR cc_start: 0.2950 (m-80) cc_final: 0.2647 (m-80) outliers start: 32 outliers final: 17 residues processed: 193 average time/residue: 2.4089 time to fit residues: 527.2747 Evaluate side-chains 168 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 356 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 169 optimal weight: 0.0030 chunk 182 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 167 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 overall best weight: 2.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15218 Z= 0.253 Angle : 0.538 7.085 20634 Z= 0.279 Chirality : 0.043 0.362 2330 Planarity : 0.004 0.052 2572 Dihedral : 11.912 177.537 2365 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.94 % Allowed : 15.16 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.32 (0.19), residues: 1880 helix: 0.98 (0.17), residues: 876 sheet: -0.95 (0.38), residues: 173 loop : -0.25 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.007 0.001 HIS F 356 PHE 0.017 0.001 PHE B 213 TYR 0.018 0.002 TYR B 360 ARG 0.003 0.001 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 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. Evaluate side-chains 188 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8190 (mtt-85) REVERT: B 34 PHE cc_start: 0.6675 (m-10) cc_final: 0.6298 (m-80) REVERT: C 253 ASP cc_start: 0.6203 (OUTLIER) cc_final: 0.5655 (p0) REVERT: E 9 VAL cc_start: 0.7813 (OUTLIER) cc_final: 0.7609 (t) REVERT: F 126 GLU cc_start: 0.3281 (tp30) cc_final: 0.2869 (mt-10) REVERT: F 200 TYR cc_start: 0.2984 (m-80) cc_final: 0.2731 (m-80) REVERT: F 383 MET cc_start: 0.3255 (ttt) cc_final: 0.2652 (mmp) outliers start: 30 outliers final: 13 residues processed: 183 average time/residue: 2.1573 time to fit residues: 448.4610 Evaluate side-chains 161 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 356 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 179 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN F 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15218 Z= 0.205 Angle : 0.514 7.411 20634 Z= 0.266 Chirality : 0.042 0.390 2330 Planarity : 0.004 0.047 2572 Dihedral : 11.302 177.488 2362 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.55 % Allowed : 15.80 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.36 (0.19), residues: 1880 helix: 1.02 (0.18), residues: 881 sheet: -0.93 (0.38), residues: 175 loop : -0.24 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.007 0.001 HIS F 356 PHE 0.016 0.001 PHE B 213 TYR 0.017 0.001 TYR B 360 ARG 0.004 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 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. Evaluate side-chains 175 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8229 (mtt-85) REVERT: B 34 PHE cc_start: 0.6670 (m-10) cc_final: 0.6309 (m-80) REVERT: C 253 ASP cc_start: 0.6188 (OUTLIER) cc_final: 0.5659 (p0) REVERT: E 9 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7558 (t) REVERT: F 126 GLU cc_start: 0.3275 (tp30) cc_final: 0.2864 (mt-10) REVERT: F 200 TYR cc_start: 0.2896 (m-80) cc_final: 0.2668 (m-80) REVERT: F 305 MET cc_start: 0.5912 (mmt) cc_final: 0.5272 (mmt) outliers start: 24 outliers final: 15 residues processed: 172 average time/residue: 2.2174 time to fit residues: 432.7391 Evaluate side-chains 165 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 292 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 153 optimal weight: 30.0000 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 ASN F 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15218 Z= 0.306 Angle : 0.568 7.397 20634 Z= 0.294 Chirality : 0.044 0.393 2330 Planarity : 0.004 0.046 2572 Dihedral : 11.173 179.872 2362 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.20 % Allowed : 15.48 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.10 (0.19), residues: 1880 helix: 0.86 (0.17), residues: 879 sheet: -0.97 (0.38), residues: 171 loop : -0.47 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 103 HIS 0.012 0.001 HIS F 356 PHE 0.022 0.002 PHE B 213 TYR 0.019 0.002 TYR B 360 ARG 0.004 0.001 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 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. Evaluate side-chains 179 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8455 (mtt-85) REVERT: B 34 PHE cc_start: 0.6678 (m-10) cc_final: 0.6320 (m-80) REVERT: C 253 ASP cc_start: 0.6190 (OUTLIER) cc_final: 0.5639 (p0) REVERT: E 9 VAL cc_start: 0.7779 (OUTLIER) cc_final: 0.7571 (t) REVERT: F 126 GLU cc_start: 0.3265 (tp30) cc_final: 0.2796 (mt-10) REVERT: F 200 TYR cc_start: 0.2920 (m-80) cc_final: 0.2715 (m-80) REVERT: F 305 MET cc_start: 0.5900 (mmt) cc_final: 0.5449 (mmt) outliers start: 34 outliers final: 19 residues processed: 172 average time/residue: 2.2083 time to fit residues: 431.0709 Evaluate side-chains 162 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 199 HIS Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 292 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 149 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.0040 chunk 94 optimal weight: 9.9990 overall best weight: 3.