Starting phenix.real_space_refine on Fri Feb 16 08:29:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk4_33243/02_2024/7xk4_33243_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk4_33243/02_2024/7xk4_33243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk4_33243/02_2024/7xk4_33243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk4_33243/02_2024/7xk4_33243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk4_33243/02_2024/7xk4_33243_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk4_33243/02_2024/7xk4_33243_updated.pdb" } resolution = 3.1 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= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 4 7.16 5 P 6 5.49 5 S 92 5.16 5 C 9608 2.51 5 N 2409 2.21 5 O 2714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "D PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E GLU 95": "OE1" <-> "OE2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 206": "OE1" <-> "OE2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F GLU 329": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14834 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3421 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Conformer: "B" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} bond proxies already assigned to first conformer: 3474 Chain: "B" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2964 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 14, 'TRANS': 372} Chain: "C" Number of atoms: 1902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1902 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "D" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1562 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "E" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1511 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "F" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3153 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 383} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 194 Unusual residues: {'FMN': 1, 'LMT': 1, 'PEE': 2, 'RBF': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 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 10059 SG CYS E 26 44.968 71.154 67.325 1.00 30.11 S ATOM 8454 SG CYS D 29 43.216 68.000 63.365 1.00 31.69 S ATOM 10781 SG CYS E 120 41.788 71.960 60.755 1.00 37.71 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA A 338 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA A 338 " occ=0.50 Time building chain proxies: 10.67, per 1000 atoms: 0.72 Number of scatterers: 14834 At special positions: 0 Unit cell: (90.64, 124.96, 154.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 1 19.99 S 92 16.00 P 6 15.00 O 2714 8.00 N 2409 7.00 C 9608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.60 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 301 " pdb="FE2 FES D 301 " - pdb=" SG CYS D 29 " pdb="FE2 FES D 301 " - pdb=" SG CYS E 120 " pdb="FE1 FES D 301 " - pdb=" SG CYS E 26 " pdb="FE1 FES D 301 " - pdb=" SG CYS D 112 " pdb=" FES F 501 " pdb="FE1 FES F 501 " - pdb=" SG CYS F 111 " Number of angles added : 7 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3422 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 14 sheets defined 44.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 109 through 112 Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 163 through 167 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 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' 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 419 through 423 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'B' and resid 28 through 33 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 96 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 118 through 150 removed outlier: 3.616A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 159 through 168 Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 204 through 215 removed outlier: 3.597A pdb=" N ARG B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 4.089A pdb=" N ALA B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 277 through 289 removed outlier: 4.099A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.899A 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 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 327 through 330 No H-bonds generated for 'chain 'B' and resid 327 through 330' Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 354 through 373 removed outlier: 3.722A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 409 removed outlier: 3.658A pdb=" N ILE B 386 " --> pdb=" O MET B 382 " (cutoff:3.500A) Proline residue: B 394 - end of helix removed outlier: 3.755A pdb=" N ARG B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 53 removed outlier: 3.514A pdb=" N THR C 11 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ASP