Starting phenix.real_space_refine on Thu Jul 31 01:50:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5q_35990/07_2025/8j5q_35990.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5q_35990/07_2025/8j5q_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/cci-nas-00/data/ceres_data/8j5q_35990/07_2025/8j5q_35990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5q_35990/07_2025/8j5q_35990.map" model { file = "/net/cci-nas-00/data/ceres_data/8j5q_35990/07_2025/8j5q_35990.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5q_35990/07_2025/8j5q_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.20, per 1000 atoms: 0.62 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: 3.87 Conformation dependent library (CDL) restraints added in 2.0 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: 1.42 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: 4.09 Time building geometry restraints manager: 4.39 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: 1.340 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: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.890 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.040 ------------------------------------------------------------------------------- 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 : 0.009 0.153 13440 Z= 0.407 Angle : 0.981 23.459 18315 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 Details of bonding type rmsd hydrogen bonds : bond 0.14215 ( 680) hydrogen bonds : angle 6.78600 ( 1941) metal coordination : bond 0.12709 ( 4) metal coordination : angle 12.19713 ( 12) covalent geometry : bond 0.00845 (13436) covalent geometry : angle 0.92979 (18303) *********************** 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 : 1.472 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: 0.2846 time to fit residues: 68.6410 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 : 1.462 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106783 restraints weight = 19207.524| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.90 r_work: 0.3123 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 13440 Z= 0.136 Angle : 0.645 15.356 18315 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 Details of bonding type rmsd hydrogen bonds : bond 0.04816 ( 680) hydrogen bonds : angle 4.98479 ( 1941) metal coordination : bond 0.00795 ( 4) metal coordination : angle 7.38331 ( 12) covalent geometry : bond 0.00288 (13436) covalent geometry : angle 0.61702 (18303) *********************** 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 : 1.392 Fit side-chains REVERT: A 180 HIS cc_start: 0.8234 (t70) cc_final: 0.7837 (t70) REVERT: A 245 PHE cc_start: 0.7612 (t80) cc_final: 0.7337 (t80) REVERT: C 233 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7646 (t0) REVERT: D 223 ASP cc_start: 0.7750 (m-30) cc_final: 0.7470 (m-30) REVERT: D 247 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6684 (mtm180) REVERT: D 406 GLU cc_start: 0.8244 (tt0) cc_final: 0.7971 (tt0) REVERT: D 590 ASN cc_start: 0.8422 (t0) cc_final: 0.8055 (t0) outliers start: 14 outliers final: 8 residues processed: 176 average time/residue: 0.3085 time to fit residues: 77.5901 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 : 1.521 ------------------------------------------------------------------------------- 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 87 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 170 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103400 restraints weight = 19515.275| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.94 r_work: 0.3083 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13440 Z= 0.176 Angle : 0.613 11.528 18315 Z= 0.306 Chirality : 0.043 0.175 2161 Planarity : 0.005 0.043 2375 Dihedral : 4.665 56.284 1918 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.53 % Allowed : 10.66 % Favored : 87.80 % 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: 0.31 (0.20), residues: 1729 helix: 1.20 (0.18), residues: 832 sheet: -0.35 (0.39), residues: 159 loop : -0.76 (0.22), residues: 738 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 0.025 0.002 TYR B 4 ARG 0.004 0.001 ARG D 147 Details of bonding type rmsd hydrogen bonds : bond 0.04908 ( 680) hydrogen bonds : angle 4.74553 ( 1941) metal coordination : bond 0.00939 ( 4) metal coordination : angle 6.54224 ( 12) covalent geometry : bond 0.00419 (13436) covalent geometry : angle 0.58949 (18303) *********************** 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 177 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.414 Fit side-chains REVERT: A 148 ARG cc_start: 0.8605 (ttm-80) cc_final: 0.8225 (tpp80) REVERT: B 12 TYR cc_start: 0.9235 (m-10) cc_final: 0.8863 (m-80) REVERT: B 250 MET cc_start: 0.8783 (mmp) cc_final: 0.8247 (mmp) REVERT: C 233 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7846 (t0) REVERT: D 223 ASP cc_start: 0.7823 (m-30) cc_final: 0.7554 (m-30) REVERT: D 517 GLN cc_start: 0.8424 (mt0) cc_final: 0.7997 (pm20) REVERT: D 590 ASN cc_start: 0.8471 (t0) cc_final: 0.8126 (t0) outliers start: 21 outliers final: 14 residues processed: 171 average time/residue: 0.2713 time to fit residues: 66.6747 Evaluate side-chains 162 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 