Starting phenix.real_space_refine on Wed Jul 30 03:51:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rwc_24714/07_2025/7rwc_24714.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rwc_24714/07_2025/7rwc_24714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rwc_24714/07_2025/7rwc_24714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rwc_24714/07_2025/7rwc_24714.map" model { file = "/net/cci-nas-00/data/ceres_data/7rwc_24714/07_2025/7rwc_24714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rwc_24714/07_2025/7rwc_24714.cif" } resolution = 3.8 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= 0.006 sd= 0.117 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 7857 2.51 5 N 2070 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12110 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4551 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 22, 'TRANS': 590} Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 17, 'GLU:plan': 22, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 196 Chain: "B" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 3760 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 201} Link IDs: {'PTRANS': 26, 'TRANS': 530} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 663 Unresolved non-hydrogen angles: 817 Unresolved non-hydrogen dihedrals: 525 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 29, 'TYR:plan': 2, 'ASN:plan1': 21, 'HIS:plan': 2, 'GLU:plan': 35, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 402 Chain: "M" Number of atoms: 2644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 2644 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 17, 'TRANS': 375} Chain breaks: 2 Unresolved non-hydrogen bonds: 540 Unresolved non-hydrogen angles: 646 Unresolved non-hydrogen dihedrals: 453 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 325 Chain: "S" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1115 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 141} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 60 Chain: "P" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 7.59, per 1000 atoms: 0.63 Number of scatterers: 12110 At special positions: 0 Unit cell: (128.76, 115.44, 108.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 2136 8.00 N 2070 7.00 C 7857 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: 2.89 Conformation dependent library (CDL) restraints added in 1.7 seconds 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3312 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 10 sheets defined 62.1% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.663A pdb=" N VAL A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 45 Processing helix chain 'A' and resid 51 through 69 removed outlier: 3.859A pdb=" N GLY A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.749A pdb=" N VAL A 80 " --> pdb=" O HIS A 76 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.509A pdb=" N ALA A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 139 removed outlier: 4.009A pdb=" N VAL A 138 " --> pdb=" O CYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.794A pdb=" N VAL A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 188 through 197 removed outlier: 4.040A pdb=" N ASN A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 218 Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.891A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 273 through 293 Processing helix chain 'A' and resid 299 through 321 removed outlier: 3.940A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.742A pdb=" N ARG A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.045A pdb=" N HIS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 384 through 397 Processing helix chain 'A' and resid 401 through 415 removed outlier: 3.770A pdb=" N THR A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 6.030A pdb=" N SER A 419 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 420 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 421 " --> pdb=" O TYR A 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 416 through 421' Processing helix chain 'A' and resid 422 through 435 Processing helix chain 'A' and resid 438 through 453 removed outlier: 3.960A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.855A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 3.950A pdb=" N GLN A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'A' and resid 508 through 511 removed outlier: 3.644A pdb=" N ILE A 511 " --> pdb=" O GLY A 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 508 through 511' Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.505A pdb=" N GLN A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.982A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 