Starting phenix.real_space_refine on Sat Jun 14 09:16:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vnz_43362/06_2025/8vnz_43362.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vnz_43362/06_2025/8vnz_43362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vnz_43362/06_2025/8vnz_43362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vnz_43362/06_2025/8vnz_43362.map" model { file = "/net/cci-nas-00/data/ceres_data/8vnz_43362/06_2025/8vnz_43362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vnz_43362/06_2025/8vnz_43362.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1328 atoms to isotropic. 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 95 5.16 5 C 9363 2.51 5 N 2650 2.21 5 O 2663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14771 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3340 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 19, 'TRANS': 419} Chain breaks: 7 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 356 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 9, 'ASN:plan1': 9, 'HIS:plan': 1, 'GLU:plan': 16, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 184 Chain: "L" Number of atoms: 2874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2874 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 349} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "N" Number of atoms: 3080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3080 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 22, 'TRANS': 372} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 4288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4288 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 33, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 594 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 477 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'ASP:plan': 15, 'PHE:plan': 6, 'GLU:plan': 27, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 367 Chain: "B" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 290 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 36} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'M3L:plan-1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "P" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 873 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 7, 'TRANS': 109} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 10.25, per 1000 atoms: 0.69 Number of scatterers: 14771 At special positions: 0 Unit cell: (157.5, 110.25, 109.2, 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 95 16.00 O 2663 8.00 N 2650 7.00 C 9363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 523 " - pdb=" SG CYS C 534 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.90 Conformation dependent library (CDL) restraints added in 3.0 seconds 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3752 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 25 sheets defined 25.0% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 83 through 107 removed outlier: 3.770A pdb=" N LYS A 92 " --> pdb=" O GLN A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix removed outlier: 3.567A pdb=" N TYR A 97 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 134 through 146 Processing helix chain 'A' and resid 459 through 471 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 539 through 543 removed outlier: 3.679A pdb=" N GLU A 542 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 removed outlier: 4.005A pdb=" N GLU A 580 " --> pdb=" O GLN A 577 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 581 " --> pdb=" O GLU A 578 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 577 through 581' Processing helix chain 'A' and resid 589 through 603 removed outlier: 3.608A pdb=" N ILE A 597 " --> pdb=" O ARG A 593 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 603 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 625 removed outlier: 5.017A pdb=" N VAL A 613 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 618 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 651 removed outlier: 3.700A pdb=" N HIS A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A 637 " --> pdb=" O ASN A 633 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLN A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LYS A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 666 removed outlier: 3.681A pdb=" N LEU A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 680 removed outlier: 3.797A pdb=" N ASP A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 676 " --> pdb=" O MET A 672 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 677 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 279 Processing helix chain 'L' and resid 395 through 399 removed outlier: 3.556A pdb=" N ALA L 399 " --> pdb=" O PRO L 396 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 27 Processing helix chain 'N' and resid 348 through 350 No H-bonds generated for 'chain 'N' and resid 348 through 350' Processing helix chain 'N' and resid 355 through 362 removed outlier: 3.616A pdb=" N ASP N 361 " --> pdb=" O GLU N 357 " (cutoff:3.500A) Processing helix chain 'N' and resid 406 through 409 Processing helix chain 'C' and resid 18 through 34 Processing helix chain 'C' and resid 34 through 63 removed outlier: 4.125A pdb=" N ILE C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 removed outlier: 4.065A pdb=" N ARG C 78 " --> pdb=" O SER C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 removed outlier: 3.626A pdb=" N GLN C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 154 removed outlier: 4.066A pdb=" N GLU C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 176 removed outlier: 3.730A pdb=" N VAL C 175 " --> pdb=" O PHE C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 231 Processing helix chain 'C' and resid 238 through 250 removed outlier: 4.112A pdb=" N GLU C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 removed outlier: 4.194A pdb=" N SER C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 