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 ASN F 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15218 Z= 0.290 Angle : 0.561 7.650 20634 Z= 0.290 Chirality : 0.043 0.410 2330 Planarity : 0.004 0.046 2572 Dihedral : 11.030 179.635 2362 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.33 % Allowed : 15.61 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: -0.01 (0.19), residues: 1880 helix: 0.79 (0.17), residues: 880 sheet: -1.05 (0.38), residues: 171 loop : -0.54 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 103 HIS 0.010 0.001 HIS F 356 PHE 0.023 0.002 PHE D 50 TYR 0.017 0.002 TYR B 360 ARG 0.004 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 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. Evaluate side-chains 181 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8488 (mtt-85) REVERT: B 34 PHE cc_start: 0.6686 (m-10) cc_final: 0.6320 (m-80) REVERT: C 253 ASP cc_start: 0.6195 (OUTLIER) cc_final: 0.5679 (p0) REVERT: D 8 LYS cc_start: 0.3452 (tttt) cc_final: 0.3228 (tptt) REVERT: D 133 ASP cc_start: 0.6808 (OUTLIER) cc_final: 0.6004 (t0) REVERT: E 9 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7557 (t) REVERT: F 126 GLU cc_start: 0.3233 (tp30) cc_final: 0.2814 (mt-10) REVERT: F 305 MET cc_start: 0.5852 (mmt) cc_final: 0.5403 (mmt) outliers start: 36 outliers final: 20 residues processed: 174 average time/residue: 2.1855 time to fit residues: 431.8569 Evaluate side-chains 164 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 306 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15218 Z= 0.216 Angle : 0.524 7.775 20634 Z= 0.270 Chirality : 0.042 0.385 2330 Planarity : 0.004 0.045 2572 Dihedral : 10.736 179.311 2362 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.62 % Allowed : 16.65 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.14 (0.19), residues: 1880 helix: 0.93 (0.18), residues: 875 sheet: -1.05 (0.38), residues: 173 loop : -0.46 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.010 0.001 HIS F 356 PHE 0.021 0.001 PHE D 50 TYR 0.018 0.001 TYR B 360 ARG 0.002 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 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. Evaluate side-chains 168 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: A 395 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8407 (mtt-85) REVERT: B 34 PHE cc_start: 0.6643 (m-10) cc_final: 0.6298 (m-80) REVERT: C 253 ASP cc_start: 0.6171 (OUTLIER) cc_final: 0.5692 (p0) REVERT: D 8 LYS cc_start: 0.3419 (tttt) cc_final: 0.3210 (tptt) REVERT: D 133 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6049 (t0) REVERT: E 9 VAL cc_start: 0.7742 (OUTLIER) cc_final: 0.7530 (t) REVERT: F 126 GLU cc_start: 0.3259 (tp30) cc_final: 0.2871 (tt0) REVERT: F 305 MET cc_start: 0.5821 (mmt) cc_final: 0.5377 (mmt) outliers start: 25 outliers final: 14 residues processed: 163 average time/residue: 2.2900 time to fit residues: 421.6598 Evaluate side-chains 156 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 137 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 279 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15218 Z= 0.256 Angle : 0.540 7.882 20634 Z= 0.279 Chirality : 0.042 0.358 2330 Planarity : 0.004 0.045 2572 Dihedral : 10.696 179.880 2359 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.94 % Allowed : 16.52 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.06 (0.19), residues: 1880 helix: 0.85 (0.17), residues: 883 sheet: -1.01 (0.39), residues: 171 loop : -0.52 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 103 HIS 0.010 0.001 HIS F 356 PHE 0.024 0.002 PHE D 50 TYR 0.018 0.002 TYR B 360 ARG 0.004 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 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. Evaluate side-chains 168 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8424 (mtt-85) REVERT: B 22 LYS cc_start: 0.2222 (OUTLIER) cc_final: 0.1985 (mmmm) REVERT: B 34 PHE cc_start: 0.6658 (m-10) cc_final: 0.6315 (m-80) REVERT: C 253 ASP cc_start: 0.6230 (OUTLIER) cc_final: 0.5694 (p0) REVERT: D 8 LYS cc_start: 0.3525 (tttt) cc_final: 0.3148 (tptp) REVERT: D 133 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6005 (t0) REVERT: E 9 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7552 (t) REVERT: F 126 GLU cc_start: 0.3327 (tp30) cc_final: 0.2920 (tt0) REVERT: F 305 MET cc_start: 0.5840 (mmt) cc_final: 0.5346 (mmt) outliers start: 30 outliers final: 18 residues processed: 162 average time/residue: 2.3401 time to fit residues: 428.7232 Evaluate side-chains 