Starting phenix.real_space_refine on Fri Feb 16 08:30:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk5_33244/02_2024/7xk5_33244_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk5_33244/02_2024/7xk5_33244.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/7xk5_33244/02_2024/7xk5_33244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk5_33244/02_2024/7xk5_33244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk5_33244/02_2024/7xk5_33244_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xk5_33244/02_2024/7xk5_33244_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= 0.091 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 34": "OE1" <-> "OE2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "E ARG 100": "NH1" <-> "NH2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E ARG 174": "NH1" <-> "NH2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 102": "OE1" <-> "OE2" Residue "F GLU 107": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F GLU 186": "OE1" <-> "OE2" Residue "F GLU 206": "OE1" <-> "OE2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F GLU 316": "OE1" <-> "OE2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F GLU 361": "OE1" <-> "OE2" Residue "F GLU 368": "OE1" <-> "OE2" Residue "F GLU 374": "OE1" <-> "OE2" 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: 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': 1, 'PTRANS': 22, 'TRANS': 422} Conformer: "B" Number of residues, atoms: 446, 3416 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, '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 9093 SG CYS D 112 42.766 75.174 64.039 1.00 43.00 S ATOM 10059 SG CYS E 26 44.768 71.143 65.164 1.00 32.42 S ATOM 8454 SG CYS D 29 43.082 68.001 61.049 1.00 37.23 S ATOM 10781 SG CYS E 120 41.531 71.815 58.684 1.00 38.33 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: 10.14, per 1000 atoms: 0.68 Number of scatterers: 14834 At special positions: 0 Unit cell: (92.4, 124.08, 152.24, 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: 5.83 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 301 " pdb="FE2 FES D 301 " - pdb=" SG CYS D 29 " pdb="FE1 FES D 301 " - pdb=" SG CYS E 26 " pdb="FE1 FES D 301 " - pdb=" SG CYS D 112 " pdb="FE2 FES D 301 " - pdb=" SG CYS E 120 " pdb=" FES F 501 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 79 " pdb="FE2 FES F 501 " - pdb=" SG CYS F 70 " Number of angles added : 9 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: 80 helices and 15 sheets defined 44.9% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 163 through 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 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 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 390 through 398 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 34 removed outlier: 4.671A pdb=" N LEU B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 86 removed outlier: 4.038A pdb=" N VAL B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE B 65 " --> pdb=" O TRP B 61 " (cutoff:3.500A) Proline residue: B 66 - end of helix Processing helix chain 'B' and resid 90 through 96 removed outlier: 3.584A pdb=" N ALA B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 118 through 150 removed outlier: 3.615A pdb=" N LEU B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 3.653A 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 204 through 215 Processing helix chain 'B' and resid 240 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 289 removed outlier: 4.123A pdb=" N PHE B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.937A 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 332 removed outlier: 3.549A pdb=" N LEU B 331 " --> pdb=" O TRP B 327 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 332' Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 354 through 374 removed outlier: 3.948A pdb=" N TRP B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 409 Proline residue: B 394 - end of helix removed outlier: 3.813A pdb=" N ARG B 407 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 32 Processing helix chain 'C' and resid 34 through 53 removed outlier: 3.983A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'C' and resid 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: 3.993A pdb=" N TRP C 189 " --> pdb=" O TRP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 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 28 through 33 Processing helix chain 'D' and resid 38 through 61 Processing helix chain 'D' and resid 71 through 93 removed outlier: 3.879A pdb=" N ILE D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 102 through 108 removed outlier: 4.475A pdb=" N GLY