563 Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.544A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 590 removed outlier: 3.632A pdb=" N ALA A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.522A pdb=" N LEU A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 620 removed outlier: 3.704A pdb=" N ALA A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 62 through 78 removed outlier: 3.655A pdb=" N TYR B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.892A pdb=" N ILE B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 4.651A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 3.862A pdb=" N LYS B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 149 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.900A pdb=" N GLN B 159 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 removed outlier: 3.725A pdb=" N VAL B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 removed outlier: 3.549A pdb=" N GLU B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 227 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 254 through 266 Processing helix chain 'B' and resid 276 through 291 Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 295 through 313 Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.616A pdb=" N VAL B 323 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE B 325 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 350 through 362 Processing helix chain 'B' and resid 366 through 384 removed outlier: 3.785A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.515A pdb=" N ARG B 419 " --> pdb=" O ARG B 415 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 434 removed outlier: 3.960A pdb=" N THR B 431 " --> pdb=" O SER B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 455 Processing helix chain 'B' and resid 461 through 470 removed outlier: 3.525A pdb=" N LEU B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 516 through 533 Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.596A pdb=" N LEU B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 565 removed outlier: 3.768A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 removed outlier: 4.046A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 Processing helix chain 'M' and resid 25 through 38 removed outlier: 3.530A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.572A pdb=" N VAL M 78 " --> pdb=" O ASN M 74 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 104 through 115 Processing helix chain 'M' and resid 125 through 131 removed outlier: 3.955A pdb=" N THR M 131 " --> pdb=" O GLY M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 383 removed outlier: 3.603A pdb=" N ALA M 382 " --> pdb=" O LYS M 379 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG M 383 " --> pdb=" O LYS M 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 379 through 383' Processing helix chain 'M' and resid 414 through 418 Processing helix chain 'S' and resid 24 through 42 removed outlier: 3.902A pdb=" N GLN S 29 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 96 Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 118 Processing helix chain 'S' and resid 127 through 137 removed outlier: 3.604A pdb=" N VAL S 131 " --> pdb=" O SER S 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 19 removed outlier: 3.999A pdb=" N ILE M 16 " --> pdb=" O ILE M 7 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL M 68 " --> pdb=" O GLY M 4 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE M 56 " --> pdb=" O ALA M 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 116 through 117 removed outlier: 3.793A pdb=" N ASP M 117 " --> pdb=" O TYR M 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 172 through 173 removed outlier: 4.268A pdb=" N GLU M 172 " --> pdb=" O TYR M 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 176 through 185 removed outlier: 3.653A pdb=" N VAL M 201 " --> pdb=" O ASP M 176 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU M 178 " --> pdb=" O ARG M 199 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER M 193 " --> pdb=" O LEU M 184 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY M 198 " --> pdb=" O ARG M 276 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG M 276 " --> pdb=" O GLY M 198 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL M 200 " --> pdb=" O LEU M 274 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET M 202 " --> pdb=" O PHE M 272 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE M 272 " --> pdb=" O MET M 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 264 through 265 removed outlier: 3.930A pdb=" N PHE M 265 " --> pdb=" O CYS M 212 