313 removed outlier: 3.501A pdb=" N THR C 313 " --> pdb=" O ASN C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 339 Processing helix chain 'C' and resid 433 through 444 Processing helix chain 'C' and resid 450 through 458 removed outlier: 3.941A pdb=" N ILE C 454 " --> pdb=" O ASN C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 477 removed outlier: 3.984A pdb=" N TYR C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU C 468 " --> pdb=" O ARG C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 513 removed outlier: 3.735A pdb=" N LYS C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP C 511 " --> pdb=" O GLN C 507 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER C 513 " --> pdb=" O LYS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 571 through 576 Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 648 through 662 removed outlier: 4.189A pdb=" N VAL C 657 " --> pdb=" O ARG C 653 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 687 removed outlier: 3.519A pdb=" N ARG C 685 " --> pdb=" O ASN C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 737 Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.805A pdb=" N ARG B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 209 Processing helix chain 'P' and resid 255 through 259 Processing helix chain 'P' and resid 276 through 281 removed outlier: 4.159A pdb=" N LEU P 279 " --> pdb=" O THR P 276 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU P 280 " --> pdb=" O ALA P 277 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP P 281 " --> pdb=" O LEU P 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 276 through 281' Processing sheet with id=AA1, first strand: chain 'A' and resid 230 through 232 removed outlier: 6.604A pdb=" N GLN A 356 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N PHE A 164 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR A 354 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 314 " --> pdb=" O LYS P 231 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU P 241 " --> pdb=" O VAL P 252 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL P 252 " --> pdb=" O LEU P 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 207 Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 207 removed outlier: 3.646A pdb=" N VAL A 189 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 249 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 428 through 433 removed outlier: 6.082A pdb=" N PHE A 429 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL A 489 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN A 431 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ILE A 491 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N LEU A 433 " --> pdb=" O ILE A 491 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 557 through 560 removed outlier: 3.556A pdb=" N THR A 526 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 525 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL N 35 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU N 34 " --> pdb=" O GLN N 403 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE N 398 " --> pdb=" O SER N 394 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER N 394 " --> pdb=" O ILE N 398 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE N 390 " --> pdb=" O TRP N 402 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER N 381 " --> pdb=" O CYS N 391 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP N 379 " --> pdb=" O VAL N 393 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 82 through 83 removed outlier: 3.940A pdb=" N TRP L 435 " --> pdb=" O ALA L 427 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 89 through 90 Processing sheet with id=AA8, first strand: chain 'L' and resid 99 through 101 Processing sheet with id=AA9, first strand: chain 'L' and resid 99 through 101 Processing sheet with id=AB1, first strand: chain 'L' and resid 147 through 154 removed outlier: 3.540A pdb=" N ALA L 166 " --> pdb=" O THR L 149 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE L 171 " --> pdb=" O GLY L 167 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASN L 176 " --> pdb=" O CYS L 182 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N CYS L 182 " --> pdb=" O ASN L 176 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 196 through 198 removed outlier: 3.716A pdb=" N LYS L 197 " --> pdb=" O LEU L 207 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU L 217 " --> pdb=" O VAL L 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 239 through 244 removed outlier: 3.635A pdb=" N SER L 241 " --> pdb=" O CYS L 254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 309 through 315 removed outlier: 3.676A pdb=" N CYS L 311 " --> pdb=" O LYS L 322 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER L 323 " --> pdb=" O ALA L 327 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA L 327 " --> pdb=" O SER L 323 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY L 354 " --> pdb=" O CYS L 330 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LYS L 332 " --> pdb=" O ILE L 352 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE L 352 " --> pdb=" O LYS L 332 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 368 through 370 removed outlier: 4.192A pdb=" N SER L 369 " --> pdb=" O ALA L 378 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA L 378 " --> pdb=" O SER L 369 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR L 402 " --> pdb=" O VAL L 388 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 48 through 49 removed outlier: 3.701A pdb=" N GLN N 48 " --> pdb=" O VAL N 67 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL N 80 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE N 119 " --> pdb=" O ILE N 81 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER N 83 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE N 117 " --> pdb=" O SER N 83 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLN N 85 " --> pdb=" O ILE N 115 