Starting phenix.real_space_refine on Fri Dec 8 21:24:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd1_0440/12_2023/6nd1_0440.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd1_0440/12_2023/6nd1_0440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd1_0440/12_2023/6nd1_0440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd1_0440/12_2023/6nd1_0440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd1_0440/12_2023/6nd1_0440.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nd1_0440/12_2023/6nd1_0440.pdb" } resolution = 4.1 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= 0.008 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5990 2.51 5 N 1514 2.21 5 O 1646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 24": "OE1" <-> "OE2" Residue "B ARG 25": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 270": "NH1" <-> "NH2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B GLU 413": "OE1" <-> "OE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A ARG 485": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "E GLU 102": "OE1" <-> "OE2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F GLU 157": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F ARG 165": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F GLU 182": "OE1" <-> "OE2" Residue "F ARG 185": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9186 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3031 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 17, 'TRANS': 372} Chain breaks: 5 Chain: "A" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3565 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 27, 'TRANS': 433} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 443 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "D" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 270 Classifications: {'peptide': 41} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1143 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain breaks: 1 Chain: "F" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 734 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU A 284 " occ=0.88 ... (6 atoms not shown) pdb=" CD2 LEU A 284 " occ=0.75 residue: pdb=" N GLY A 316 " occ=0.88 ... (2 atoms not shown) pdb=" O GLY A 316 " occ=0.88 residue: pdb=" N LEU A 398 " occ=0.88 ... (6 atoms not shown) pdb=" CD2 LEU A 398 " occ=0.75 residue: pdb=" N ALA A 413 " occ=0.88 ... (3 atoms not shown) pdb=" CB ALA A 413 " occ=0.88 Time building chain proxies: 5.39, per 1000 atoms: 0.59 Number of scatterers: 9186 At special positions: 0 Unit cell: (108, 106.65, 121.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1646 8.00 N 1514 7.00 C 5990 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=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 2.1 seconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 65.8% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'B' and resid 28 through 48 removed outlier: 3.743A pdb=" N ILE B 34 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.073A pdb=" N MET B 69 " --> pdb=" O TRP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.731A pdb=" N ILE B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER B 88 " --> pdb=" O PRO B 84 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE B 92 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 137 Processing helix chain 'B' and resid 146 through 174 removed outlier: 4.015A pdb=" N CYS B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 197 removed outlier: 3.878A pdb=" N LEU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 184 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 223 removed outlier: 3.998A pdb=" N LEU B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 222 " --> pdb=" O PHE B 218 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 223 " --> pdb=" O PHE B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 238 removed outlier: 4.208A pdb=" N VAL B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 262 removed outlier: 4.016A pdb=" N ALA B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 289 removed outlier: 3.722A pdb=" N SER B 289 " --> pdb=" O PHE B 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 289' Processing helix chain 'B' and resid 290 through 314 removed outlier: 3.707A pdb=" N MET B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 