146 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 468 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.132087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104148 restraints weight = 19330.599| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.94 r_work: 0.3081 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13440 Z= 0.147 Angle : 0.569 10.442 18315 Z= 0.284 Chirality : 0.042 0.166 2161 Planarity : 0.004 0.042 2375 Dihedral : 4.485 58.434 1918 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.97 % Allowed : 13.08 % Favored : 84.95 % 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: 1.36 (0.18), residues: 840 sheet: -0.41 (0.40), residues: 159 loop : -0.64 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 280 HIS 0.004 0.001 HIS D 558 PHE 0.017 0.001 PHE C 177 TYR 0.022 0.001 TYR B 4 ARG 0.007 0.001 ARG D 247 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 680) hydrogen bonds : angle 4.55562 ( 1941) metal coordination : bond 0.00753 ( 4) metal coordination : angle 6.03516 ( 12) covalent geometry : bond 0.00345 (13436) covalent geometry : angle 0.54809 (18303) *********************** 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 182 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.175 Fit side-chains REVERT: A 148 ARG cc_start: 0.8709 (ttm-80) cc_final: 0.8347 (tpp80) REVERT: B 12 TYR cc_start: 0.9239 (m-10) cc_final: 0.8891 (m-80) REVERT: B 250 MET cc_start: 0.8800 (mmp) cc_final: 0.8248 (mmp) REVERT: C 179 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8400 (ttt-90) REVERT: C 233 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7943 (t0) REVERT: D 135 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7560 (mp) REVERT: D 223 ASP cc_start: 0.7845 (m-30) cc_final: 0.7569 (m-30) REVERT: D 517 GLN cc_start: 0.8422 (mt0) cc_final: 0.7981 (pm20) REVERT: D 590 ASN cc_start: 0.8471 (t0) cc_final: 0.8148 (t0) outliers start: 27 outliers final: 19 residues processed: 174 average time/residue: 0.2902 time to fit residues: 71.2772 Evaluate side-chains 165 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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 74 VAL 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 179 ARG Chi-restraints excluded: chain C residue 233 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 92 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 126 optimal weight: 0.0770 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 88 optimal weight: 0.0970 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 overall best weight: 0.7938 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.133930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106411 restraints weight = 19404.862| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.92 r_work: 0.3116 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13440 Z= 0.106 Angle : 0.528 8.873 18315 Z= 0.265 Chirality : 0.040 0.172 2161 Planarity : 0.004 0.041 2375 Dihedral : 4.286 58.004 1918 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.75 % Allowed : 14.32 % Favored : 83.93 % 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: 0.77 (0.20), residues: 1729 helix: 1.59 (0.18), residues: 840 sheet: -0.48 (0.39), residues: 172 loop : -0.47 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 280 HIS 0.004 0.001 HIS D 558 PHE 0.015 0.001 PHE C 177 TYR 0.018 0.001 TYR B 4 ARG 0.005 0.000 ARG D 247 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 680) hydrogen bonds : angle 4.38963 ( 1941) metal coordination : bond 0.00420 ( 4) metal coordination : angle 5.12285 ( 12) covalent geometry : bond 0.00229 (13436) covalent geometry : angle 0.51176 (18303) *********************** 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 180 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 1.559 Fit side-chains REVERT: B 12 TYR cc_start: 0.9211 (m-10) cc_final: 0.8824 (m-80) REVERT: B 250 MET cc_start: 0.8709 (mmp) cc_final: 0.8153 (mmp) REVERT: C 233 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7815 (t0) REVERT: D 223 ASP cc_start: 0.7826 (m-30) cc_final: 0.7567 (m-30) REVERT: D 517 GLN cc_start: 0.8412 (mt0) cc_final: 0.8042 (pm20) REVERT: D 590 ASN cc_start: 0.8447 (t0) cc_final: 0.8191 (t0) outliers start: 24 outliers final: 15 residues processed: 173 average time/residue: 0.2703 time to fit residues: 67.2869 Evaluate side-chains 165 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 1.469 ------------------------------------------------------------------------------- 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 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 D residue 21 VAL Chi-restraints excluded: chain D residue 39 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.106167 restraints weight = 19637.380| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.97 r_work: 0.3105 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13440 Z= 0.118 Angle : 0.523 8.987 18315 Z= 0.262 Chirality : 0.041 0.175 2161 Planarity : 0.004 0.042 2375 Dihedral : 4.202 58.366 1918 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.97 % Allowed : 15.56 % Favored : 82.47 % 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: 0.86 (0.20), residues: 1729 helix: 1.67 (0.18), residues: 840 sheet: -0.46 (0.40), residues: 172 