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE N 115 " --> pdb=" O GLN N 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 131 through 132 removed outlier: 3.505A pdb=" N ARG N 131 " --> pdb=" O ALA N 141 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA N 141 " --> pdb=" O ARG N 131 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU N 171 " --> pdb=" O VAL N 151 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ARG N 172 " --> pdb=" O VAL N 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 183 through 185 removed outlier: 3.758A pdb=" N SER N 195 " --> pdb=" O CYS N 203 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR N 221 " --> pdb=" O LEU N 204 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 230 through 236 removed outlier: 3.729A pdb=" N ASP N 232 " --> pdb=" O VAL N 246 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU N 242 " --> pdb=" O HIS N 236 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 276 through 281 removed outlier: 4.483A pdb=" N HIS N 311 " --> pdb=" O LEU N 300 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 320 through 325 removed outlier: 3.762A pdb=" N VAL N 344 " --> pdb=" O PHE N 368 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE N 368 " --> pdb=" O VAL N 344 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASP N 346 " --> pdb=" O LEU N 366 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU N 366 " --> pdb=" O ASP N 346 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.090A pdb=" N SER C 114 " --> pdb=" O GLY C 681 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 614 through 618 Processing sheet with id=AC5, first strand: chain 'C' and resid 637 through 638 removed outlier: 3.831A pdb=" N ILE C 710 " --> pdb=" O ILE C 638 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C 709 " --> pdb=" O LYS C 698 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N CYS C 695 " --> pdb=" O ASP C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 644 through 647 removed outlier: 3.608A pdb=" N ILE C 646 " --> pdb=" O VAL C 674 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 219 through 223 491 hydrogen bonds defined for protein. 1362 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: 5.42 Time building geometry restraints manager: 4.65 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: 4901 1.34 - 1.46: 3211 1.46 - 1.58: 6890 1.58 - 1.70: 1 1.70 - 1.82: 131 Bond restraints: 15134 Sorted by residual: bond pdb=" C2 SAH C 801 " pdb=" N3 SAH C 801 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.52e+00 bond pdb=" CB PRO P 282 " pdb=" CG PRO P 282 " ideal model delta sigma weight residual 1.492 1.625 -0.133 5.00e-02 4.00e+02 7.13e+00 bond pdb=" C8 SAH C 801 " pdb=" N7 SAH C 801 " ideal model delta sigma weight residual 1.299 1.350 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" C2 SAH C 801 " pdb=" N1 SAH C 801 " ideal model delta sigma weight residual 1.330 1.380 -0.050 2.00e-02 2.50e+03 6.33e+00 bond pdb=" C6 SAH C 801 " pdb=" N1 SAH C 801 " ideal model delta sigma weight residual 1.338 1.379 -0.041 2.00e-02 2.50e+03 4.23e+00 ... (remaining 15129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 20352 2.52 - 5.05: 209 5.05 - 7.57: 26 7.57 - 10.09: 5 10.09 - 12.61: 3 Bond angle restraints: 20595 Sorted by residual: angle pdb=" CA PRO P 282 " pdb=" N PRO P 282 " pdb=" CD PRO P 282 " ideal model delta sigma weight residual 112.00 100.55 11.45 1.40e+00 5.10e-01 6.69e+01 angle pdb=" N ILE N 207 " pdb=" CA ILE N 207 " pdb=" C ILE N 207 " ideal model delta sigma weight residual 111.91 107.95 3.96 8.90e-01 1.26e+00 1.98e+01 angle pdb=" C ASN L 93 " pdb=" N GLN L 94 " pdb=" CA GLN L 94 " ideal model delta sigma weight residual 122.71 110.10 12.61 3.03e+00 1.09e-01 1.73e+01 angle pdb=" CG SAH C 801 " pdb=" SD SAH C 801 " pdb=" C5' SAH C 801 " ideal model delta sigma weight residual 101.77 90.88 10.89 3.00e+00 1.11e-01 1.32e+01 angle pdb=" N VAL L 383 " pdb=" CA VAL L 383 " pdb=" C VAL L 383 " ideal model delta sigma weight residual 112.29 108.95 3.34 9.40e-01 1.13e+00 1.26e+01 ... (remaining 20590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8257 17.99 - 35.97: 614 35.97 - 53.96: 117 53.96 - 71.95: 17 71.95 - 89.93: 4 Dihedral angle restraints: 9009 sinusoidal: 3261 harmonic: 5748 Sorted by residual: dihedral pdb=" CA CYS L 324 " pdb=" C CYS L 324 " pdb=" N GLU L 325 " pdb=" CA GLU L 325 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PHE C 667 " pdb=" C PHE C 667 " pdb=" N ASN C 668 " pdb=" CA ASN C 668 " ideal model delta harmonic sigma weight residual 180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LEU C 666 " pdb=" C LEU C 666 " pdb=" N PHE C 667 " pdb=" CA PHE C 667 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 9006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1775 0.047 - 0.094: 389 0.094 - 0.141: 130 0.141 - 0.188: 5 0.188 - 0.235: 1 Chirality restraints: 2300 Sorted by residual: chirality pdb=" CA PRO P 282 " pdb=" N PRO P 282 " pdb=" C PRO P 282 " pdb=" CB PRO P 282 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ASN L 119 " pdb=" N ASN L 119 " pdb=" C ASN L 119 " pdb=" CB ASN L 119 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA VAL C 157 " pdb=" N VAL C 157 " pdb=" C VAL C 157 " pdb=" CB VAL C 157 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 2297 not shown) Planarity restraints: 2668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP P 281 " -0.078 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO P 282 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO P 282 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO P 282 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET N 133 " -0.058 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO N 134 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO N 134 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO N 134 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 534 " -0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO C 535 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 535 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 535 " -0.031 5.00e-02 4.00e+02 ... (remaining 2665 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 600 2.71 - 3.26: 15538 3.26 - 3.81: 25232 3.81 - 4.35: 31038 4.35 - 4.90: 50313 Nonbonded interactions: 122721 Sorted by model distance: nonbonded pdb=" O LEU A 311 " pdb=" OH TYR A 315 " model vdw 2.163 3.040 nonbonded pdb=" O GLU N 118 " pdb=" OG SER N 159 " model vdw 2.202 3.040 nonbonded pdb=" O TYR A 248 " pdb=" OG1 THR A 300 " model vdw 2.230 3.040 nonbonded pdb=" ND2 ASN L 326 " pdb=" O TYR L 358 " model vdw 2.233 3.120 nonbonded pdb=" OG1 THR N 72 " pdb=" O GLU N 75 " model vdw 2.234 3.040 ... (remaining 122716 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: 59.