C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LYS C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 183 through 189 removed outlier: 4.130A pdb=" N TRP C 189 " --> pdb=" O TRP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 238 Processing helix chain 'C' and resid 245 through 253 Processing helix chain 'D' and resid 9 through 16 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' 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 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 38 through 61 Processing helix chain 'D' and resid 71 through 93 removed outlier: 3.755A pdb=" N ALA D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 removed outlier: 3.579A pdb=" N GLN D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 108 removed outlier: 4.435A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'D' and resid 127 through 157 removed outlier: 3.844A pdb=" N VAL D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 185 through 201 removed outlier: 3.718A pdb=" N PHE D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.596A pdb=" N SER E 6 " --> pdb=" O GLU E 2 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU E 7 " --> pdb=" O HIS E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 35 through 62 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 76 through 101 removed outlier: 4.722A pdb=" N PHE E 80 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE E 81 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE E 101 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 removed outlier: 5.642A pdb=" N ILE E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 136 through 166 removed outlier: 4.135A pdb=" N LYS E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 4.937A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 29 removed outlier: 3.976A pdb=" N PHE F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 62 Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'F' and resid 100 through 105 removed outlier: 3.649A pdb=" N ARG F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 100 through 105' 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 189 through 195 Processing helix chain 'F' and resid 244 through 251 Processing helix chain 'F' and resid 282 through 297 removed outlier: 4.054A pdb=" N MET F 285 " --> pdb=" O GLY F 282 " (cutoff:3.500A) Proline residue: F 287 - end of helix removed outlier: 3.566A pdb=" N PHE F 293 " --> pdb=" O SER F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 316 No H-bonds generated for 'chain 'F' and resid 314 through 316' Processing helix chain 'F' and resid 320 through 329 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 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 393 Processing sheet with id= A, first strand: chain 'A' and resid 2 through 4 Processing sheet with id= B, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.619A pdb=" N SER A 89 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.876A 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: 6.970A 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: 6.525A pdb=" N ALA A 148 " --> pdb=" O TRP A 237 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE A 239 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N PHE A 150 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS A 188 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 151 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR A 190 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 306 through 308 removed outlier: 5.750A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N SER A 17 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N ARG A 276 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 12.785A pdb=" N VAL A 19 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 14.228A pdb=" N VAL A 278 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 14.295A pdb=" N SER A 21 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.587A pdb=" N ASP C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 14.616A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.571A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR C 125 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASP C 129 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N THR C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 169 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU C 165 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= H, first strand: chain 'C' and resid 204 through 206 Processing sheet with id= I, first strand: chain 'F' and resid 35 through 38 Processing sheet with id= J, first strand: chain 'F' and resid 107 through 109 removed outlier: 3.820A pdb=" N LYS F 82 " --> pdb=" O GLU F 122 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP F 120 " --> pdb=" O LYS F 84 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 223 through 229 removed outlier: 3.577A pdb=" N ILE F 224 " --> pdb=" O LEU F 152 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA F 153 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL F 137 " --> pdb=" O ALA F 153 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 208 through 213 removed outlier: 4.480A pdb=" N GLN F 169 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N GLY F 262 " --> pdb=" O GLN F 169 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLU F 171 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE F 260 " --> pdb=" O GLU F 171 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 175 through 178 Processing sheet with id= N, first strand: chain 'F' and resid 333 through 339 removed outlier: 6.923A pdb=" N MET F 305 " --> pdb=" O VAL F 334 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N HIS F 336 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N TYR F 307 " --> pdb=" O HIS F 336 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ALA F 338 " --> pdb=" O TYR F 307 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR F 309 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET F 276 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N TRP F 308 " --> pdb=" O MET F 276 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE F 278 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N GLY F 310 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY F 280 " --> pdb=" O GLY F 310 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLU F 374 " --> pdb=" O VAL F 277 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE F 279 " --> pdb=" O GLU F 374 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR F 376 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY F 281 " --> pdb=" O TYR F 376 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS F 378 " --> pdb=" O GLY F 281 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 6.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.36: 4709 1.36 - 1.57: 10292 1.57 - 1.78: 12 1.78 - 1.99: 152 1.99 - 2.20: 8 Bond restraints: 15173 Sorted by residual: bond pdb=" CA SER B 239 " pdb=" CB SER B 239 " ideal model delta sigma weight residual 1.536 1.420 0.116 1.42e-02 4.96e+03 6.69e+01 bond pdb=" C4A RBF B 502 " pdb=" N5 RBF B 502 " ideal model delta sigma weight residual 1.288 1.450 -0.162 2.00e-02 2.50e+03 6.57e+01 bond pdb=" C10 RBF B 502 " pdb=" N1 RBF B 502 " ideal model delta sigma weight residual 1.304 1.462 -0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" C5A RBF B 502 " pdb=" N5 RBF B 502 " ideal model delta sigma weight residual 1.350 1.490 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" CA SER C 228 " pdb=" CB SER C 228 " ideal model delta sigma weight residual 1.531 1.423 0.107 1.59e-02 3.96e+03 4.57e+01 ... (remaining 15168 not shown) Histogram of bond angle deviations from ideal: 88.71 - 97.83: 10 97.83 - 106.96: 530 106.96 - 116.08: 9501 116.08 - 125.20: 10269 125.20 - 134.33: 260 Bond angle restraints: 20570 Sorted by residual: angle pdb=" S1 FES F 501 " pdb="FE2 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 90.85 13.48 1.14e+00 7.69e-01 1.40e+02 angle pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " pdb="FE2 FES F 501 " ideal model delta sigma weight residual 75.66 89.09 -13.43 1.14e+00 7.69e-01 1.39e+02 angle pdb="FE1 FES D 301 " pdb=" S2 FES D 301 " pdb="FE2 FES D 301 " ideal model delta sigma weight residual 75.66 88.74 -13.08 1.14e+00 7.69e-01 1.32e+02 angle pdb=" S1 FES D 301 " pdb="FE2 FES D 301 " pdb=" S2 FES D 301 " ideal model delta sigma weight residual 104.33 91.32 13.01 1.14e+00 7.69e-01 1.30e+02 angle pdb=" S1 FES F 501 " pdb="FE1 FES F 501 " pdb=" S2 FES F 501 " ideal model delta sigma weight residual 104.33 90.85 13.48 1.20e+00 6.94e-01 1.26e+02 ... (remaining 20565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 8803 35.47 - 70.93: 208 70.93 - 106.40: 9 106.40 - 141.87: 10 141.87 - 177.34: 4 Dihedral angle restraints: 9034 sinusoidal: 3668 harmonic: 5366 Sorted by residual: dihedral pdb=" C10 FMN B 501 " pdb=" C1' FMN B 501 " pdb=" N10 FMN B 501 " pdb=" C2' FMN B 501 " ideal model delta sinusoidal sigma weight residual -102.41 74.93 -177.34 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C10 FMN C 301 " pdb=" C1' FMN C 301 " pdb=" N10 FMN C 301 " pdb=" C2' FMN C 301 " ideal model delta sinusoidal sigma weight residual -102.41 60.89 -163.30 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C PRO B 217 " pdb=" N PRO B 217 " pdb=" CA PRO B 217 " pdb=" CB PRO B 217 " ideal model delta harmonic sigma weight residual -120.70 -105.90 -14.80 0 2.50e+00 1.60e-01 3.51e+01 ... (remaining 9031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2171 0.095 - 0.189: 