D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 108 " --> pdb=" O PHE D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'D' and resid 122 through 124 No H-bonds generated for 'chain 'D' and resid 122 through 124' Processing helix chain 'D' and resid 127 through 157 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 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: 3.511A pdb=" N PHE D 201 " --> pdb=" O ALA D 197 " (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 2 through 13 removed outlier: 3.595A pdb=" N SER E 6 " --> pdb=" O GLU E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 35 through 63 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 76 through 100 removed outlier: 3.557A pdb=" N ASN E 79 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE E 80 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 81 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 100 " --> pdb=" O ILE E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 removed outlier: 5.303A pdb=" N ILE E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) removed outlier: 5.774A 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 165 removed outlier: 4.222A pdb=" N LYS E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 4.952A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N PHE E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 28 removed outlier: 3.552A 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 95 No H-bonds generated for 'chain 'F' and resid 92 through 95' Processing helix chain 'F' and resid 102 through 105 No H-bonds generated for 'chain 'F' and resid 102 through 105' Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'F' and resid 186 through 194 removed outlier: 4.858A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (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 244 through 251 Processing helix chain 'F' and resid 282 through 297 removed outlier: 3.820A pdb=" N MET F 285 " --> pdb=" O GLY F 282 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA F 286 " --> pdb=" O ALA F 283 " (cutoff:3.500A) Proline residue: F 287 - end of helix removed outlier: 3.559A pdb=" N PHE F 293 " --> pdb=" O SER F 290 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS F 297 " --> pdb=" O ASP F 294 " (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 355 through 362 Processing helix chain 'F' and resid 381 through 394 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 30 removed outlier: 3.668A pdb=" N SER A 89 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 78 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.673A 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: 7.208A 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: 6.807A pdb=" N LYS A 188 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL A 151 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.222A 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: 5.892A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL A 323 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N SER A 263 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL A 325 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA A 265 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 9.267A pdb=" N ARG A 327 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N SER A 17 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N ARG A 276 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 12.452A pdb=" N VAL A 19 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 14.448A pdb=" N VAL A 278 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 14.211A pdb=" N SER A 21 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 71 through 77 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 135 through 138 Processing sheet with id= I, first strand: chain 'C' and resid 141 through 143 Processing sheet with id= J, first strand: chain 'C' and resid 204 through 206 Processing sheet with id= K, first strand: chain 'F' and resid 35 through 38 Processing sheet with id= L, first strand: chain 'F' and resid 133 through 136 removed outlier: 4.013A pdb=" N THR F 259 " --> pdb=" O GLU F 171 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU F 171 " --> pdb=" O THR F 259 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 147 through 153 Processing sheet with id= N, first strand: chain 'F' and resid 175 through 178 Processing sheet with id= O, first strand: chain 'F' and resid 401 through 404 removed outlier: 6.694A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP F 404 " --> pdb=" O TYR F 375 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N MET F 377 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL F 334 " --> pdb=" O MET F 305 " (cutoff:3.500A) 586 hydrogen bonds defined for protein. 