Starting phenix.real_space_refine on Sun Nov 17 05:41:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5q_35990/11_2024/8j5q_35990.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5q_35990/11_2024/8j5q_35990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5q_35990/11_2024/8j5q_35990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5q_35990/11_2024/8j5q_35990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5q_35990/11_2024/8j5q_35990.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5q_35990/11_2024/8j5q_35990.cif" } resolution = 3.25 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= 0.008 sd= 0.079 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 41 5.16 5 C 8365 2.51 5 N 2355 2.21 5 O 2422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 224 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13187 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4003 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 28, 'TRANS': 498} Chain: "B" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2476 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 313} Chain: "C" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2070 Classifications: {'peptide': 274} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 260} Chain: "D" Number of atoms: 4584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4584 Classifications: {'peptide': 611} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 575} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 46 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10656 SG CYS D 286 16.028 52.203 22.637 1.00 72.25 S ATOM 10889 SG CYS D 317 16.301 50.748 16.183 1.00 79.80 S ATOM 10703 SG CYS D 292 19.087 55.724 18.421 1.00 68.73 S ATOM 10756 SG CYS D 299 12.432 55.636 17.637 1.00 87.74 S Time building chain proxies: 8.08, per 1000 atoms: 0.61 Number of scatterers: 13187 At special positions: 0 Unit cell: (80.704, 96.512, 166.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 41 16.00 O 2422 8.00 N 2355 7.00 C 8365 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 - 3.00 Amino acid : True - 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: 3.38 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 D2001 " pdb="FE3 SF4 D2001 " - pdb=" SG CYS D 292 " pdb="FE1 SF4 D2001 " - pdb=" SG CYS D 286 " pdb="FE4 SF4 D2001 " - pdb=" SG CYS D 299 " pdb="FE2 SF4 D2001 " - pdb=" SG CYS D 317 " Number of angles added : 12 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3180 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 13 sheets defined 53.1% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 171 through 182 removed outlier: 3.726A pdb=" N ILE A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 226 removed outlier: 4.502A pdb=" N ARG A 224 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 226 " --> pdb=" O TRP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.271A pdb=" N ALA A 240 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 316 through 326 Processing helix chain 'A' and resid 350 through 353 Processing helix chain 'A' and resid 354 through 363 Processing helix chain 'A' and resid 366 through 375 removed outlier: 3.513A pdb=" N ILE A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 407 through 418 Processing helix chain 'A' and resid 443 through 461 removed outlier: 3.900A pdb=" N GLN A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 496 through 499 Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 518 through 530 Processing helix chain 'A' and resid 533 through 552 removed outlier: 3.952A pdb=" N ALA A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 31 removed outlier: 3.556A pdb=" N ASN B 11 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 61 through 74 Processing helix chain 'B' and resid 87 through 123 removed outlier: 4.203A pdb=" N GLY B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ARG B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 142 Processing helix chain 'B' and resid 143 through 163 removed outlier: 3.702A pdb=" N ASN B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 220 removed outlier: 4.141A pdb=" N ARG B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU B 194 " --> pdb=" O GLN B 190 " (cutoff:3.500A) Proline residue: B 195 - end of helix removed outlier: 3.536A pdb=" N LEU B 199 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 233 through 273 removed outlier: 4.443A pdb=" N ARG B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 245 " --> pdb=" O HIS B 241 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 248 " --> pdb=" O ARG B 244 " (cutoff:3.500A) Proline residue: B 249 - end of helix removed outlier: 3.813A pdb=" N THR B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 254 " --> pdb=" O MET B 250 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ALA B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N TYR B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 287 removed outlier: 3.505A pdb=" N VAL B 282 " --> pdb=" O GLY B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 319 removed outlier: 3.573A pdb=" N VAL B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 17 Processing helix chain 'C' and resid 18 through 38 removed outlier: 3.906A pdb=" N TYR C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 42 Processing helix chain 'C' and resid 72 through 110 removed outlier: 3.515A pdb=" N GLN C 76 