127 0.189 - 0.284: 17 0.284 - 0.379: 3 0.379 - 0.473: 5 Chirality restraints: 2323 Sorted by residual: chirality pdb=" CA PRO C 174 " pdb=" N PRO C 174 " pdb=" C PRO C 174 " pdb=" CB PRO C 174 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CA ILE B 272 " pdb=" N ILE B 272 " pdb=" C ILE B 272 " pdb=" CB ILE B 272 " both_signs ideal model delta sigma weight residual False 2.43 2.00 0.44 2.00e-01 2.50e+01 4.73e+00 chirality pdb=" CA THR C 173 " pdb=" N THR C 173 " pdb=" C THR C 173 " pdb=" CB THR C 173 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.16e+00 ... (remaining 2320 not shown) Planarity restraints: 2571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " 0.057 2.00e-02 2.50e+03 2.34e-02 2.61e+01 pdb=" C10 FMN C 301 " 0.007 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " -0.024 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " 0.013 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " 0.013 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " 0.012 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " 0.012 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " -0.015 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " -0.032 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " -0.017 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " -0.015 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " 0.011 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " 0.011 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " -0.002 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " -0.005 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " -0.009 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " 0.012 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " -0.055 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 210 " 0.017 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C ALA B 210 " -0.062 2.00e-02 2.50e+03 pdb=" O ALA B 210 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE B 211 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN B 501 " -0.017 2.00e-02 2.50e+03 1.55e-02 1.15e+01 pdb=" C10 FMN B 501 " -0.005 2.00e-02 2.50e+03 pdb=" C2 FMN B 501 " 0.009 2.00e-02 2.50e+03 pdb=" C4 FMN B 501 " 0.003 2.00e-02 2.50e+03 pdb=" C4A FMN B 501 " -0.001 2.00e-02 2.50e+03 pdb=" C5A FMN B 501 " -0.020 2.00e-02 2.50e+03 pdb=" C6 FMN B 501 " -0.016 2.00e-02 2.50e+03 pdb=" C7 FMN B 501 " 0.009 2.00e-02 2.50e+03 pdb=" C7M FMN B 501 " 0.015 2.00e-02 2.50e+03 pdb=" C8 FMN B 501 " 0.012 2.00e-02 2.50e+03 pdb=" C8M FMN B 501 " 0.031 2.00e-02 2.50e+03 pdb=" C9 FMN B 501 " -0.011 2.00e-02 2.50e+03 pdb=" C9A FMN B 501 " -0.012 2.00e-02 2.50e+03 pdb=" N1 FMN B 501 " 0.002 2.00e-02 2.50e+03 pdb=" N10 FMN B 501 " -0.019 2.00e-02 2.50e+03 pdb=" N3 FMN B 501 " 0.002 2.00e-02 2.50e+03 pdb=" N5 FMN B 501 " -0.023 2.00e-02 2.50e+03 pdb=" O2 FMN B 501 " 0.028 2.00e-02 2.50e+03 pdb=" O4 FMN B 501 " 0.011 2.00e-02 2.50e+03 ... (remaining 2568 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 819 2.72 - 3.27: 14434 3.27 - 3.81: 23519 3.81 - 4.36: 30020 4.36 - 4.90: 52123 Nonbonded interactions: 120915 Sorted by model distance: nonbonded pdb=" O SER F 68 " pdb=" NE2 GLN F 169 " model vdw 2.180 2.520 nonbonded pdb=" ND2 ASN C 40 " pdb=" O ALA D 92 " model vdw 2.223 2.520 nonbonded pdb=" O SER A 289 " pdb=" OG SER A 289 " model vdw 2.231 2.440 nonbonded pdb=" OE2 GLU F 275 " pdb=" OH TYR F 363 " model vdw 2.250 2.440 nonbonded pdb=" O4' FMN B 501 " pdb=" O5' FMN B 501 " model vdw 2.254 2.432 ... (remaining 120910 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.770 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 46.540 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.162 15173 Z= 0.468 Angle : 0.993 17.846 20570 Z= 0.599 Chirality : 0.054 0.473 2323 Planarity : 0.005 0.060 2571 Dihedral : 16.208 177.336 5612 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.50 % Favored : 97.40 % Rotamer: Outliers : 0.71 % Allowed : 3.70 % Favored : 95.59 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.17), residues: 1885 helix: -0.80 (0.16), residues: 841 sheet: -1.49 (0.36), residues: 162 loop : -2.20 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.030 0.002 PHE B 213 TYR 0.018 0.001 TYR F 217 ARG 0.005 0.000 ARG B 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 236 time to evaluate : 1.607 Fit side-chains REVERT: A 77 VAL cc_start: 0.8514 (p) cc_final: 0.8307 (m) REVERT: A 343 ASN cc_start: 0.8055 (m-40) cc_final: 0.7837 (p0) REVERT: B 224 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8568 (mp) REVERT: C 172 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: D 44 MET cc_start: 0.8987 (tpt) cc_final: 0.8562 (tpt) REVERT: E 51 ILE cc_start: 0.8541 (mt) cc_final: 0.8333 (mt) REVERT: F 20 LEU cc_start: 0.8003 (mt) cc_final: 0.7786 (mt) outliers start: 