306 " --> pdb=" O ASN B 302 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 384 removed outlier: 4.000A pdb=" N THR B 362 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 363 " --> pdb=" O PRO B 359 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 399 removed outlier: 4.170A pdb=" N LYS B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 440 removed outlier: 3.870A pdb=" N LYS B 416 " --> pdb=" O ARG B 412 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 417 " --> pdb=" O GLU B 413 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.628A pdb=" N ASP B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 464 removed outlier: 3.595A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 454 " --> pdb=" O MET B 450 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS B 464 " --> pdb=" O GLU B 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 21 removed outlier: 4.027A pdb=" N THR A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 59 through 64 removed outlier: 4.385A pdb=" N GLU A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 removed outlier: 3.590A pdb=" N PHE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 110 Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.541A pdb=" N VAL A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 246 removed outlier: 3.678A pdb=" N VAL A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.861A pdb=" N ASN A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.828A pdb=" N ILE A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.794A pdb=" N GLU A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N HIS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 328 Processing helix chain 'A' and resid 328 through 341 removed outlier: 3.893A pdb=" N LEU A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.855A pdb=" N PHE A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 4.100A pdb=" N LEU A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 373 " --> pdb=" O CYS A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 378 through 386 Processing helix chain 'A' and resid 391 through 397 removed outlier: 3.616A pdb=" N LEU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 407 Processing helix chain 'A' and resid 411 through 424 Processing helix chain 'A' and resid 480 through 484 Processing helix chain 'A' and resid 486 through 494 removed outlier: 3.986A pdb=" N ALA A 489 " --> pdb=" O ASP A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 43 through 80 removed outlier: 3.523A pdb=" N TYR C 47 " --> pdb=" O ASP C 43 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS C 52 " --> pdb=" O THR C 48 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) Proline residue: C 74 - end of helix removed outlier: 3.682A pdb=" N TYR C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 removed outlier: 3.767A pdb=" N ALA D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 75 removed outlier: 3.818A pdb=" N PHE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 73 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 60 removed outlier: 4.378A pdb=" N LEU E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 59 " --> pdb=" O GLN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 81 removed outlier: 4.198A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE E 78 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N MET E 81 " --> pdb=" O GLN E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 124 Proline residue: E 115 - end of helix removed outlier: 3.862A pdb=" N GLY E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 153 removed outlier: 3.680A pdb=" N TRP E 131 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 149 " --> pdb=" O PHE E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 176 removed outlier: 4.282A pdb=" N VAL E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N CYS E 167 " --> pdb=" O PHE E 163 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS E 168 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU E 169 " --> pdb=" O MET E 165 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN E 174 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 120 Processing helix chain 'F' and resid 122 through 136 removed outlier: 3.792A pdb=" N LEU F 126 " --> pdb=" O HIS F 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE F 131 " --> pdb=" O GLN F 127 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 152 removed outlier: 4.120A pdb=" N PHE F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 170 Processing helix chain 'F' and resid 175 through 192 removed outlier: 3.629A pdb=" N LEU F 179 " --> pdb=" O LYS F 175 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 198 through 203 removed outlier: 5.832A pdb=" N THR B 201 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU B 212 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU B 210 " --> pdb=" O VAL B 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 264 through 269 Processing sheet with id=AA3, first strand: chain 'A' and resid 430 through 436 removed outlier: 3.969A pdb=" N LYS A 432 " --> pdb=" O LYS A 454 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 525 removed outlier: 3.575A pdb=" N LYS A 524 " --> pdb=" O SER A 519 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 524 through 525 removed outlier: 3.575A pdb=" N LYS A 524 " --> pdb=" O SER A 519 " (cutoff:3.500A) 506 hydrogen bonds defined for protein. 1473 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: 2.42 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2687 1.34 - 1.46: 1685 1.46 - 1.58: 4938 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 9366 Sorted by residual: bond pdb=" C THR B 379 " pdb=" N TRP B 380 " ideal model delta sigma weight residual 1.335 1.226 0.110 1.38e-02 5.25e+03 6.30e+01 bond pdb=" C TRP A 566 " pdb=" N GLU A 567 " ideal model delta sigma weight residual 1.331 1.238 0.093 1.37e-02 5.33e+03 4.61e+01 bond pdb=" C GLY A 576 " pdb=" N GLN A 577 " ideal model delta sigma weight residual 1.331 1.221 0.110 2.07e-02 2.33e+03 2.83e+01 bond pdb=" C GLN B 398 " pdb=" N GLY B 399 " ideal model delta sigma weight residual 1.330 1.258 0.072 1.42e-02 4.96e+03 2.56e+01 bond pdb=" N ILE C 79 " pdb=" CA ILE C 79 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.10e+00 ... (remaining 9361 not shown) Histogram of bond angle deviations from ideal: 91.69 - 100.30: 8 100.30 - 108.91: 716 108.91 - 117.53: 6171 117.53 - 126.14: 5666 126.14 - 134.75: 124 Bond angle restraints: 12685 Sorted by residual: angle pdb=" C ILE C 75 " pdb=" CA ILE C 75 " pdb=" CB ILE C 75 " ideal model delta sigma weight residual 112.14 129.12 -16.98 1.35e+00 5.49e-01 1.58e+02 angle pdb=" C GLU F 124 " pdb=" CA GLU F 124 " pdb=" CB GLU F 124 " ideal model delta sigma weight residual 110.85 130.99 -20.14 1.70e+00 3.46e-01 1.40e+02 angle pdb=" C ALA B 463 " pdb=" CA ALA B 463 " pdb=" CB ALA B 463 " ideal model delta sigma weight residual 110.68 125.60 -14.92 1.70e+00 3.46e-01 7.70e+01 angle pdb=" C GLU A 440 " pdb=" CA GLU A 440 " pdb=" CB GLU A 440 " ideal model delta sigma weight residual 110.45 91.69 18.76 2.15e+00 2.16e-01 7.61e+01 angle pdb=" C PHE B 218 " pdb=" CA PHE B 218 " pdb=" CB PHE B 218 " ideal model delta sigma weight residual 109.56 123.30 -13.74 1.65e+00 3.67e-01 6.94e+01 ... (remaining 12680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 4902 17.48 - 34.95: 569 34.95 - 52.43: 124 52.43 - 69.91: 28 69.91 - 87.39: 14 Dihedral angle restraints: 5637 sinusoidal: 2211 harmonic: 3426 Sorted by residual: dihedral pdb=" C GLU A 440 " pdb=" N GLU A 440 " pdb=" CA GLU A 440 " pdb=" CB GLU A 440 " ideal model delta harmonic sigma weight residual -122.60 -100.10 -22.50 0 2.50e+00 1.60e-01 8.10e+01 dihedral pdb=" C GLU F 124 " pdb=" N GLU F 124 " pdb=" CA GLU F 124 " pdb=" CB GLU F 124 " ideal model delta harmonic sigma weight residual -122.60 -143.24 20.64 0 2.50e+00 1.60e-01 6.82e+01 dihedral pdb=" CA PRO B 62 " pdb=" C PRO B 62 " pdb=" N LEU B 63 " pdb=" CA LEU B 63 " ideal model delta harmonic sigma weight residual 180.00 140.65 39.35 0 5.00e+00 4.00e-02 6.19e+01 ... (remaining 5634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1385 0.131 - 0.261: 89 0.261 - 0.392: 11 0.392 - 0.523: 6 0.523 - 0.654: 2 Chirality restraints: 1493 Sorted by residual: chirality pdb=" CA GLU F 124 " pdb=" N GLU F 124 " pdb=" C GLU F 124 " pdb=" CB GLU F 124 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA PHE B 236 " pdb=" N PHE B 236 " pdb=" C PHE B 236 " pdb=" CB PHE B 236 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" CA ALA B 462 " pdb=" N ALA B 462 " pdb=" C ALA B 462 " pdb=" CB ALA B 462 " both_signs ideal model delta sigma weight residual False 2.48 1.96 0.52 2.00e-01 2.50e+01 6.80e+00 ... (remaining 1490 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 444 " -0.059 5.00e-02 4.00e+02 9.00e-02 1.30e+01 pdb=" N PRO A 445 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 265 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.43e+00 pdb=" C TYR B 265 " 0.053 2.00e-02 2.50e+03 pdb=" O TYR B 265 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU B 266 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 160 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00 pdb=" C VAL E 160 " 0.053 2.00e-02 2.50e+03 pdb=" O VAL E 160 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN E 161 " -0.018 2.00e-02 2.50e+03 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2168 2.78 - 3.31: 8588 3.31 - 3.84: 14120 3.84 - 4.37: 15051 4.37 - 4.90: 26046 Nonbonded interactions: 65973 Sorted by model distance: nonbonded pdb=" OG1 THR A 599 " pdb=" N THR A 600 " model vdw 2.249 2.520 nonbonded pdb=" OG1 THR A 444 " pdb=" OG SER A 447 " model vdw 2.287 2.440 nonbonded pdb=" O HIS A 390 " pdb=" OH TYR F 190 " model vdw 2.295 2.440 nonbonded pdb=" O SER A 483 " pdb=" OG SER A 483 " model vdw 2.301 2.440 nonbonded pdb=" O ASN B 290 " pdb=" OD1 ASN B 290 " model vdw 2.302 3.040 ... (remaining 65968 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 0.000 Extract box with map and model: 1.450 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.110 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.009 0.110 9366 Z= 0.580 Angle : 1.231 20.144 12685 Z= 0.718 Chirality : 0.079 0.654 1493 Planarity : 0.009 0.090 1586 Dihedral : 16.242 87.386 3409 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 0.10 % Allowed : 15.61 % Favored : 84.29 % Cbeta Deviations : 1.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.89 (0.20), residues: 1145 helix: -2.28 (0.15), residues: 689 sheet: -2.93 (0.45), residues: 80 loop : -2.70 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 242 HIS 0.011 0.002 HIS A 334 PHE 0.041 0.003 PHE E 66 TYR 0.030 0.002 TYR B 287 ARG 0.009 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.2410 time to fit residues: 80.9004 Evaluate side-chains 189 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 30.0000 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 220 HIS B 261 GLN B 296 GLN B 347 GLN A 55 ASN A 255 HIS A 261 ASN A 307 GLN A 334 HIS A 361 GLN A 376 ASN A 427 ASN A 494 GLN E 173 ASN F 106 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9366 Z= 0.179 Angle : 0.623 9.825 12685 Z= 0.316 Chirality : 0.042 0.157 1493 Planarity : 0.005 0.061 1586 Dihedral : 5.366 68.719 1242 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.41 % Allowed : 5.20 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.74 (0.24), residues: 1145 helix: -0.41 (0.18), residues: 712 sheet: -2.27 (0.50), residues: 77 loop : -2.23 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 65 HIS 0.006 0.001 HIS A 255 PHE 0.021 0.001 PHE E 66 TYR 0.017 0.001 TYR B 344 ARG 0.006 0.000 ARG B 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 252 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 256 average time/residue: 0.2024 time to fit residues: 72.0377 Evaluate side-chains 193 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0867 time to fit residues: 1.6694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 114 optimal weight: 0.0980 chunk 93 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 ASN A 261 ASN A 330 HIS E 123 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9366 Z= 0.174 Angle : 0.586 9.061 12685 Z= 0.293 Chirality : 0.042 0.189 1493 Planarity : 0.004 0.058 1586 Dihedral : 4.856 60.928 1242 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.25), residues: 1145 helix: 0.29 (0.19), residues: 718 sheet: -1.69 (0.55), residues: 76 loop : -2.01 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 65 HIS 0.003 0.001 HIS A 288 PHE 0.016 0.001 PHE E 66 TYR 0.016 0.001 TYR B 344 ARG 0.006 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2090 time to fit residues: 73.6466 Evaluate side-chains 196 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.0370 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 overall best weight: 1.0264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS B 246 GLN ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN A 330 HIS E 72 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9366 Z= 0.163 Angle : 0.580 10.756 12685 Z= 0.287 Chirality : 0.042 0.196 1493 Planarity : 0.004 0.059 1586 Dihedral : 4.596 58.598 1242 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.25), residues: 1145 helix: 0.72 (0.19), residues: 710 sheet: -1.50 (0.56), residues: 77 loop : -1.65 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 65 HIS 0.004 0.001 HIS D 72 PHE 0.014 0.001 PHE B 376 TYR 0.019 0.001 TYR B 456 ARG 0.004 0.000 ARG F 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2064 time to fit residues: 69.6110 Evaluate side-chains 197 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 0.0970 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN A 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9366 Z= 0.168 Angle : 0.576 11.119 12685 Z= 0.284 Chirality : 0.042 0.185 1493 Planarity : 0.004 0.059 1586 Dihedral : 4.461 56.623 1242 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.25), residues: 1145 helix: 0.93 (0.19), residues: 720 sheet: -1.46 (0.56), residues: 79 loop : -1.45 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 159 HIS 0.003 0.001 HIS D 72 PHE 0.014 0.001 PHE B 376 TYR 0.014 0.001 TYR B 344 ARG 0.002 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.183 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.2225 time to fit residues: 74.8256 Evaluate side-chains 185 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 0.0670 chunk 112 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 overall best weight: 3.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9366 Z= 0.314 Angle : 0.686 12.335 12685 Z= 0.343 Chirality : 0.046 0.200 1493 Planarity : 0.004 0.059 1586 Dihedral : 4.775 52.691 1242 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.25), residues: 1145 helix: 0.82 (0.19), residues: 720 sheet: -1.44 (0.56), residues: 77 loop : -1.53 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 35 HIS 0.004 0.001 HIS A 424 PHE 0.020 0.002 PHE E 47 TYR 0.016 0.001 TYR B 344 ARG 0.005 0.001 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.2251 time to fit residues: 69.0581 Evaluate side-chains 181 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.8868 > 50: distance: 27 - 62: 24.657 distance: 30 - 59: 11.585 distance: 55 - 59: 8.036 distance: 59 - 60: 7.089 distance: 60 - 61: 6.511 distance: 60 - 63: 10.800 distance: 61 - 62: 24.790 distance: 61 - 67: 12.302 distance: 63 - 64: 10.769 distance: 63 - 65: 7.134 distance: 64 - 66: 10.100 distance: 67 - 68: 7.882 distance: 67 - 73: 12.411 distance: 68 - 69: 3.350 distance: 68 - 71: 13.311 distance: 69 - 70: 8.398 distance: 69 - 74: 16.427 distance: 71 - 72: 15.160 distance: 72 - 73: 11.473 distance: 74 - 75: 10.850 distance: 75 - 76: 11.026 distance: 75 - 78: 12.540 distance: 76 - 77: 18.288 distance: 76 - 82: 34.208 distance: 78 - 79: 14.189 distance: 79 - 80: 14.676 distance: 79 - 81: 15.514 distance: 82 - 83: 23.432 distance: 83 - 84: 21.097 distance: 84 - 85: 19.373 distance: 84 - 86: 26.389 distance: 86 - 87: 17.366 distance: 87 - 88: 10.785 distance: 87 - 90: 10.139 distance: 88 - 89: 14.275 distance: 88 - 95: 23.610 distance: 90 - 91: 20.319 distance: 91 - 92: 4.108 distance: 92 - 93: 5.796 distance: 92 - 94: 8.377 distance: 95 - 96: 19.453 distance: 95 - 101: 16.856 distance: 96 - 97: 15.402 distance: 96 - 99: 21.579 distance: 97 - 98: 23.767 distance: 97 - 102: 28.566 distance: 99 - 100: 14.761 distance: 100 - 101: 36.446 distance: 102 - 103: 13.859 distance: 103 - 104: 20.474 distance: 103 - 106: 6.195 distance: 104 - 105: 12.787 distance: 104 - 107: 23.892 distance: 107 - 108: 19.989 distance: 107 - 113: 9.985 distance: 108 - 109: 19.020 distance: 108 - 111: 39.511 distance: 109 - 110: 7.192 distance: 109 - 114: 9.073 distance: 111 - 112: 20.213 distance: 112 - 113: 28.112 distance: 114 - 115: 10.424 distance: 115 - 116: 8.471 distance: 115 - 118: 5.942 distance: 116 - 117: 12.350 distance: 116 - 123: 9.749 distance: 118 - 119: 14.044 distance: 119 - 120: 6.366 distance: 120 - 121: 8.406 distance: 120 - 122: 10.280 distance: 123 - 124: 12.771 distance: 124 - 125: 6.546 distance: 124 - 127: 15.135 distance: 125 - 126: 10.001 distance: 125 - 130: 16.860 distance: 127 - 128: 22.786 distance: 127 - 129: 10.472