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS M 212 " --> pdb=" O PHE M 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 289 through 291 removed outlier: 3.574A pdb=" N VAL M 306 " --> pdb=" O ILE M 290 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL M 303 " --> pdb=" O ALA M 368 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE M 366 " --> pdb=" O VAL M 305 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE M 307 " --> pdb=" O SER M 364 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER M 364 " --> pdb=" O ILE M 307 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN M 334 " --> pdb=" O GLU M 369 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU M 371 " --> pdb=" O GLY M 332 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 341 through 345 removed outlier: 3.669A pdb=" N LYS M 341 " --> pdb=" O LYS M 354 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 341 through 345 removed outlier: 3.669A pdb=" N LYS M 341 " --> pdb=" O LYS M 354 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.998A pdb=" N THR S 14 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ASN S 9 " --> pdb=" O THR S 14 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU S 16 " --> pdb=" O ILE S 7 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2232 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: 3.48 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3895 1.34 - 1.45: 1375 1.45 - 1.57: 6994 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 12334 Sorted by residual: bond pdb=" CA THR A 238 " pdb=" CB THR A 238 " ideal model delta sigma weight residual 1.524 1.547 -0.023 1.62e-02 3.81e+03 2.00e+00 bond pdb=" CB VAL A 483 " pdb=" CG1 VAL A 483 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.69e+00 bond pdb=" CA MET A 10 " pdb=" C MET A 10 " ideal model delta sigma weight residual 1.520 1.534 -0.014 1.20e-02 6.94e+03 1.27e+00 bond pdb=" N ILE M 430 " pdb=" CA ILE M 430 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.17e+00 bond pdb=" CB GLU S 82 " pdb=" CG GLU S 82 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.11e+00 ... (remaining 12329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 16438 1.56 - 3.12: 395 3.12 - 4.68: 51 4.68 - 6.24: 19 6.24 - 7.80: 5 Bond angle restraints: 16908 Sorted by residual: angle pdb=" N VAL B 506 " pdb=" CA VAL B 506 " pdb=" C VAL B 506 " ideal model delta sigma weight residual 113.53 108.45 5.08 9.80e-01 1.04e+00 2.69e+01 angle pdb=" N LEU A 201 " pdb=" CA LEU A 201 " pdb=" C LEU A 201 " ideal model delta sigma weight residual 114.75 109.12 5.63 1.26e+00 6.30e-01 2.00e+01 angle pdb=" N GLU B 501 " pdb=" CA GLU B 501 " pdb=" C GLU B 501 " ideal model delta sigma weight residual 114.16 108.36 5.80 1.48e+00 4.57e-01 1.54e+01 angle pdb=" CA GLN A 199 " pdb=" C GLN A 199 " pdb=" O GLN A 199 " ideal model delta sigma weight residual 121.67 117.91 3.76 1.26e+00 6.30e-01 8.91e+00 angle pdb=" N SER A 384 " pdb=" CA SER A 384 " pdb=" C SER A 384 " ideal model delta sigma weight residual 113.88 110.43 3.45 1.23e+00 6.61e-01 7.86e+00 ... (remaining 16903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 6755 17.52 - 35.03: 491 35.03 - 52.55: 81 52.55 - 70.07: 6 70.07 - 87.58: 10 Dihedral angle restraints: 7343 sinusoidal: 2267 harmonic: 5076 Sorted by residual: dihedral pdb=" CA SER A 458 " pdb=" C SER A 458 " pdb=" N GLU A 459 " pdb=" CA GLU A 459 " ideal model delta harmonic sigma weight residual 180.00 157.89 22.11 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA GLU A 460 " pdb=" C GLU A 460 " pdb=" N VAL A 461 " pdb=" CA VAL A 461 " ideal model delta harmonic sigma weight residual 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASN M 74 " pdb=" C ASN M 74 " pdb=" N ALA M 75 " pdb=" CA ALA M 75 " ideal model delta harmonic sigma weight residual -180.00 -162.64 -17.36 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 7340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1461 0.038 - 0.075: 511 0.075 - 0.113: 134 0.113 - 0.151: 25 0.151 - 0.188: 3 Chirality restraints: 2134 Sorted by residual: chirality pdb=" CG LEU A 201 " pdb=" CB LEU A 201 " pdb=" CD1 LEU A 201 " pdb=" CD2 LEU A 201 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CB THR A 238 " pdb=" CA THR A 238 " pdb=" OG1 THR A 238 " pdb=" CG2 THR A 238 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA ILE S 58 " pdb=" N ILE S 58 " pdb=" C ILE S 58 " pdb=" CB ILE S 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 2131 not shown) Planarity restraints: 2134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 268 " 0.061 5.00e-02 4.00e+02 9.20e-02 1.35e+01 pdb=" N PRO A 269 " -0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 269 