11 outliers final: 4 residues processed: 245 average time/residue: 0.2628 time to fit residues: 95.7237 Evaluate side-chains 193 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 187 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 209 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 109 GLN A 215 HIS B 178 GLN B 219 GLN B 240 GLN B 243 GLN B 313 ASN C 37 GLN C 68 ASN C 116 GLN D 88 GLN D 100 GLN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 GLN E 16 ASN F 216 ASN F 227 ASN F 239 ASN F 244 GLN F 295 GLN F 332 ASN F 367 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15173 Z= 0.214 Angle : 0.534 8.162 20570 Z= 0.280 Chirality : 0.042 0.166 2323 Planarity : 0.005 0.055 2571 Dihedral : 13.821 178.891 2321 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.76 % Favored : 97.18 % Rotamer: Outliers : 1.56 % Allowed : 8.30 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.10 (0.18), residues: 1885 helix: 0.25 (0.18), residues: 842 sheet: -0.93 (0.38), residues: 160 loop : -1.67 (0.18), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.017 0.001 PHE D 50 TYR 0.017 0.001 TYR F 217 ARG 0.003 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 193 time to evaluate : 1.645 Fit side-chains REVERT: A 46 ARG cc_start: 0.7476 (ttm110) cc_final: 0.7129 (mtm-85) REVERT: A 170 GLN cc_start: 0.7381 (mt0) cc_final: 0.7171 (mt0) REVERT: D 44 MET cc_start: 0.8986 (tpt) cc_final: 0.8783 (tpp) REVERT: E 34 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8004 (mmtm) REVERT: E 95 GLU cc_start: 0.6634 (tt0) cc_final: 0.6420 (tt0) REVERT: F 360 TYR cc_start: 0.8108 (t80) cc_final: 0.7746 (t80) outliers start: 24 outliers final: 14 residues processed: 208 average time/residue: 0.2519 time to fit residues: 79.4407 Evaluate side-chains 200 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 186 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 242 GLN B 74 ASN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN F 112 GLN ** F 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN F 356 HIS F 367 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.073 15173 Z= 0.652 Angle : 0.769 9.467 20570 Z= 0.392 Chirality : 0.053 0.307 2323 Planarity : 0.006 0.079 2571 Dihedral : 13.844 174.303 2312 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.05 % Favored : 94.85 % Rotamer: Outliers : 2.33 % Allowed : 11.28 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.22 (0.18), residues: 1885 helix: 0.02 (0.18), residues: 842 sheet: -0.80 (0.39), residues: 160 loop : -1.61 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 103 HIS 0.006 0.002 HIS B 101 PHE 0.028 0.003 PHE E 28 TYR 0.022 0.003 TYR F 217 ARG 0.012 0.001 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 1.656 Fit side-chains REVERT: A 46 ARG cc_start: 0.7626 (ttm110) cc_final: 0.7232 (mtm-85) REVERT: C 110 GLN cc_start: 0.8429 (mt0) cc_final: 0.8109 (mt0) REVERT: E 34 LYS cc_start: 0.8471 (mtpp) cc_final: 0.8008 (mmtm) outliers start: 36 outliers final: 23 residues processed: 211 average time/residue: 0.2498 time to fit residues: 79.7241 Evaluate side-chains 199 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 133 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 405 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 169 optimal weight: 0.8980 chunk 179 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 160 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15173 Z= 0.157 Angle : 0.500 8.458 20570 Z= 0.261 Chirality : 0.041 0.178 2323 Planarity : 0.004 0.054 2571 Dihedral : 12.677 175.871 2312 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.56 % Rotamer: Outliers : 1.95 % Allowed : 12.84 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.52 (0.19), residues: 1885 helix: 0.76 (0.19), residues: 832 sheet: -0.63 (0.38), residues: 160 loop : -1.35 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.004 0.001 HIS B 46 PHE 0.017 0.001 PHE D 50 TYR 0.023 0.001 TYR F 248 ARG 0.002 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 1.527 Fit side-chains REVERT: A 46 ARG cc_start: 0.7506 (ttm110) cc_final: 0.7187 (mtm-85) REVERT: C 110 GLN cc_start: 0.8325 (mt0) cc_final: 0.7994 (mt0) REVERT: E 34 LYS cc_start: 0.8442 (mtpp) cc_final: 0.7973 (mmtm) outliers start: 30 outliers final: 19 residues processed: 206 average time/residue: 0.2375 time to fit residues: 74.2403 Evaluate side-chains 199 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 195 PHE Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.0970 chunk 102 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 161 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15173 Z= 0.158 Angle : 0.475 7.864 20570 Z= 0.247 Chirality : 0.041 0.175 2323 Planarity : 0.004 0.054 2571 Dihedral : 12.101 174.694 2312 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.35 % Favored : 96.60 % Rotamer: Outliers : 2.01 % Allowed : 13.49 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.08 (0.19), residues: 1885 helix: 1.14 (0.19), residues: 835 sheet: -0.49 (0.38), residues: 167 loop : -1.13 (0.19), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 103 HIS 0.004 0.001 HIS D 65 PHE 0.015 0.001 PHE B 213 TYR 0.023 0.001 TYR F 248 ARG 0.002 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 1.493 Fit side-chains REVERT: A 46 ARG cc_start: 0.7512 (ttm110) cc_final: 0.7214 (mtm-85) REVERT: C 110 GLN cc_start: 0.8288 (mt0) cc_final: 0.7974 (mt0) REVERT: E 17 MET cc_start: 0.7999 (ttm) cc_final: 0.7790 (ttm) REVERT: E 34 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8034 (mmtm) REVERT: E 95 GLU cc_start: 0.6516 (tt0) cc_final: 0.6219 (tt0) REVERT: F 131 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6949 (pttt) outliers start: 31 outliers final: 21 residues processed: 212 average time/residue: 0.2526 time to fit residues: 80.8700 Evaluate side-chains 203 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 131 LYS Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 405 ASP 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: 0.9990 chunk 35 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN F 175 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 15173 Z= 0.456 Angle : 0.635 9.128 20570 Z= 0.326 Chirality : 0.047 0.248 2323 Planarity : 0.005 0.054 2571 Dihedral : 12.611 178.430 2312 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.14 % Favored : 95.75 % Rotamer: Outliers : 2.40 % Allowed : 13.68 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.41 (0.19), residues: 1885 helix: 0.69 (0.18), residues: 838 sheet: -0.45 (0.40), residues: 153 loop : -1.16 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 103 HIS 0.005 0.001 HIS B 101 PHE 0.024 0.002 PHE E 28 TYR 0.025 0.002 TYR F 248 ARG 0.008 0.001 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 187 time to evaluate : 1.634 Fit side-chains REVERT: A 46 ARG cc_start: 0.7600 (ttm110) cc_final: 0.7220 (mtm-85) REVERT: C 110 GLN cc_start: 0.8414 (mt0) cc_final: 0.8057 (mt0) REVERT: E 34 LYS cc_start: 0.8459 (mtpp) cc_final: 0.7990 (mmtm) REVERT: F 108 ARG cc_start: 0.6795 (mtm-85) cc_final: 0.6449 (mtp180) outliers start: 37 outliers final: 30 residues processed: 214 average time/residue: 0.2446 time to fit residues: 79.5271 Evaluate side-chains 213 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 405 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 179 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.8501 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15173 Z= 0.233 Angle : 0.521 6.550 20570 Z= 0.271 Chirality : 0.043 0.235 2323 Planarity : 0.004 0.053 2571 Dihedral : 12.202 177.637 2312 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 2.27 % Allowed : 14.40 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 1885 helix: 0.93 (0.19), residues: 834 sheet: -0.40 (0.40), residues: 153 loop : -1.11 (0.19), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.018 0.001 PHE F 24 TYR 0.025 0.001 TYR F 248 ARG 0.004 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 1.576 Fit side-chains REVERT: A 46 ARG cc_start: 0.7571 (ttm110) cc_final: 0.7258 (mtm-85) REVERT: C 110 GLN cc_start: 0.8369 (mt0) cc_final: 0.8033 (mt0) REVERT: E 34 LYS cc_start: 0.8445 (mtpp) cc_final: 0.7976 (mmtm) REVERT: F 108 ARG cc_start: 0.6751 (mtm-85) cc_final: 0.6438 (mtp180) outliers start: 35 outliers final: 29 residues processed: 206 average time/residue: 0.2400 time to fit residues: 75.1742 Evaluate side-chains 207 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 405 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15173 Z= 0.264 Angle : 0.534 10.258 20570 Z= 0.275 Chirality : 0.043 0.223 2323 Planarity : 0.004 0.052 2571 Dihedral : 12.026 177.761 2310 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 2.33 % Allowed : 14.46 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.16 (0.19), residues: 1885 helix: 0.92 (0.19), residues: 842 sheet: -0.40 (0.40), residues: 154 loop : -1.03 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.018 0.001 PHE B 213 TYR 0.026 0.001 TYR F 248 ARG 0.005 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 1.718 Fit side-chains REVERT: A 46 ARG cc_start: 0.7566 (ttm110) cc_final: 0.7254 (mtm-85) REVERT: C 110 GLN cc_start: 0.8377 (mt0) cc_final: 0.8032 (mt0) REVERT: E 34 LYS cc_start: 0.8436 (mtpp) cc_final: 0.7969 (mmtm) REVERT: F 108 ARG cc_start: 0.6723 (mtm-85) cc_final: 0.6430 (mtp180) REVERT: F 257 LYS cc_start: 0.7565 (tptt) cc_final: 0.7219 (tptt) outliers start: 36 outliers final: 32 residues processed: 215 average time/residue: 0.2456 time to fit residues: 80.6171 Evaluate side-chains 218 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 