loop : -0.44 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 280 HIS 0.003 0.001 HIS D 558 PHE 0.015 0.001 PHE C 177 TYR 0.020 0.001 TYR B 4 ARG 0.004 0.000 ARG D 122 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 680) hydrogen bonds : angle 4.31966 ( 1941) metal coordination : bond 0.00578 ( 4) metal coordination : angle 4.96139 ( 12) covalent geometry : bond 0.00272 (13436) covalent geometry : angle 0.50774 (18303) *********************** 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 190 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 1.383 Fit side-chains REVERT: A 148 ARG cc_start: 0.8676 (ttm-80) cc_final: 0.8402 (ttp-110) REVERT: B 8 ARG cc_start: 0.8335 (mtp85) cc_final: 0.8011 (mtp85) REVERT: B 12 TYR cc_start: 0.9215 (m-10) cc_final: 0.8890 (m-80) REVERT: B 250 MET cc_start: 0.8711 (mmp) cc_final: 0.8130 (mmp) REVERT: C 233 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7882 (t0) REVERT: D 223 ASP cc_start: 0.7816 (m-30) cc_final: 0.7565 (m-30) REVERT: D 590 ASN cc_start: 0.8464 (t0) cc_final: 0.8232 (t0) outliers start: 27 outliers final: 21 residues processed: 179 average time/residue: 0.2548 time to fit residues: 66.4107 Evaluate side-chains 170 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 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 468 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.129089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.100856 restraints weight = 19650.060| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.96 r_work: 0.3037 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13440 Z= 0.252 Angle : 0.634 12.007 18315 Z= 0.318 Chirality : 0.045 0.196 2161 Planarity : 0.005 0.045 2375 Dihedral : 4.485 58.203 1918 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.34 % Allowed : 16.00 % Favored : 81.67 % 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: 0.49 (0.20), residues: 1729 helix: 1.37 (0.18), residues: 838 sheet: -0.65 (0.39), residues: 169 loop : -0.61 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 339 HIS 0.004 0.001 HIS D 558 PHE 0.019 0.002 PHE A 474 TYR 0.030 0.002 TYR B 4 ARG 0.005 0.001 ARG B 244 Details of bonding type rmsd hydrogen bonds : bond 0.05052 ( 680) hydrogen bonds : angle 4.57278 ( 1941) metal coordination : bond 0.01269 ( 4) metal coordination : angle 6.27323 ( 12) covalent geometry : bond 0.00606 (13436) covalent geometry : angle 0.61371 (18303) *********************** 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 179 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 1.742 Fit side-chains REVERT: C 233 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8014 (t0) REVERT: D 223 ASP cc_start: 0.7867 (m-30) cc_final: 0.7606 (m-30) REVERT: D 590 ASN cc_start: 0.8548 (t0) cc_final: 0.8280 (t0) outliers start: 32 outliers final: 25 residues processed: 169 average time/residue: 0.3024 time to fit residues: 75.8092 Evaluate side-chains 163 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 1.342 ------------------------------------------------------------------------------- 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 289 ASP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 160 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 75 optimal weight: 0.8980 chunk 142 optimal weight: 0.3980 chunk 52 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 44 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.134466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107255 restraints weight = 19384.075| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.89 r_work: 0.3121 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13440 Z= 0.100 Angle : 0.533 8.359 18315 Z= 0.268 Chirality : 0.040 0.185 2161 Planarity : 0.004 0.065 2375 Dihedral : 4.230 58.594 1918 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.68 % Allowed : 17.17 % Favored : 81.15 % 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: 0.84 (0.20), residues: 1729 helix: 1.69 (0.18), residues: 839 sheet: -0.64 (0.39), residues: 174 loop : -0.43 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 280 HIS 0.003 0.001 HIS A 106 PHE 0.014 0.001 PHE C 177 TYR 0.020 0.001 TYR D 243 ARG 0.007 0.001 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 680) hydrogen bonds : angle 4.31067 ( 1941) metal coordination : bond 0.00256 ( 4) metal coordination : angle 4.88944 ( 12) covalent geometry : bond 0.00213 (13436) covalent geometry : angle 0.51792 (18303) *********************** 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 182 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.491 Fit side-chains REVERT: B 12 TYR cc_start: 0.9198 (m-10) cc_final: 0.8918 (m-80) REVERT: B 90 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8411 (tt0) REVERT: B 288 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7616 (mt0) REVERT: C 233 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7812 (t0) REVERT: D 223 ASP cc_start: 0.7795 (m-30) cc_final: 0.7535 (m-30) outliers start: 23 outliers final: 19 residues processed: 175 average time/residue: 0.2581 time to fit residues: 65.7397 Evaluate side-chains 171 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 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 D residue 21 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 