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO A 270 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 270 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 270 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 22 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C ASN A 22 " -0.025 2.00e-02 2.50e+03 pdb=" O ASN A 22 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS A 23 " 0.008 2.00e-02 2.50e+03 ... (remaining 2131 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 417 2.72 - 3.27: 12578 3.27 - 3.81: 19597 3.81 - 4.36: 21547 4.36 - 4.90: 38183 Nonbonded interactions: 92322 Sorted by model distance: nonbonded pdb=" O LEU B 507 " pdb=" OG1 THR B 511 " model vdw 2.175 3.040 nonbonded pdb=" OG SER M 97 " pdb=" OD1 ASN M 100 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR S 62 " pdb=" ND1 HIS S 85 " model vdw 2.264 3.120 nonbonded pdb=" O PHE M 287 " pdb=" OH TYR M 431 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASP A 321 " pdb=" OG SER A 359 " model vdw 2.299 3.040 ... (remaining 92317 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.860 Find NCS groups from input model: 0.150 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 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 : 0.004 0.043 12334 Z= 0.159 Angle : 0.605 7.802 16908 Z= 0.334 Chirality : 0.041 0.188 2134 Planarity : 0.004 0.092 2134 Dihedral : 12.871 87.582 4031 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.55 % Favored : 94.39 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1693 helix: 1.43 (0.17), residues: 966 sheet: -0.16 (0.44), residues: 156 loop : -1.82 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 462 HIS 0.011 0.001 HIS A 76 PHE 0.015 0.001 PHE A 66 TYR 0.017 0.001 TYR A 463 ARG 0.004 0.000 ARG B 520 Details of bonding type rmsd hydrogen bonds : bond 0.15245 ( 750) hydrogen bonds : angle 6.19134 ( 2232) covalent geometry : bond 0.00364 (12334) covalent geometry : angle 0.60481 (16908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7544 (tp) cc_final: 0.6923 (tp) REVERT: A 552 PHE cc_start: 0.7651 (m-80) cc_final: 0.7168 (m-10) REVERT: B 379 ARG cc_start: 0.7620 (ttm170) cc_final: 0.7406 (ttp-170) REVERT: M 187 PRO cc_start: 0.7193 (Cg_exo) cc_final: 0.6852 (Cg_endo) outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 0.2273 time to fit residues: 59.4736 Evaluate side-chains 138 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 153 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 200 HIS A 387 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.227758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.218367 restraints weight = 13920.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.204020 restraints weight = 29455.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.201843 restraints weight = 33329.671| |-----------------------------------------------------------------------------| r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12334 Z= 0.136 Angle : 0.538 7.507 16908 Z= 0.284 Chirality : 0.041 0.193 2134 Planarity : 0.004 0.071 2134 Dihedral : 3.951 28.642 1818 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.67 % Allowed : 9.25 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1693 helix: 1.41 (0.17), residues: 982 sheet: -0.16 (0.46), residues: 154 loop : -1.78 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.004 0.001 HIS A 76 PHE 0.014 0.001 PHE M 93 TYR 0.012 0.001 TYR A 247 ARG 0.004 0.000 ARG A 579 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 750) hydrogen bonds : angle 4.66275 ( 2232) covalent geometry : bond 0.00318 (12334) covalent geometry : angle 0.53750 (16908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 1.331 Fit side-chains revert: symmetry clash REVERT: A 62 LEU cc_start: 0.7378 (tp) cc_final: 0.7109 (tp) REVERT: M 162 ARG cc_start: 0.4508 (ptt180) cc_final: 0.3559 (mpp80) REVERT: M 187 PRO cc_start: 0.7794 (Cg_exo) cc_final: 0.7524 (Cg_endo) REVERT: M 216 MET cc_start: 0.6728 (ppp) cc_final: 0.5969 (ppp) REVERT: M 425 ILE cc_start: 0.8562 (mm) cc_final: 0.8262 (mm) outliers start: 18 outliers final: 8 residues processed: 165 average time/residue: 0.1973 time to fit residues: 49.8653 Evaluate side-chains 152 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 46 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 113 optimal weight: 0.0470 chunk 137 optimal weight: 0.0000 chunk 149 optimal weight: 20.0000 chunk 155 optimal weight: 0.5980 chunk 133 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 151 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN M 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.235044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.222410 restraints weight = 14254.