158 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 292 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 158 optimal weight: 9.9990 chunk 166 optimal weight: 0.6980 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15218 Z= 0.280 Angle : 0.552 7.923 20634 Z= 0.286 Chirality : 0.043 0.338 2330 Planarity : 0.004 0.045 2572 Dihedral : 10.733 179.661 2359 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.94 % Allowed : 16.65 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: -0.01 (0.19), residues: 1880 helix: 0.80 (0.17), residues: 883 sheet: -1.08 (0.38), residues: 171 loop : -0.56 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 103 HIS 0.008 0.001 HIS F 356 PHE 0.025 0.002 PHE D 50 TYR 0.018 0.002 TYR B 360 ARG 0.004 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 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. Evaluate side-chains 167 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8462 (mtt-85) REVERT: B 22 LYS cc_start: 0.2239 (OUTLIER) cc_final: 0.1997 (mmmm) REVERT: B 34 PHE cc_start: 0.6623 (m-10) cc_final: 0.6303 (m-80) REVERT: C 253 ASP cc_start: 0.6194 (OUTLIER) cc_final: 0.5682 (p0) REVERT: D 8 LYS cc_start: 0.3478 (tttt) cc_final: 0.3108 (tptp) REVERT: D 133 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.6038 (t0) REVERT: E 9 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7575 (t) REVERT: F 126 GLU cc_start: 0.3342 (tp30) cc_final: 0.2920 (tt0) REVERT: F 305 MET cc_start: 0.5841 (mmt) cc_final: 0.5352 (mmt) outliers start: 30 outliers final: 21 residues processed: 163 average time/residue: 2.3156 time to fit residues: 427.0742 Evaluate side-chains 162 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 22 PHE Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 183 ASP Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 306 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 107 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 0.2980 chunk 185 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 147 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 overall best weight: 3.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15218 Z= 0.289 Angle : 0.561 7.708 20634 Z= 0.291 Chirality : 0.043 0.326 2330 Planarity : 0.004 0.046 2572 Dihedral : 10.776 179.384 2359 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.55 % Allowed : 16.90 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: -0.09 (0.19), residues: 1880 helix: 0.74 (0.17), residues: 886 sheet: -1.08 (0.39), residues: 171 loop : -0.62 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 103 HIS 0.010 0.001 HIS F 356 PHE 0.028 0.002 PHE D 50 TYR 0.018 0.002 TYR B 360 ARG 0.005 0.001 ARG C 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 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. Evaluate side-chains 160 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 2.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 395 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8476 (mtt-85) REVERT: B 22 LYS cc_start: 0.2232 (OUTLIER) cc_final: 0.1981 (mmmm) REVERT: B 34 PHE cc_start: 0.6683 (m-10) cc_final: 0.6352 (m-80) REVERT: C 198 ASN cc_start: 0.6108 (t0) cc_final: 0.5908 (p0) REVERT: C 253 ASP cc_start: 0.6196 (OUTLIER) cc_final: 0.5557 (p0) REVERT: D 8 LYS cc_start: 0.3646 (tttt) cc_final: 0.3223 (tptp) REVERT: D 133 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6036 (t0) REVERT: E 9 VAL cc_start: 0.7785 (OUTLIER) cc_final: 0.7584 (t) REVERT: F 126 GLU cc_start: 0.3288 (tp30) cc_final: 0.2872 (tt0) outliers start: 24 outliers final: 17 residues processed: 156 average time/residue: 2.3985 time to fit residues: 428.5114 Evaluate side-chains 154 residues out of total 1544 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 4.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 34 LYS Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 306 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.094403 restraints weight = 59666.044| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.89 r_work: 0.2993 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15218 Z= 0.227 Angle : 0.532 8.025 20634 Z= 0.275 Chirality : 0.042 0.307 2330 Planarity : 0.004 0.073 2572 Dihedral : 10.598 179.806 2359 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.68 % Allowed : 16.90 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.06 % 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: 0.05 (0.19), residues: 1880 helix: 0.85 (0.18), residues: 887 sheet: -1.02 (0.39), residues: 171 loop : -0.55 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.010 0.001 HIS F 356 PHE 0.024 0.001 PHE D 50 TYR 0.018 0.001 TYR B 360 ARG 0.013 0.000 ARG C 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9301.88 seconds wall clock time: 166 minutes 15.85 seconds (9975.85 seconds total)