1656 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: 4.06 Time building geometry restraints manager: 6.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.37: 4840 1.37 - 1.58: 10163 1.58 - 1.78: 11 1.78 - 1.99: 151 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 1.407 0.129 1.42e-02 4.96e+03 8.19e+01 bond pdb=" C4A RBF B 502 " pdb=" N5 RBF B 502 " ideal model delta sigma weight residual 1.288 1.448 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" C10 RBF B 502 " pdb=" N1 RBF B 502 " ideal model delta sigma weight residual 1.304 1.461 -0.157 2.00e-02 2.50e+03 6.17e+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 4.87e+01 bond pdb=" CA SER C 228 " pdb=" CB SER C 228 " ideal model delta sigma weight residual 1.532 1.427 0.106 1.53e-02 4.27e+03 4.79e+01 ... (remaining 15168 not shown) Histogram of bond angle deviations from ideal: 88.71 - 97.89: 11 97.89 - 107.06: 516 107.06 - 116.23: 9597 116.23 - 125.40: 10193 125.40 - 134.57: 253 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 90.77 13.56 1.14e+00 7.69e-01 1.42e+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 89.19 -13.53 1.14e+00 7.69e-01 1.41e+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 88.71 -13.05 1.14e+00 7.69e-01 1.31e+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 91.28 13.05 1.14e+00 7.69e-01 1.31e+02 angle pdb="FE1 FES F 501 " pdb=" S1 FES F 501 " pdb="FE2 FES F 501 " ideal model delta sigma weight residual 75.66 89.26 -13.60 1.20e+00 6.94e-01 1.28e+02 ... (remaining 20565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 8818 35.92 - 71.84: 192 71.84 - 107.76: 12 107.76 - 143.68: 7 143.68 - 179.60: 5 Dihedral angle restraints: 9034 sinusoidal: 3668 harmonic: 5366 Sorted by residual: dihedral pdb=" CA HIS A 215 " pdb=" C HIS A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta harmonic sigma weight residual 180.00 127.01 52.99 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" C THR C 227 " pdb=" N THR C 227 " pdb=" CA THR C 227 " pdb=" CB THR C 227 " ideal model delta harmonic sigma weight residual -122.00 -100.80 -21.20 0 2.50e+00 1.60e-01 7.19e+01 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 257.59 78.00 179.60 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 9031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2244 0.113 - 0.226: 70 0.226 - 0.339: 4 0.339 - 0.452: 3 0.452 - 0.565: 2 Chirality restraints: 2323 Sorted by residual: chirality pdb=" CA THR B 236 " pdb=" N THR B 236 " pdb=" C THR B 236 " pdb=" CB THR B 236 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.56 2.00e-01 2.50e+01 7.97e+00 chirality pdb=" CB ILE B 220 " pdb=" CA ILE B 220 " pdb=" CG1 ILE B 220 " pdb=" CG2 ILE B 220 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.19e+00 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 2.29 0.43 2.00e-01 2.50e+01 4.57e+00 ... (remaining 2320 not shown) Planarity restraints: 2571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN C 301 " 0.050 2.00e-02 2.50e+03 2.04e-02 1.98e+01 pdb=" C10 FMN C 301 " 0.009 2.00e-02 2.50e+03 pdb=" C2 FMN C 301 " -0.017 2.00e-02 2.50e+03 pdb=" C4 FMN C 301 " 0.008 2.00e-02 2.50e+03 pdb=" C4A FMN C 301 " 0.011 2.00e-02 2.50e+03 pdb=" C5A FMN C 301 " 0.009 2.00e-02 2.50e+03 pdb=" C6 FMN C 301 " 0.009 2.00e-02 2.50e+03 pdb=" C7 FMN C 301 " -0.014 2.00e-02 2.50e+03 pdb=" C7M FMN C 301 " -0.023 2.00e-02 2.50e+03 pdb=" C8 FMN C 301 " -0.016 2.00e-02 2.50e+03 pdb=" C8M FMN C 301 " -0.014 2.00e-02 2.50e+03 pdb=" C9 FMN C 301 " 0.008 2.00e-02 2.50e+03 pdb=" C9A FMN C 301 " 0.008 2.00e-02 2.50e+03 pdb=" N1 FMN C 301 " 0.000 2.00e-02 2.50e+03 pdb=" N10 FMN C 301 " -0.002 2.00e-02 2.50e+03 pdb=" N3 FMN C 301 " -0.007 2.00e-02 2.50e+03 pdb=" N5 FMN C 301 " 0.012 2.00e-02 2.50e+03 pdb=" O2 FMN C 301 " -0.053 2.00e-02 2.50e+03 pdb=" O4 FMN C 301 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 215 " 0.063 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO A 216 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 232 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" C TYR B 232 " -0.053 2.00e-02 2.50e+03 pdb=" O TYR B 232 " 0.020 2.00e-02 2.50e+03 pdb=" N SER B 233 " 0.018 2.00e-02 2.50e+03 ... (remaining 2568 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 322 2.69 - 3.24: 14318 3.24 - 3.80: 22355 3.80 - 4.35: 31267 4.35 - 4.90: 52180 Nonbonded interactions: 120442 Sorted by model distance: nonbonded pdb=" OE2 GLU F 275 " pdb=" OH TYR F 363 " model vdw 2.139 2.440 nonbonded pdb=" O4' FMN B 501 " pdb=" O5' FMN B 501 " model vdw 2.191 2.432 nonbonded pdb=" O GLN F 295 " pdb=" OG SER F 301 " model vdw 2.211 2.440 nonbonded pdb=" ND2 ASN F 140 " pdb=" O LEU F 252 " model vdw 2.223 