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 125 removed outlier: 3.537A pdb=" N TRP C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 141 removed outlier: 3.524A pdb=" N VAL C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 146 through 155 Processing helix chain 'C' and resid 158 through 174 removed outlier: 3.726A pdb=" N ARG C 163 " --> pdb=" O MET C 159 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 174 " --> pdb=" O MET C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.682A pdb=" N ARG C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'C' and resid 195 through 225 removed outlier: 4.726A pdb=" N SER C 202 " --> pdb=" O PRO C 198 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE C 206 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 248 removed outlier: 4.312A pdb=" N ALA C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER C 246 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 280 Proline residue: C 257 - end of helix Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.533A pdb=" N VAL D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 107 through 118 removed outlier: 3.514A pdb=" N ALA D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 139 removed outlier: 4.443A pdb=" N ARG D 130 " --> pdb=" O LYS D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'D' and resid 149 through 150 No H-bonds generated for 'chain 'D' and resid 149 through 150' Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 186 through 205 Processing helix chain 'D' and resid 214 through 222 removed outlier: 4.170A pdb=" N VAL D 218 " --> pdb=" O ASP D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 248 through 255 Processing helix chain 'D' and resid 296 through 301 removed outlier: 3.678A pdb=" N THR D 301 " --> pdb=" O GLU D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 327 through 333 Processing helix chain 'D' and resid 399 through 409 Processing helix chain 'D' and resid 429 through 437 removed outlier: 3.663A pdb=" N SER D 435 " --> pdb=" O ALA D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 451 removed outlier: 4.016A pdb=" N LEU D 451 " --> pdb=" O PRO D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 468 Proline residue: D 464 - end of helix Processing helix chain 'D' and resid 471 through 486 removed outlier: 3.895A pdb=" N HIS D 476 " --> pdb=" O LYS D 472 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA D 477 " --> pdb=" O ASN D 473 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 500 Processing helix chain 'D' and resid 501 through 514 Processing helix chain 'D' and resid 515 through 517 No H-bonds generated for 'chain 'D' and resid 515 through 517' Processing helix chain 'D' and resid 531 through 550 removed outlier: 3.785A pdb=" N GLY D 537 " --> pdb=" O SER D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 567 removed outlier: 4.019A pdb=" N HIS D 565 " --> pdb=" O SER D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 590 Processing helix chain 'D' and resid 593 through 602 Processing helix chain 'D' and resid 607 through 611 removed outlier: 3.888A pdb=" N ARG D 610 " --> pdb=" O ASP D 607 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 95 removed outlier: 6.787A pdb=" N ARG A 271 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU A 265 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A 273 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 148 removed outlier: 6.834A pdb=" N VAL A 153 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA6, first strand: chain 'A' and resid 463 through 469 removed outlier: 6.438A pdb=" N ILE A 436 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLN A 467 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP A 438 " --> pdb=" O GLN A 467 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS A 469 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE A 440 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE A 486 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG A 437 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLN A 488 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 439 " --> pdb=" O GLN A 488 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY A 490 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N TYR A 441 " --> pdb=" O GLY A 490 " (cutoff:3.500A) removed outlier: 15.811A pdb=" N VAL A 492 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N TYR A 340 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 463 through 469 removed outlier: 6.438A pdb=" N ILE A 436 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N GLN A 467 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP A 438 " --> pdb=" O GLN A 467 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS A 469 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE A 440 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N ILE A 486 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG A 437 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLN A 488 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 439 " --> pdb=" O GLN A 488 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N GLY A 490 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N TYR A 441 " --> pdb=" O GLY A 490 " (cutoff:3.500A) removed outlier: 15.811A pdb=" N VAL A 492 " --> pdb=" O TYR A 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 421 through 423 removed outlier: 3.627A