187 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 5 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 139 optimal weight: 0.0670 chunk 87 optimal weight: 2.9990 chunk 163 optimal weight: 0.0020 chunk 83 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 overall best weight: 0.9930 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105251 restraints weight = 19313.514| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.01 r_work: 0.3100 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13440 Z= 0.108 Angle : 0.531 9.922 18315 Z= 0.267 Chirality : 0.040 0.189 2161 Planarity : 0.004 0.046 2375 Dihedral : 4.147 58.583 1918 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.75 % Allowed : 17.24 % Favored : 81.01 % 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: 0.93 (0.21), residues: 1729 helix: 1.77 (0.18), residues: 839 sheet: -0.64 (0.39), residues: 174 loop : -0.39 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 280 HIS 0.003 0.001 HIS B 54 PHE 0.013 0.001 PHE C 177 TYR 0.021 0.001 TYR D 243 ARG 0.004 0.000 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 680) hydrogen bonds : angle 4.26203 ( 1941) metal coordination : bond 0.00456 ( 4) metal coordination : angle 4.61000 ( 12) covalent geometry : bond 0.00244 (13436) covalent geometry : angle 0.51754 (18303) *********************** 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 179 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 1.495 Fit side-chains REVERT: B 8 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7909 (mtp85) REVERT: B 12 TYR cc_start: 0.9139 (m-10) cc_final: 0.8840 (m-80) REVERT: B 288 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: C 233 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8004 (t0) outliers start: 24 outliers final: 20 residues processed: 171 average time/residue: 0.2591 time to fit residues: 64.7784 Evaluate side-chains 172 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 135 LEU Chi-restraints excluded: chain D residue 187 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 170 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104579 restraints weight = 19262.184| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.98 r_work: 0.3092 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13440 Z= 0.126 Angle : 0.543 9.712 18315 Z= 0.274 Chirality : 0.041 0.195 2161 Planarity : 0.004 0.045 2375 Dihedral : 4.155 58.494 1918 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.68 % Allowed : 17.82 % Favored : 80.50 % 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: 0.89 (0.20), residues: 1729 helix: 1.77 (0.18), residues: 831 sheet: -0.63 (0.39), residues: 175 loop : -0.43 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 280 HIS 0.003 0.001 HIS D 558 PHE 0.044 0.001 PHE D 444 TYR 0.021 0.001 TYR D 243 ARG 0.005 0.000 ARG B 126 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 680) hydrogen bonds : angle 4.27199 ( 1941) metal coordination : bond 0.00553 ( 4) metal coordination : angle 4.70791 ( 12) covalent geometry : bond 0.00295 (13436) covalent geometry : angle 0.52919 (18303) ********************** 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 173 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 4.664 Fit side-chains REVERT: B 8 ARG cc_start: 0.8278 (mtp85) cc_final: 0.7914 (mtp85) REVERT: B 12 TYR cc_start: 0.9141 (m-10) cc_final: 0.8825 (m-80) REVERT: B 288 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: C 233 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8010 (t0) outliers start: 23 outliers final: 19 residues processed: 165 average time/residue: 0.3114 time to fit residues: 74.5420 Evaluate side-chains 166 residues out of total 1369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 135 LEU Chi-restraints excluded: chain D residue 187 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 133 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 139 optimal weight: 0.0370 chunk 67 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 overall best weight: 2.0064 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.131492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.103289 restraints weight = 19399.304| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.05 r_work: 0.3064 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13440 Z= 0.151 Angle : 0.563 10.110 18315 Z= 0.283 Chirality : 0.042 0.199 2161 Planarity : 0.004 0.046 2375 Dihedral : 4.231 58.468 1918 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.68 % Allowed : 17.75 % Favored : 80.57 % 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: 0.80 (0.20), residues: 1729 helix: 1.70 (0.18), residues: 835 sheet: -0.74 (0.39), residues: 174 loop : -0.49 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 280 HIS 0.003 0.001 HIS D 558 PHE 0.036 0.002 PHE D 444 TYR 0.023 0.001 TYR B 4 ARG 0.007 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 680) hydrogen bonds : angle 4.31015 ( 1941) metal coordination : bond 0.00740 ( 4) metal coordination : angle 5.09081 ( 12) covalent geometry : bond 0.00360 (13436) covalent geometry : angle 0.54827 (18303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7457.92 seconds wall clock time: 130 minutes 28.17 seconds (7828.17 seconds total)