186 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 405 ASP 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: 8.9990 chunk 156 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 158 optimal weight: 0.0470 chunk 166 optimal weight: 7.9990 overall best weight: 1.4882 ------------------------------------------------------------------------------- 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: 0.8497 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15173 Z= 0.238 Angle : 0.516 8.766 20570 Z= 0.267 Chirality : 0.042 0.226 2323 Planarity : 0.004 0.052 2571 Dihedral : 11.879 177.079 2310 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 2.20 % Allowed : 14.85 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.09 (0.19), residues: 1885 helix: 0.98 (0.19), residues: 839 sheet: -0.38 (0.40), residues: 156 loop : -1.00 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.003 0.001 HIS D 65 PHE 0.017 0.001 PHE B 213 TYR 0.025 0.001 TYR F 248 ARG 0.004 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 190 time to evaluate : 1.657 Fit side-chains REVERT: A 46 ARG cc_start: 0.7544 (ttm110) cc_final: 0.7239 (mtm-85) REVERT: C 110 GLN cc_start: 0.8369 (mt0) cc_final: 0.8027 (mt0) REVERT: D 50 PHE cc_start: 0.7393 (t80) cc_final: 0.6810 (m-10) REVERT: E 34 LYS cc_start: 0.8431 (mtpp) cc_final: 0.7955 (mmtm) REVERT: F 108 ARG cc_start: 0.6696 (mtm-85) cc_final: 0.6440 (mtp180) REVERT: F 257 LYS cc_start: 0.7523 (tptt) cc_final: 0.7174 (tptt) outliers start: 34 outliers final: 33 residues processed: 218 average time/residue: 0.2689 time to fit residues: 89.0071 Evaluate side-chains 219 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 186 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 154 GLU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 405 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 107 optimal weight: 0.0060 chunk 83 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 15 optimal weight: 0.0170 chunk 113 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 overall best weight: 0.9638 ------------------------------------------------------------------------------- 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: 0.8470 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15173 Z= 0.176 Angle : 0.485 8.086 20570 Z= 0.252 Chirality : 0.041 0.224 2323 Planarity : 0.004 0.052 2571 Dihedral : 11.572 175.120 2310 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.55 % Rotamer: Outliers : 2.20 % Allowed : 15.05 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.08 (0.19), residues: 1885 helix: 1.15 (0.19), residues: 842 sheet: -0.30 (0.40), residues: 156 loop : -0.93 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 103 HIS 0.004 0.001 HIS D 65 PHE 0.022 0.001 PHE F 24 TYR 0.025 0.001 TYR F 248 ARG 0.002 0.000 ARG A 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 1.629 Fit side-chains REVERT: A 46 ARG cc_start: 0.7501 (ttm110) cc_final: 0.7210 (mtm-85) REVERT: B 28 GLU cc_start: 0.5555 (OUTLIER) cc_final: 0.4565 (pm20) REVERT: C 110 GLN cc_start: 0.8313 (mt0) cc_final: 0.8014 (mt0) REVERT: D 50 PHE cc_start: 0.7304 (t80) cc_final: 0.6777 (m-10) REVERT: E 34 LYS cc_start: 0.8428 (mtpp) cc_final: 0.7961 (mmtm) REVERT: F 108 ARG cc_start: 0.6682 (mtm-85) cc_final: 0.6433 (mtp180) REVERT: F 257 LYS cc_start: 0.7539 (tptt) cc_final: 0.7229 (tptt) REVERT: F 360 TYR cc_start: 0.8047 (t80) cc_final: 0.7561 (t80) outliers start: 34 outliers final: 28 residues processed: 217 average time/residue: 0.2453 time to fit residues: 80.8818 Evaluate side-chains 219 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 190 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 GLU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 405 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 45 optimal weight: 0.3980 chunk 136 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.140721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.101657 restraints weight = 25886.691| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.83 r_work: 0.2873 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15173 Z= 0.274 Angle : 0.529 6.586 20570 Z= 0.274 Chirality : 0.043 0.225 2323 Planarity : 0.004 0.052 2571 Dihedral : 11.729 177.714 2310 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 2.08 % Allowed : 15.50 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.01 (0.19), residues: 1885 helix: 1.00 (0.19), residues: 843 sheet: -0.26 (0.40), residues: 154 loop : -0.93 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.004 0.001 HIS B 101 PHE 0.018 0.001 PHE B 213 TYR 0.026 0.001 TYR F 248 ARG 0.005 0.000 ARG A 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3273.54 seconds wall clock time: 60 minutes 16.15 seconds (3616.15 seconds total)