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.207597 restraints weight = 35837.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.205060 restraints weight = 27890.794| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12334 Z= 0.114 Angle : 0.495 6.628 16908 Z= 0.264 Chirality : 0.040 0.197 2134 Planarity : 0.004 0.061 2134 Dihedral : 3.738 20.781 1816 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.67 % Allowed : 11.93 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1693 helix: 1.57 (0.17), residues: 978 sheet: -0.28 (0.45), residues: 154 loop : -1.76 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 462 HIS 0.003 0.001 HIS S 36 PHE 0.013 0.001 PHE A 66 TYR 0.013 0.001 TYR A 418 ARG 0.003 0.000 ARG A 579 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 750) hydrogen bonds : angle 4.31599 ( 2232) covalent geometry : bond 0.00258 (12334) covalent geometry : angle 0.49455 (16908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.325 Fit side-chains REVERT: A 615 LYS cc_start: 0.8053 (ttpp) cc_final: 0.7562 (ttpp) REVERT: B 208 LEU cc_start: 0.6815 (mm) cc_final: 0.6134 (tp) REVERT: B 357 GLU cc_start: 0.7145 (tp30) cc_final: 0.6836 (tp30) REVERT: B 361 TYR cc_start: 0.6943 (m-10) cc_final: 0.6529 (m-10) REVERT: M 77 MET cc_start: 0.7731 (ttp) cc_final: 0.7144 (ttp) REVERT: M 162 ARG cc_start: 0.4877 (ptt180) cc_final: 0.3837 (mpp80) REVERT: M 187 PRO cc_start: 0.7879 (Cg_exo) cc_final: 0.7626 (Cg_endo) REVERT: M 216 MET cc_start: 0.6717 (ppp) cc_final: 0.5724 (ppp) outliers start: 18 outliers final: 12 residues processed: 163 average time/residue: 0.2019 time to fit residues: 50.8229 Evaluate side-chains 152 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain M residue 349 ASN Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 128 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 61 optimal weight: 20.0000 chunk 89 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 130 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 133 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN M 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.231260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.222195 restraints weight = 14060.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.203512 restraints weight = 23453.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.200750 restraints weight = 20682.257| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12334 Z= 0.149 Angle : 0.518 6.738 16908 Z= 0.274 Chirality : 0.041 0.212 2134 Planarity : 0.004 0.059 2134 Dihedral : 3.759 19.072 1816 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.78 % Allowed : 13.14 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1693 helix: 1.56 (0.17), residues: 977 sheet: -0.36 (0.45), residues: 154 loop : -1.79 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 462 HIS 0.004 0.001 HIS S 85 PHE 0.014 0.001 PHE A 66 TYR 0.018 0.001 TYR A 88 ARG 0.003 0.000 ARG S 42 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 750) hydrogen bonds : angle 4.19779 ( 2232) covalent geometry : bond 0.00364 (12334) covalent geometry : angle 0.51813 (16908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.403 Fit side-chains REVERT: A 615 LYS cc_start: 0.8105 (ttpp) cc_final: 0.7548 (ttpp) REVERT: M 1 MET cc_start: 0.7650 (ptp) cc_final: 0.7432 (mtm) REVERT: M 77 MET cc_start: 0.7752 (ttp) cc_final: 0.7247 (ttp) REVERT: M 162 ARG cc_start: 0.4986 (ptt180) cc_final: 0.4061 (mpp80) REVERT: M 187 PRO cc_start: 0.8024 (Cg_exo) cc_final: 0.7768 (Cg_endo) REVERT: M 216 MET cc_start: 0.6751 (ppp) cc_final: 0.5631 (ppp) outliers start: 30 outliers final: 20 residues processed: 173 average time/residue: 0.2040 time to fit residues: 54.5697 Evaluate side-chains 159 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 107 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 349 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.230383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.220975 restraints weight = 14064.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.201624 restraints weight = 22919.