2.520 nonbonded pdb=" O3' RBF B 502 " pdb=" O5' RBF B 502 " model vdw 2.223 2.440 ... (remaining 120437 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: 1.450 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: 7.990 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 45.880 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 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 0.160 15173 Z= 0.411 Angle : 0.947 18.711 20570 Z= 0.563 Chirality : 0.051 0.565 2323 Planarity : 0.005 0.094 2571 Dihedral : 16.031 179.595 5612 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.13 % Favored : 96.76 % Rotamer: Outliers : 0.45 % Allowed : 4.28 % Favored : 95.27 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -2.20 (0.17), residues: 1885 helix: -0.73 (0.16), residues: 860 sheet: -1.52 (0.38), residues: 177 loop : -2.19 (0.17), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 146 HIS 0.006 0.001 HIS A 215 PHE 0.045 0.001 PHE B 213 TYR 0.016 0.001 TYR C 167 ARG 0.002 0.000 ARG A 40 *********************** 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 252 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 245 time to evaluate : 1.661 Fit side-chains revert: symmetry clash REVERT: A 444 LYS cc_start: 0.7468 (ttmm) cc_final: 0.7095 (tmmt) REVERT: B 367 MET cc_start: 0.8399 (mmm) cc_final: 0.7886 (mmm) REVERT: C 207 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8562 (ttpt) REVERT: C 252 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7636 (mtm110) REVERT: E 151 MET cc_start: 0.7995 (ttp) cc_final: 0.7741 (ttp) REVERT: E 197 GLN cc_start: 0.7891 (pt0) cc_final: 0.7453 (mm-40) REVERT: F 105 GLU cc_start: 0.4882 (mt-10) cc_final: 0.4031 (tt0) REVERT: F 133 TRP cc_start: 0.6882 (m100) cc_final: 0.5755 (m100) REVERT: F 178 LYS cc_start: 0.6804 (mtmm) cc_final: 0.6449 (tptp) REVERT: F 312 ARG cc_start: 0.6469 (mtp-110) cc_final: 0.6162 (ttm-80) outliers start: 7 outliers final: 4 residues processed: 252 average time/residue: 0.2666 time to fit residues: 98.6157 Evaluate side-chains 195 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 PRO Chi-restraints excluded: chain C residue 207 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 0.0370 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 0.0170 chunk 168 optimal weight: 8.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS A 225 HIS A 259 GLN B 74 ASN B 219 GLN B 240 GLN B 243 GLN B 251 ASN B 252 ASN B 313 ASN C 37 GLN C 216 HIS D 56 ASN D 88 GLN D 171 ASN D 176 GLN E 79 ASN F 175 HIS F 176 HIS F 216 ASN F 330 ASN F 356 HIS F 367 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15173 Z= 0.162 Angle : 0.499 7.540 20570 Z= 0.262 Chirality : 0.041 0.284 2323 Planarity : 0.005 0.107 2571 Dihedral : 13.235 176.968 2317 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.91 % Allowed : 8.63 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.99 (0.18), residues: 1885 helix: 0.34 (0.18), residues: 876 sheet: -0.88 (0.39), residues: 169 loop : -1.67 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.004 0.001 HIS A 215 PHE 0.015 0.001 PHE B 213 TYR 0.016 0.001 TYR F 319 ARG 0.011 0.000 ARG A 46 *********************** 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 212 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 198 time to evaluate : 1.768 Fit side-chains revert: symmetry clash REVERT: C 252 ARG cc_start: 0.8165 (ttm110) cc_final: 0.7843 (mtm110) REVERT: D 157 SER cc_start: 0.8837 (t) cc_final: 0.8230 (p) REVERT: E 151 MET cc_start: 0.7919 (ttp) cc_final: 0.7629 (ttp) REVERT: E 197 GLN cc_start: 0.7908 (pt0) cc_final: 0.7454 (mm-40) REVERT: F 105 GLU cc_start: 0.4669 (mt-10) cc_final: 0.4057 (tt0) REVERT: F 133 TRP cc_start: 0.7238 (m100) cc_final: 0.6684 (m100) REVERT: F 178 LYS cc_start: 0.6787 (mtmm) cc_final: 0.6408 (tptp) outliers start: 14 outliers final: 7 residues processed: 203 average time/residue: 0.2505 time to fit residues: 77.4738 Evaluate side-chains 188 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 181 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 209 ILE Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 169 optimal weight: 0.0010 chunk 182 optimal weight: 6.9990 chunk 150 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN C 40 ASN F 142 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15173 Z= 0.300 Angle : 0.560 9.199 20570 Z= 0.289 Chirality : 0.044 0.309 2323 Planarity : 0.005 0.117 2571 Dihedral : 12.438 179.289 2305 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.36 % Allowed : 10.77 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.18), residues: 1885 helix: 0.45 (0.18), residues: 872 sheet: -0.71 (0.39), residues: 167 loop : -1.50 (0.18), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.009 0.001 HIS A 215 PHE 0.020 0.002 PHE B 213 TYR 0.014 0.002 TYR F 217 ARG 0.003 0.000 ARG D 63 *********************** 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 196 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 175 time to evaluate : 1.713 Fit side-chains revert: symmetry clash REVERT: B 367 MET cc_start: 0.8437 (mmm) cc_final: 0.7924 (mmm) REVERT: C 252 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7590 (mtm110) REVERT: E 151 MET cc_start: 0.7974 (ttp) cc_final: 0.7680 (ttp) REVERT: E 197 GLN cc_start: 0.7942 (pt0) cc_final: 0.7483 (mm-40) REVERT: F 105 GLU cc_start: 0.4677 (mt-10) cc_final: 0.4047 (tt0) REVERT: F 133 TRP cc_start: 0.7211 (m100) cc_final: 0.6688 (m100) REVERT: F 178 LYS cc_start: 0.6773 (mtmm) cc_final: 0.6424 (tptp) REVERT: F 295 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7058 (mm-40) outliers start: 21 outliers final: 18 residues processed: 190 average time/residue: 0.2457 time to fit residues: 70.6013 Evaluate side-chains 186 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 366 ASP Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 179 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8425 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15173 Z= 0.246 Angle : 0.517 8.046 20570 Z= 0.268 Chirality : 0.043 0.317 2323 Planarity : 0.005 0.118 2571 Dihedral : 11.477 179.786 2305 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.56 % Allowed : 11.35 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.55 (0.18), residues: 1885 helix: 0.63 (0.18), residues: 872 sheet: -0.61 (0.39), residues: 167 loop : -1.35 (0.18), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.007 0.001 HIS A 215 PHE 0.019 0.001 PHE B 213 TYR 0.015 0.001 TYR F 248 ARG 0.004 0.000 ARG B 408 *********************** 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 191 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 1.669 Fit side-chains REVERT: B 367 MET cc_start: 0.8444 (mmm) cc_final: 0.7918 (mmm) REVERT: C 252 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7646 (mtm110) REVERT: E 151 MET cc_start: 0.7966 (ttp) cc_final: 0.7655 (ttp) REVERT: E 197 GLN cc_start: 0.8008 (pt0) cc_final: 0.7538 (mm-40) REVERT: F 102 GLU cc_start: 0.5849 (pm20) cc_final: 0.5422 (pt0) REVERT: F 133 TRP cc_start: 0.7223 (m100) cc_final: 0.6694 (m100) REVERT: F 295 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7046 (mm-40) outliers start: 24 outliers final: 17 residues processed: 184 average time/residue: 0.2557 time to fit residues: 71.8365 Evaluate side-chains 180 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 10.0000 chunk 102 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 133 optimal weight: 0.0970 chunk 74 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15173 Z= 0.260 Angle : 0.525 8.775 20570 Z= 0.271 Chirality : 0.043 0.327 2323 Planarity : 0.005 0.121 2571 Dihedral : 11.129 178.848 2305 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.75 % Allowed : 12.71 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: 0.71 (0.18), residues: 866 sheet: -0.51 (0.40), residues: 167 loop : -1.22 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.007 0.001 HIS A 215 PHE 0.020 0.001 PHE B 213 TYR 0.010 0.001 TYR B 360 ARG 0.003 0.000 ARG D 63 *********************** 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 200 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 1.579 Fit side-chains REVERT: B 367 MET cc_start: 0.8436 (mmm) cc_final: 0.7919 (mmm) REVERT: B 380 GLU cc_start: 0.8234 (tt0) cc_final: 0.8011 (tt0) REVERT: C 252 ARG cc_start: 0.8129 (ttm110) cc_final: 0.7626 (mtm110) REVERT: E 151 MET cc_start: 0.7968 (ttp) cc_final: 0.7621 (ttp) REVERT: E 197 GLN cc_start: 0.8038 (pt0) cc_final: 0.7548 (mm-40) REVERT: F 133 TRP cc_start: 0.7258 (m100) cc_final: 0.6744 (m100) REVERT: F 295 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7111 (mm-40) outliers start: 27 outliers final: 21 residues processed: 193 average time/residue: 0.2462 time to fit residues: 72.2037 Evaluate side-chains 187 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 79 CYS Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 149 optimal weight: 0.0970 chunk 83 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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: 0.8440 moved from start: 0.1607 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= 0.282 Angle : 0.537 9.787 20570 Z= 0.276 Chirality : 0.043 0.280 2323 Planarity : 0.005 0.126 2571 Dihedral : 10.946 178.219 2305 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.95 % Allowed : 13.23 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: 1885 helix: 0.68 (0.18), residues: 