pdb=" N PHE A 426 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 570 through 571 removed outlier: 3.520A pdb=" N GLY A 587 " --> pdb=" O ALA A 571 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 21 through 31 removed outlier: 6.412A pdb=" N ALA D 23 " --> pdb=" O THR D 13 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N THR D 13 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG D 25 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA D 11 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE D 27 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N VAL D 7 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ARG D 69 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASP D 9 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER D 67 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.425A pdb=" N LEU D 176 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE D 211 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N CYS D 178 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL D 36 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU D 226 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ALA D 38 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N MET D 228 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL D 40 " --> pdb=" O MET D 228 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA D 225 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER D 236 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 227 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA D 315 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASP D 308 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 369 through 385 removed outlier: 7.772A pdb=" N GLY D 372 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ALA D 362 " --> pdb=" O GLY D 372 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL D 374 " --> pdb=" O ARG D 360 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ARG D 360 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ALA D 376 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N THR D 358 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP D 378 " --> pdb=" O VAL D 356 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL D 356 " --> pdb=" O ASP D 378 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE D 380 " --> pdb=" O HIS D 354 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 350 " --> pdb=" O LEU D 384 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU D 355 " --> pdb=" O SER D 415 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N SER D 415 " --> pdb=" O LEU D 355 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 440 through 443 removed outlier: 3.583A pdb=" N GLN D 441 " --> pdb=" O ILE D 520 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 570 " --> pdb=" O GLN D 581 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN D 581 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL D 572 " --> pdb=" O VAL D 579 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1941 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: 3.89 Time building geometry restraints manager: 3.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 5372 1.41 - 1.63: 7986 1.63 - 1.85: 66 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 13436 Sorted by residual: bond pdb=" C GLU D 525 " pdb=" O GLU D 525 " ideal model delta sigma weight residual 1.234 1.260 -0.026 5.00e-03 4.00e+04 2.68e+01 bond pdb=" N VAL B 177 " pdb=" CA VAL B 177 " ideal model delta sigma weight residual 1.457 1.495 -0.038 9.30e-03 1.16e+04 1.71e+01 bond pdb=" CA SER B 311 " pdb=" CB SER B 311 " ideal model delta sigma weight residual 1.528 1.466 0.062 1.59e-02 3.96e+03 1.54e+01 bond pdb=" C SER B 311 " pdb=" O SER B 311 " ideal model delta sigma weight residual 1.237 1.191 0.045 1.19e-02 7.06e+03 1.45e+01 bond pdb=" N VAL D 164 " pdb=" CA VAL D 164 " ideal model delta sigma weight residual 1.460 1.503 -0.044 1.21e-02 6.83e+03 1.32e+01 ... (remaining 13431 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 17722 2.36 - 4.73: 512 4.73 - 7.09: 61 7.09 - 9.46: 7 9.46 - 11.82: 1 Bond angle restraints: 18303 Sorted by residual: angle pdb=" N ALA D 170 " pdb=" CA ALA D 170 " pdb=" C ALA D 170 " ideal model delta sigma weight residual 110.43 103.80 6.63 1.31e+00 5.83e-01 2.56e+01 angle pdb=" CA GLY B 176 " pdb=" C GLY B 176 " pdb=" O GLY B 176 " ideal model delta sigma weight residual 121.88 118.12 3.76 7.80e-01 1.64e+00 2.32e+01 angle pdb=" N VAL B 177 " pdb=" CA VAL B 177 " pdb=" C VAL B 177 " ideal model delta sigma weight residual 113.20 108.68 4.52 9.60e-01 1.09e+00 2.21e+01 angle pdb=" N PHE C 177 " pdb=" CA PHE C 177 " pdb=" C PHE C 177 " ideal model delta sigma weight residual 111.71 106.33 5.38 1.15e+00 7.56e-01 2.19e+01 angle pdb=" N ALA B 307 " pdb=" CA ALA B 307 " pdb=" C ALA B 307 " ideal model delta sigma weight residual 111.28 106.21 5.07 1.09e+00 8.42e-01 2.16e+01 ... (remaining 18298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7125 18.00 - 36.00: 712 36.00 - 53.99: 161 53.99 - 71.99: 32 71.99 - 89.99: 6 Dihedral angle restraints: 8036 sinusoidal: 3077 harmonic: 4959 Sorted by residual: dihedral pdb=" CD ARG D 246 " pdb=" NE ARG D 246 " pdb=" CZ ARG D 246 " pdb=" NH1 ARG D 246 " ideal model delta sinusoidal sigma weight residual 0.00 -51.12 51.12 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CA TYR D 553 " pdb=" C TYR D 553 " pdb=" N LEU D 554 " pdb=" CA LEU D 554 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ALA A 120 " pdb=" C ALA A 120 " pdb=" N THR A 121 " pdb=" CA THR A 121 " ideal model delta harmonic sigma weight residual 180.00 -157.34 -22.66 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 8033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1520 0.053 - 0.106: 498 0.106 - 0.159: 127 0.159 - 0.212: 12 0.212 - 0.265: 4 Chirality restraints: 2161 Sorted by residual: chirality pdb=" CA ARG D 246 " pdb=" N ARG D 246 " pdb=" C ARG D 246 " pdb=" CB ARG D 246 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA SER B 41 " pdb=" N SER B 41 " pdb=" C SER B 41 " pdb=" CB SER B 41 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE C 178 " pdb=" N ILE C 178 " pdb=" C ILE C 178 " pdb=" CB ILE C 178 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2158 not shown) Planarity restraints: 2375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 246 " -0.854 9.50e-02 1.11e+02 3.83e-01 8.89e+01 pdb=" NE ARG D 246 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG D 246 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 246 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 246 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 167 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ILE D 167 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE D 167 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA D 168 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 92 " -0.261 9.50e-02 1.11e+02 1.17e-01 8.37e+00 pdb=" NE ARG A 92 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 92 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 92 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 92 " -0.009 2.00e-02 2.50e+03 ... (remaining 2372 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2088 2.75 - 3.29: 13379 3.29 - 3.83: 20944 3.83 - 4.36: 25273 4.36 - 4.90: 43601 Nonbonded interactions: 105285 Sorted by model distance: nonbonded pdb=" OG SER C 45 " pdb=" O TYR C 46 " model vdw 2.216 3.040 nonbonded pdb=" N GLU D 395 " pdb=" OE1 GLU D 395 " model vdw 2.220 3.120 nonbonded pdb=" O VAL D 420 " pdb=" OG1 THR D 423 " model vdw 2.223 3.040 nonbonded pdb=" O HIS A 180 " pdb=" OG SER A 183 " model vdw 2.270 3.040 nonbonded pdb=" O ALA A 303 " pdb=" OG1 THR A 308 " model vdw 2.277 3.040 ... (remaining 105280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.500 Find NCS groups from input model: 0.170 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: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 : 0.008 0.086 13436 Z= 0.558 Angle : 0.930 11.821 18303 Z= 0.554 Chirality : 0.055 0.265 2161 Planarity : 0.010 0.383 2375 Dihedral : 15.303 89.990 4856 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.19), residues: 1729 helix: -0.39 (0.17), residues: 813 sheet: -0.21 (0.40), residues: 156 loop : -1.09 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 223 HIS 0.007 0.001 HIS A 106 PHE 0.023 0.003 PHE A 474 TYR 0.027 0.004 TYR B 315 ARG 0.011 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 1.602 Fit side-chains REVERT: A 122 LEU cc_start: 0.9129 (mm) cc_final: 0.8927 (mm) REVERT: A 451 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8195 (mt0) REVERT: B 222 ASP cc_start: 0.7803 (m-30) cc_final: 0.7471 (t0) REVERT: D 174 ASP cc_start: 0.6849 (t70) cc_final: 0.6391 (m-30) outliers start: 4 outliers final: 2 residues processed: 168 average time/residue: 0.2716 time to fit residues: 65.3665 Evaluate side-chains 151 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 246 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.0870 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 69 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN A 307 ASN A 387 ASN A 451 GLN B 54 HIS B 190 GLN D 468 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13436 Z= 0.186 Angle : 0.617 9.315 18303 Z= 0.321 Chirality : 0.043 0.166 2161 Planarity : 0.005 0.045 2375 Dihedral : 5.151 59.658 1923 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.02 % Allowed : 7.09 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.03 (0.20), residues: 1729 helix: 0.85 (0.18), residues: 825 sheet: -0.21 (0.39), residues: 159 loop : -0.81 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 223 HIS 0.004 0.001 HIS B 54 PHE 0.016 0.002 PHE C 177 TYR 0.022 0.002 TYR B 4 ARG 0.007 0.001 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 1.426 Fit side-chains REVERT: A 180 HIS cc_start: 0.8165 (t70) cc_final: 0.7765 (t70) REVERT: A 245 PHE cc_start: 0.7475 (t80) cc_final: 0.7244 (t80) REVERT: B 8 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7549 (mtp85) REVERT: C 233 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7195 (t0) REVERT: D 247 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6380 (mtm180) REVERT: D 406 GLU cc_start: 0.7658 (tt0) cc_final: 0.7347 (tt0) REVERT: D 590 ASN cc_start: 0.8368 (t0) cc_final: 0.8060 (t0) outliers start: 14 outliers final: 8 residues processed: 176 average time/residue: 0.2992 time to fit residues: 74.7755 Evaluate side-chains 158 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 468 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 106 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN B 72 HIS B 288 GLN D 111 GLN ** D 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13436 Z= 0.236 Angle : 0.575 7.906 18303 Z= 0.298 Chirality : 0.043 0.172 2161 Planarity : 0.005 0.041 2375 Dihedral : 4.625 56.643 1918 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.53 % Allowed : 10.01 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.38 (0.20), residues: 1729 helix: 1.25 (0.18), residues: 833 sheet: -0.33 (0.39), residues: 159 loop : -0.73 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 280 HIS 0.006 0.001 HIS D 558 PHE 0.016 0.002 PHE C 177 TYR 0.023 0.001 TYR B 4 ARG 0.004 0.001 ARG D 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 1.418 Fit side-chains REVERT: A 148 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7963 (tpp80) REVERT: B 250 MET cc_start: 0.8038 (mmp) cc_final: 0.7451 (mmp) REVERT: C 233 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7334 (t0) REVERT: D 590 ASN cc_start: 0.8404 (t0) cc_final: 0.8133 (t0) outliers start: 21 outliers final: 14 residues processed: 174 average time/residue: 0.2841 time to fit residues: 70.7098 Evaluate side-chains 159 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 440 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 ASN B 54 HIS ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN D 171 ASN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13436 Z= 0.153 Angle : 0.522 7.914 18303 Z= 0.269 Chirality : 0.040 0.159 2161 Planarity : 0.004 0.044 2375 Dihedral : 4.345 59.244 1918 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.68 % Allowed : 12.71 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.70 (0.20), residues: 1729 helix: 1.53 (0.18), residues: 840 sheet: -0.41 (0.39), residues: 164 loop : -0.55 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 280 HIS 0.004 0.001 HIS D 558 PHE 0.016 0.001 PHE C 177 TYR 0.018 0.001 TYR B 4 ARG 0.007 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.353 Fit side-chains REVERT: A 148 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7964 (tpp80) REVERT: B 250 MET cc_start: 0.8007 (mmp) cc_final: 0.7408 (mmp) REVERT: C 233 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7270 (t0) REVERT: D 590 ASN cc_start: 0.8349 (t0) cc_final: 0.8134 (t0) outliers start: 23 outliers final: 13 residues processed: 178 average time/residue: 0.2874 time to fit residues: 72.1112 Evaluate side-chains 158 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 468 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 114 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13436 Z= 0.335 Angle : 0.582 7.650 18303 Z= 0.302 Chirality : 0.044 0.180 2161 Planarity : 0.005 0.044 2375 Dihedral : 4.451 57.879 1918 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.34 % Allowed : 14.32 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.54 (0.20), residues: 1729 helix: 1.39 (0.18), residues: 837 sheet: -0.38 (0.40), residues: 159 loop : -0.62 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 280 HIS 0.004 0.001 HIS D 558 PHE 0.017 0.002 PHE A 474 TYR 0.028 0.002 TYR B 4 ARG 0.004 0.001 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 1.551 Fit side-chains REVERT: B 90 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7926 (mt-10) REVERT: B 250 MET cc_start: 0.8043 (mmp) cc_final: 0.7442 (mmp) REVERT: C 233 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7441 (t0) REVERT: D 174 ASP cc_start: 0.7628 (t0) cc_final: 0.7192 (t0) REVERT: D 590 ASN cc_start: 0.8372 (t0) cc_final: 0.8168 (t0) outliers start: 32 outliers final: 24 residues processed: 175 average time/residue: 0.2635 time to fit residues: 67.1048 Evaluate side-chains 162 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 19 ASP Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 468 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 166 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13436 Z= 0.295 Angle : 0.566 7.762 18303 Z= 0.294 Chirality : 0.043 0.233 2161 Planarity : 0.004 0.044 2375 Dihedral : 4.446 58.361 1918 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.26 % Allowed : 15.70 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.51 (0.20), residues: 1729 helix: 1.39 (0.18), residues: 837 sheet: -0.48 (0.41), residues: 159 loop : -0.66 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 280 HIS 0.004 0.001 HIS D 558 PHE 0.015 0.001 PHE C 177 TYR 0.025 0.002 TYR B 4 ARG 0.004 0.000 ARG D 122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 1.479 Fit side-chains REVERT: C 233 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7414 (t0) outliers start: 31 outliers final: 25 residues processed: 168 average time/residue: 0.2754 time to fit residues: 67.5043 Evaluate side-chains 168 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 468 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN D 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13436 Z= 0.228 Angle : 0.541 7.636 18303 Z= 0.281 Chirality : 0.042 0.188 2161 Planarity : 0.004 0.045 2375 Dihedral : 4.356 58.670 1918 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.97 % Allowed : 16.73 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.62 (0.20), residues: 1729 helix: 1.50 (0.18), residues: 838 sheet: -0.57 (0.40), residues: 169 loop : -0.59 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 280 HIS 0.004 0.001 HIS D 558 PHE 0.014 0.001 PHE C 177 TYR 0.022 0.001 TYR B 4 ARG 0.005 0.000 ARG D 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.484 Fit side-chains REVERT: B 250 MET cc_start: 0.7972 (mmp) cc_final: 0.7412 (mmp) REVERT: B 288 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7450 (mt0) REVERT: C 233 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7359 (t0) outliers start: 27 outliers final: 23 residues processed: 170 average time/residue: 0.2691 time to fit residues: 66.4254 Evaluate side-chains 167 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 468 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN D 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13436 Z= 0.309 Angle : 0.574 7.364 18303 Z= 0.298 Chirality : 0.043 0.196 2161 Planarity : 0.004 0.049 2375 Dihedral : 4.423 58.721 1918 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.56 % Allowed : 16.36 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1729 helix: 1.43 (0.18), residues: 837 sheet: -0.67 (0.40), residues: 169 loop : -0.63 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 280 HIS 0.004 0.001 HIS D 558 PHE 0.015 0.001 PHE C 177 TYR 0.027 0.002 TYR B 4 ARG 0.008 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.471 Fit side-chains REVERT: B 90 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7922 (tt0) REVERT: B 288 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7526 (mt0) REVERT: C 233 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7361 (t0) outliers start: 35 outliers final: 28 residues processed: 174 average time/residue: 0.2691 time to fit residues: 68.0278 Evaluate side-chains 177 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 468 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 121 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 20.0000 chunk 153 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN D 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13436 Z= 0.232 Angle : 0.552 7.246 18303 Z= 0.286 Chirality : 0.042 0.201 2161 Planarity : 0.005 0.064 2375 Dihedral : 4.371 58.865 1918 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.41 % Allowed : 16.73 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.62 (0.20), residues: 1729 helix: 1.52 (0.18), residues: 838 sheet: -0.68 (0.40), residues: 169 loop : -0.59 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 280 HIS 0.004 0.001 HIS D 558 PHE 0.014 0.001 PHE C 177 TYR 0.024 0.001 TYR B 4 ARG 0.007 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 1.467 Fit side-chains REVERT: B 12 TYR cc_start: 0.9087 (m-10) cc_final: 0.8785 (m-80) REVERT: B 90 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7907 (tt0) REVERT: B 288 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7429 (mt0) REVERT: C 233 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7328 (t0) outliers start: 33 outliers final: 29 residues processed: 175 average time/residue: 0.2576 time to fit residues: 65.8474 Evaluate side-chains 175 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 468 ASN Chi-restraints excluded: chain D residue 516 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 157 optimal weight: 0.2980 chunk 136 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN D 468 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13436 Z= 0.188 Angle : 0.535 7.603 18303 Z= 0.277 Chirality : 0.041 0.196 2161 Planarity : 0.004 0.050 2375 Dihedral : 4.291 59.058 1918 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.05 % Allowed : 17.24 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.71 (0.20), residues: 1729 helix: 1.61 (0.18), residues: 840 sheet: -0.74 (0.39), residues: 174 loop : -0.54 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 280 HIS 0.003 0.001 HIS D 558 PHE 0.014 0.001 PHE C 177 TYR 0.021 0.001 TYR D 243 ARG 0.007 0.000 ARG A 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: B 12 TYR cc_start: 0.9076 (m-10) cc_final: 0.8844 (m-80) REVERT: B 90 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7907 (tt0) REVERT: B 288 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7365 (mt0) REVERT: C 233 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7325 (t0) REVERT: D 122 ARG cc_start: 0.6208 (mtm-85) cc_final: 0.5754 (mtm-85) outliers start: 28 outliers final: 24 residues processed: 173 average time/residue: 0.2680 time to fit residues: 67.5354 Evaluate side-chains 175 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 403 THR Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 516 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 4.9990 chunk 125 optimal weight: 0.0060 chunk 20 optimal weight: 0.0770 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 57 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN D 468 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.106125 restraints weight = 19204.524| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.14 r_work: 0.3107 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13436 Z= 0.137 Angle : 0.514 7.790 18303 Z= 0.266 Chirality : 0.040 0.191 2161 Planarity : 0.004 0.046 2375 Dihedral : 4.124 58.944 1918 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.39 % Allowed : 17.97 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.96 (0.21), residues: 1729 helix: 1.81 (0.18), residues: 839 sheet: -0.59 (0.40), residues: 175 loop : -0.41 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 280 HIS 0.003 0.001 HIS D 558 PHE 0.013 0.001 PHE C 177 TYR 0.024 0.001 TYR D 243 ARG 0.007 0.000 ARG A 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2806.80 seconds wall clock time: 51 minutes 47.14 seconds (3107.14 seconds total)