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.199400 restraints weight = 27283.029| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12334 Z= 0.146 Angle : 0.518 6.720 16908 Z= 0.273 Chirality : 0.041 0.215 2134 Planarity : 0.004 0.056 2134 Dihedral : 3.782 18.614 1816 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.96 % Favored : 94.98 % Rotamer: Outliers : 3.24 % Allowed : 15.26 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1693 helix: 1.54 (0.17), residues: 978 sheet: -0.37 (0.45), residues: 154 loop : -1.83 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 462 HIS 0.005 0.001 HIS B 566 PHE 0.013 0.001 PHE M 93 TYR 0.016 0.001 TYR A 418 ARG 0.004 0.000 ARG S 42 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 750) hydrogen bonds : angle 4.13215 ( 2232) covalent geometry : bond 0.00354 (12334) covalent geometry : angle 0.51780 (16908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 1.350 Fit side-chains REVERT: A 249 TYR cc_start: 0.8434 (t80) cc_final: 0.8017 (t80) REVERT: B 208 LEU cc_start: 0.6536 (mm) cc_final: 0.5881 (tp) REVERT: B 562 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8135 (tm-30) REVERT: M 1 MET cc_start: 0.7775 (ptp) cc_final: 0.7563 (mtm) REVERT: M 162 ARG cc_start: 0.5032 (ptt180) cc_final: 0.3979 (mpp80) REVERT: M 216 MET cc_start: 0.6656 (ppp) cc_final: 0.5619 (ppp) REVERT: S 42 ARG cc_start: 0.8012 (mtp85) cc_final: 0.7656 (mtp85) outliers start: 35 outliers final: 24 residues processed: 170 average time/residue: 0.1999 time to fit residues: 52.5390 Evaluate side-chains 166 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 25 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 109 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 139 optimal weight: 10.0000 chunk 161 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.230118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.220603 restraints weight = 14310.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.201640 restraints weight = 24143.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.199056 restraints weight = 25195.447| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12334 Z= 0.139 Angle : 0.514 7.313 16908 Z= 0.272 Chirality : 0.041 0.229 2134 Planarity : 0.004 0.054 2134 Dihedral : 3.758 19.876 1816 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.73 % Favored : 95.22 % Rotamer: Outliers : 3.33 % Allowed : 16.65 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1693 helix: 1.56 (0.17), residues: 978 sheet: -0.40 (0.45), residues: 154 loop : -1.82 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 PHE 0.014 0.001 PHE S 55 TYR 0.015 0.001 TYR A 418 ARG 0.007 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 750) hydrogen bonds : angle 4.07701 ( 2232) covalent geometry : bond 0.00338 (12334) covalent geometry : angle 0.51380 (16908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.251 Fit side-chains REVERT: A 249 TYR cc_start: 0.8413 (t80) cc_final: 0.8077 (t80) REVERT: A 577 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.6794 (tt0) REVERT: B 313 ARG cc_start: 0.7695 (tpp80) cc_final: 0.7222 (tpp-160) REVERT: B 562 GLU cc_start: 0.8785 (tm-30) cc_final: 0.7976 (tm-30) REVERT: M 162 ARG cc_start: 0.5278 (ptt180) cc_final: 0.4344 (mpp80) REVERT: M 216 MET cc_start: 0.6553 (ppp) cc_final: 0.5434 (ppp) REVERT: S 42 ARG cc_start: 0.8004 (mtp85) cc_final: 0.7674 (mtp85) outliers start: 36 outliers final: 28 residues processed: 176 average time/residue: 0.2056 time to fit residues: 55.2686 Evaluate side-chains 165 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain S residue 135 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 127 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.231226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.221927 restraints weight = 14226.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.200711 restraints weight = 22762.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.201249 restraints weight = 19025.623| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12334 Z= 0.126 Angle : 0.509 7.350 16908 Z= 0.267 Chirality : 0.041 0.204 2134 Planarity : 0.004 0.053 2134 Dihedral : 3.708 18.033 1816 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.73 % Favored : 95.22 % Rotamer: Outliers : 3.61 % Allowed : 17.39 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1693 helix: 1.61 (0.17), residues: 979 sheet: -0.35 (0.45), residues: 154 loop : -1.83 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 PHE 0.014 0.001 PHE M 93 TYR 0.013 0.001 TYR A 418 ARG 0.005 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 750) hydrogen bonds : angle 4.00184 ( 2232) covalent geometry : bond 0.00301 (12334) covalent geometry : angle 0.50935 (16908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 1.349 Fit side-chains REVERT: A 62 LEU cc_start: 0.7079 (tp) cc_final: 0.6727 (tp) REVERT: A 249 TYR cc_start: 0.8289 (t80) cc_final: 0.7963 (t80) REVERT: A 577 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.6740 (tt0) REVERT: B 208 LEU cc_start: 0.6407 (OUTLIER) cc_final: 0.5975 (tp) REVERT: B 313 ARG cc_start: 0.7682 (tpp80) cc_final: 0.7261 (tpp-160) REVERT: B 340 ASP cc_start: 0.8167 (t0) cc_final: 0.7948 (t0) REVERT: B 562 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8008 (tm-30) REVERT: M 77 MET cc_start: 0.7579 (ttp) cc_final: 0.6807 (ttp) REVERT: M 162 ARG cc_start: 0.5457 (ptt180) cc_final: 0.4476 (mpp80) REVERT: M 216 MET cc_start: 0.6549 (ppp) cc_final: 0.5418 (ppp) REVERT: M 425 ILE cc_start: 0.8606 (mt) cc_final: 0.8370 (mt) REVERT: S 42 ARG cc_start: 0.8004 (mtp85) cc_final: 0.7700 (mtp85) outliers start: 39 outliers final: 31 residues processed: 176 average time/residue: 0.2243 time to fit residues: 62.1396 Evaluate side-chains 174 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain S residue 135 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 160 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 131 optimal weight: 0.2980 chunk 127 optimal weight: 2.9990 chunk 136 optimal weight: 0.0470 chunk 168 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 91 optimal weight: 0.0870 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.233112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.222005 restraints weight = 14208.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.206555 restraints weight = 29403.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.203640 restraints weight = 21854.413| |-----------------------------------------------------------------------------| r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12334 Z= 0.110 Angle : 0.494 6.664 16908 Z= 0.259 Chirality : 0.040 0.255 2134 Planarity : 0.003 0.052 2134 Dihedral : 3.634 17.339 1816 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 3.33 % Allowed : 18.32 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1693 helix: 1.70 (0.17), residues: 983 sheet: -0.38 (0.44), residues: 156 loop : -1.77 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 PHE 0.022 0.001 PHE S 55 TYR 0.015 0.001 TYR A 418 ARG 0.004 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.03295 ( 750) hydrogen bonds : angle 3.91551 ( 2232) covalent geometry : bond 0.00254 (12334) covalent geometry : angle 0.49375 (16908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 1.231 Fit side-chains REVERT: A 577 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.6720 (tt0) REVERT: B 208 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6042 (tp) REVERT: B 313 ARG cc_start: 0.7695 (tpp80) cc_final: 0.7289 (tpp-160) REVERT: B 340 ASP cc_start: 0.8136 (t0) cc_final: 0.7894 (t0) REVERT: B 542 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8058 (mp) REVERT: B 562 GLU cc_start: 0.8799 (tm-30) cc_final: 0.7928 (tm-30) REVERT: M 162 ARG cc_start: 0.5469 (ptt180) cc_final: 0.4423 (mpp80) REVERT: M 216 MET cc_start: 0.6630 (ppp) cc_final: 0.5579 (ppp) REVERT: M 425 ILE cc_start: 0.8636 (mt) cc_final: 0.8388 (mt) REVERT: S 42 ARG cc_start: 0.8015 (mtp85) cc_final: 0.7675 (mtp85) outliers start: 36 outliers final: 25 residues processed: 179 average time/residue: 0.1963 time to fit residues: 53.7085 Evaluate side-chains 180 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 342 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 135 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 162 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 87 optimal weight: 0.0270 chunk 166 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 160 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.0770 chunk 167 optimal weight: 0.7980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.232715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.224057 restraints weight = 14119.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.206083 restraints weight = 27576.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.204644 restraints weight = 26002.094| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12334 Z= 0.117 Angle : 0.504 6.857 16908 Z= 0.264 Chirality : 0.041 0.249 2134 Planarity : 0.004 0.051 2134 Dihedral : 3.620 16.833 1816 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 3.05 % Allowed : 19.61 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.21), residues: 1693 helix: 1.72 (0.17), residues: 981 sheet: -0.37 (0.44), residues: 156 loop : -1.80 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 462 HIS 0.003 0.001 HIS M 57 PHE 0.021 0.001 PHE A 66 TYR 0.012 0.001 TYR A 88 ARG 0.004 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 750) hydrogen bonds : angle 3.90913 ( 2232) covalent geometry : bond 0.00276 (12334) covalent geometry : angle 0.50415 (16908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.342 Fit side-chains REVERT: A 577 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.6720 (tt0) REVERT: B 208 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6041 (tp) REVERT: B 340 ASP cc_start: 0.8091 (t0) cc_final: 0.7854 (t0) REVERT: B 542 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8093 (mp) REVERT: B 562 GLU cc_start: 0.8746 (tm-30) cc_final: 0.7993 (tm-30) REVERT: M 1 MET cc_start: 0.7652 (ptp) cc_final: 0.7112 (mtm) REVERT: M 162 ARG cc_start: 0.5364 (ptt180) cc_final: 0.4314 (mpp80) REVERT: M 216 MET cc_start: 0.6447 (ppp) cc_final: 0.5481 (ppp) REVERT: M 425 ILE cc_start: 0.8624 (mt) cc_final: 0.8368 (mt) REVERT: S 42 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7694 (mtp85) outliers start: 33 outliers final: 27 residues processed: 173 average time/residue: 0.2056 time to fit residues: 54.8755 Evaluate side-chains 173 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 414 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain M residue 303 VAL Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 135 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 6 optimal weight: 0.0470 chunk 127 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 125 optimal weight: 0.0980 chunk 149 optimal weight: 0.0010 chunk 49 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.235783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.227018 restraints weight = 14141.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.211915 restraints weight = 25437.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.208988 restraints weight = 27493.061| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 12334 Z= 0.101 Angle : 0.494 9.443 16908 Z= 0.258 Chirality : 0.041 0.246 2134 Planarity : 0.004 0.050 2134 Dihedral : 3.521 16.345 1816 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 2.68 % Allowed : 19.98 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1693 helix: 1.84 (0.17), residues: 984 sheet: -0.28 (0.45), residues: 152 loop : -1.78 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 462 HIS 0.003 0.001 HIS S 36 PHE 0.035 0.001 PHE A 66 TYR 0.012 0.001 TYR A 418 ARG 0.006 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 750) hydrogen bonds : angle 3.82491 ( 2232) covalent geometry : bond 0.00227 (12334) covalent geometry : angle 0.49436 (16908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3386 Ramachandran restraints generated. 1693 Oldfield, 0 Emsley, 1693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 1.235 Fit side-chains REVERT: A 185 MET cc_start: 0.8155 (mmt) cc_final: 0.7921 (mmt) REVERT: A 577 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.6742 (tt0) REVERT: B 208 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6101 (tp) REVERT: B 313 ARG cc_start: 0.7740 (tpp80) cc_final: 0.7192 (tpp-160) REVERT: B 340 ASP cc_start: 0.8006 (t0) cc_final: 0.7760 (t0) REVERT: B 542 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8070 (mp) REVERT: B 562 GLU cc_start: 0.8665 (tm-30) cc_final: 0.7906 (tm-30) REVERT: M 162 ARG cc_start: 0.5192 (ptt180) cc_final: 0.4156 (mpp80) REVERT: M 216 MET cc_start: 0.6269 (ppp) cc_final: 0.5417 (ppp) REVERT: M 425 ILE cc_start: 0.8572 (mt) cc_final: 0.8293 (mt) REVERT: S 42 ARG cc_start: 0.7966 (mtp85) cc_final: 0.7652 (mtp85) outliers start: 29 outliers final: 22 residues processed: 168 average time/residue: 0.1946 time to fit residues: 50.4327 Evaluate side-chains 169 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 550 ASN Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 316 LEU Chi-restraints excluded: chain M residue 320 ILE Chi-restraints excluded: chain S residue 135 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN M 349 ASN S 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.230015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.220827 restraints weight = 14173.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.205172 restraints weight = 28629.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.202820 restraints weight = 27994.985| |-----------------------------------------------------------------------------| r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12334 Z= 0.156 Angle : 0.547 15.201 16908 Z= 0.282 Chirality : 0.042 0.254 2134 Planarity : 0.004 0.052 2134 Dihedral : 3.639 16.419 1816 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 2.78 % Allowed : 20.35 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1693 helix: 1.66 (0.17), residues: 985 sheet: -0.28 (0.45), residues: 152 loop : -1.77 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 353 HIS 0.005 0.001 HIS S 85 PHE 0.032 0.002 PHE A 66 TYR 0.013 0.001 TYR A 418 ARG 0.006 0.000 ARG B 313 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 750) hydrogen bonds : angle 3.93246 ( 2232) covalent geometry : bond 0.00385 (12334) covalent geometry : angle 0.54748 (16908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.40 seconds wall clock time: 60 minutes 10.37 seconds (3610.37 seconds total)