865 sheet: -0.54 (0.39), residues: 167 loop : -1.19 (0.18), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.008 0.001 HIS A 215 PHE 0.021 0.001 PHE B 213 TYR 0.012 0.001 TYR F 248 ARG 0.004 0.000 ARG D 63 *********************** 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 196 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 166 time to evaluate : 1.756 Fit side-chains REVERT: B 367 MET cc_start: 0.8440 (mmm) cc_final: 0.7910 (mmm) REVERT: C 170 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6555 (pt0) REVERT: C 252 ARG cc_start: 0.8152 (ttm110) cc_final: 0.7667 (mtm110) REVERT: E 151 MET cc_start: 0.7941 (ttp) cc_final: 0.7600 (ttp) REVERT: E 197 GLN cc_start: 0.8034 (pt0) cc_final: 0.7553 (mm-40) REVERT: F 133 TRP cc_start: 0.7235 (m100) cc_final: 0.6715 (m100) REVERT: F 295 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7089 (mm-40) outliers start: 30 outliers final: 23 residues processed: 187 average time/residue: 0.2499 time to fit residues: 71.3164 Evaluate side-chains 186 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 0.0370 chunk 131 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 overall best weight: 0.8660 ------------------------------------------------------------------------------- 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: 0.8395 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15173 Z= 0.169 Angle : 0.482 7.630 20570 Z= 0.248 Chirality : 0.041 0.266 2323 Planarity : 0.005 0.114 2571 Dihedral : 10.283 179.116 2305 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.56 % Allowed : 14.40 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: 1885 helix: 0.94 (0.18), residues: 868 sheet: -0.46 (0.39), residues: 167 loop : -1.08 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.004 0.001 HIS A 215 PHE 0.017 0.001 PHE B 213 TYR 0.014 0.001 TYR F 248 ARG 0.004 0.000 ARG D 63 *********************** 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 201 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 1.635 Fit side-chains REVERT: B 367 MET cc_start: 0.8419 (mmm) cc_final: 0.7898 (mmm) REVERT: C 170 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6510 (pt0) REVERT: C 252 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7647 (mtm110) REVERT: E 81 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7344 (tp) REVERT: E 197 GLN cc_start: 0.8016 (pt0) cc_final: 0.7552 (mm-40) REVERT: F 6 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8006 (t80) REVERT: F 133 TRP cc_start: 0.7214 (m100) cc_final: 0.6718 (m100) REVERT: F 295 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7055 (mm-40) outliers start: 24 outliers final: 14 residues processed: 193 average time/residue: 0.2452 time to fit residues: 72.5405 Evaluate side-chains 182 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 378 CYS Chi-restraints excluded: chain F residue 382 MET 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: 10.0000 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15173 Z= 0.317 Angle : 0.563 10.750 20570 Z= 0.287 Chirality : 0.044 0.315 2323 Planarity : 0.005 0.132 2571 Dihedral : 10.413 177.387 2305 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.69 % Allowed : 14.79 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: -0.31 (0.19), residues: 1885 helix: 0.73 (0.18), residues: 869 sheet: -0.52 (0.39), residues: 167 loop : -1.10 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 103 HIS 0.009 0.001 HIS A 215 PHE 0.022 0.002 PHE B 213 TYR 0.015 0.001 TYR F 248 ARG 0.004 0.000 ARG D 63 *********************** 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 188 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 1.544 Fit side-chains REVERT: A 179 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.7132 (m-30) REVERT: B 367 MET cc_start: 0.8433 (mmm) cc_final: 0.7923 (mmm) REVERT: C 170 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6578 (pt0) REVERT: C 252 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7677 (mtm110) REVERT: E 151 MET cc_start: 0.7954 (ttp) cc_final: 0.7622 (ttp) REVERT: E 197 GLN cc_start: 0.8046 (pt0) cc_final: 0.7563 (mm-40) REVERT: F 6 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8038 (t80) REVERT: F 133 TRP cc_start: 0.7259 (m100) cc_final: 0.6714 (m100) REVERT: F 295 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7046 (mm-40) outliers start: 26 outliers final: 18 residues processed: 180 average time/residue: 0.2459 time to fit residues: 67.2126 Evaluate side-chains 178 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN B 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 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 : 0.005 0.042 15173 Z= 0.355 Angle : 0.585 10.788 20570 Z= 0.299 Chirality : 0.045 0.385 2323 Planarity : 0.005 0.133 2571 Dihedral : 10.638 177.758 2305 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.82 % Allowed : 14.53 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 1885 helix: 0.58 (0.18), residues: 866 sheet: -0.63 (0.39), residues: 167 loop : -1.15 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 103 HIS 0.009 0.001 HIS A 215 PHE 0.023 0.002 PHE B 213 TYR 0.017 0.002 TYR F 248 ARG 0.004 0.000 ARG D 63 *********************** 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 185 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 157 time to evaluate : 1.703 Fit side-chains REVERT: A 179 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7194 (m-30) REVERT: B 367 MET cc_start: 0.8451 (mmm) cc_final: 0.7884 (mmm) REVERT: C 170 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6602 (pt0) REVERT: C 252 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7701 (mtm110) REVERT: E 151 MET cc_start: 0.7971 (ttp) cc_final: 0.7661 (ttp) REVERT: E 197 GLN cc_start: 0.8054 (pt0) cc_final: 0.7565 (mm-40) REVERT: F 125 GLU cc_start: 0.6956 (tp30) cc_final: 0.6699 (tp30) REVERT: F 133 TRP cc_start: 0.7253 (m100) cc_final: 0.6694 (m100) REVERT: F 295 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7027 (mm-40) outliers start: 28 outliers final: 20 residues processed: 174 average time/residue: 0.2596 time to fit residues: 68.1211 Evaluate side-chains 177 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 58 LYS Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 107 optimal weight: 0.0070 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 113 optimal weight: 0.2980 chunk 90 optimal weight: 10.0000 overall best weight: 0.8604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15173 Z= 0.171 Angle : 0.493 9.272 20570 Z= 0.253 Chirality : 0.042 0.341 2323 Planarity : 0.005 0.123 2571 Dihedral : 10.082 178.709 2305 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.17 % Allowed : 15.37 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: 1885 helix: 0.99 (0.19), residues: 860 sheet: -0.51 (0.39), residues: 167 loop : -0.97 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.004 0.001 HIS A 215 PHE 0.019 0.001 PHE B 213 TYR 0.020 0.001 TYR F 248 ARG 0.004 0.000 ARG D 63 ********************** 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 188 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 1.726 Fit side-chains REVERT: A 179 ASP cc_start: 0.7322 (m-30) cc_final: 0.7114 (m-30) REVERT: B 367 MET cc_start: 0.8429 (mmm) cc_final: 0.7902 (mmm) REVERT: C 170 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6506 (pt0) REVERT: C 252 ARG cc_start: 0.8140 (ttm110) cc_final: 0.7736 (mtm110) REVERT: E 151 MET cc_start: 0.7872 (ttp) cc_final: 0.7548 (ttp) REVERT: E 197 GLN cc_start: 0.8034 (pt0) cc_final: 0.7561 (mm-40) REVERT: F 6 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8055 (t80) REVERT: F 125 GLU cc_start: 0.6887 (tp30) cc_final: 0.6638 (tp30) REVERT: F 133 TRP cc_start: 0.7152 (m100) cc_final: 0.6598 (m100) REVERT: F 295 GLN cc_start: 0.7550 (mm-40) cc_final: 0.6980 (mm-40) REVERT: F 317 MET cc_start: 0.6900 (ptm) cc_final: 0.6394 (ptp) outliers start: 18 outliers final: 13 residues processed: 184 average time/residue: 0.2534 time to fit residues: 71.0554 Evaluate side-chains 182 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 170 GLN Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain F residue 6 PHE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 382 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 41 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 18 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 overall best weight: 1.6964 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.174504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.133584 restraints weight = 26127.353| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.13 r_work: 0.3325 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15173 Z= 0.268 Angle : 0.544 11.094 20570 Z= 0.276 Chirality : 0.043 0.376 2323 Planarity : 0.005 0.134 2571 Dihedral : 10.256 177.287 2305 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.23 % Allowed : 15.18 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 1.19 % 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: 0.87 (0.18), residues: 860 sheet: -0.53 (0.39), residues: 167 loop : -0.99 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 103 HIS 0.009 0.001 HIS A 215 PHE 0.021 0.001 PHE B 213 TYR 0.018 0.001 TYR F 248 ARG 0.004 0.000 ARG D 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3233.35 seconds wall clock time: 59 minutes 33.38 seconds (3573.38 seconds total)