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 39.250 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 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:4.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 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 : 0.003 0.133 15135 Z= 0.130 Angle : 0.648 12.614 20597 Z= 0.336 Chirality : 0.043 0.235 2300 Planarity : 0.005 0.109 2668 Dihedral : 13.113 89.933 5254 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.35 % Allowed : 17.82 % Favored : 81.84 % 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: -1.00 (0.19), residues: 1924 helix: 0.25 (0.25), residues: 445 sheet: -0.44 (0.27), residues: 366 loop : -1.12 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 301 HIS 0.007 0.001 HIS P 268 PHE 0.024 0.001 PHE L 299 TYR 0.013 0.001 TYR C 448 ARG 0.006 0.000 ARG C 741 Details of bonding type rmsd hydrogen bonds : bond 0.23937 ( 479) hydrogen bonds : angle 8.93069 ( 1362) SS BOND : bond 0.00369 ( 1) SS BOND : angle 1.18830 ( 2) covalent geometry : bond 0.00287 (15134) covalent geometry : angle 0.64759 (20595) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 125 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8131 (mmp) cc_final: 0.7798 (mmp) REVERT: C 47 GLN cc_start: 0.8469 (mm-40) cc_final: 0.7572 (tm-30) REVERT: P 195 LEU cc_start: 0.8035 (mm) cc_final: 0.7588 (tt) outliers start: 5 outliers final: 4 residues processed: 127 average time/residue: 0.2452 time to fit residues: 49.1447 Evaluate side-chains 124 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 593 HIS Chi-restraints excluded: chain C residue 628 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 175 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 ASN A 659 HIS L 136 GLN ** L 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.084806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.073503 restraints weight = 93465.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.074845 restraints weight = 59440.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.075758 restraints weight = 42950.901| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15135 Z= 0.183 Angle : 0.651 8.991 20597 Z= 0.341 Chirality : 0.045 0.172 2300 Planarity : 0.005 0.061 2668 Dihedral : 5.189 40.313 2099 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.59 % Allowed : 16.09 % Favored : 80.32 % 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: -1.07 (0.19), residues: 1924 helix: 0.27 (0.25), residues: 451 sheet: -0.73 (0.26), residues: 359 loop : -1.11 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 235 HIS 0.009 0.001 HIS C 129 PHE 0.021 0.002 PHE C 724 TYR 0.022 0.002 TYR N 32 ARG 0.006 0.001 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.04902 ( 479) hydrogen bonds : angle 6.59223 ( 1362) SS BOND : bond 0.00585 ( 1) SS BOND : angle 1.71287 ( 2) covalent geometry : bond 0.00406 (15134) covalent geometry : angle 0.65114 (20595) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 123 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8287 (mmp) cc_final: 0.8030 (mmp) REVERT: N 253 MET cc_start: 0.6189 (mmt) cc_final: 0.5543 (mmt) REVERT: C 47 GLN cc_start: 0.8582 (mm-40) cc_final: 0.7784 (tm-30) REVERT: P 195 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7635 (tt) outliers start: 52 outliers final: 34 residues processed: 168 average time/residue: 0.2420 time to fit residues: 65.9318 Evaluate side-chains 143 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 258 HIS Chi-restraints excluded: chain L residue 308 TYR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 356 PHE Chi-restraints excluded: chain L residue 383 VAL Chi-restraints excluded: chain L residue 438 ASP Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 593 HIS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 278 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 96 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** L 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 GLN P 223 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.085657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.074397 restraints weight = 93027.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.075785 restraints weight = 58921.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.076728 restraints weight = 41996.639| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15135 Z= 0.130 Angle : 0.593 9.961 20597 Z= 0.307 Chirality : 0.044 0.155 2300 Planarity : 0.004 0.066 2668 Dihedral : 5.015 39.316 2097 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.35 % Allowed : 16.37 % Favored : 79.28 % 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: -1.12 (0.19), residues: 1924 helix: 0.30 (0.25), residues: 458 sheet: -0.80 (0.26), residues: 359 loop : -1.16 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 388 HIS 0.010 0.001 HIS C 129 PHE 0.013 0.001 PHE C 667 TYR 0.020 0.002 TYR L 244 ARG 0.005 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 479) hydrogen bonds : angle 6.19264 ( 1362) SS BOND : bond 0.00424 ( 1) SS BOND : angle 1.74610 ( 2) covalent geometry : bond 0.00288 (15134) covalent geometry : angle 0.59235 (20595) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 115 time to evaluate : 1.773 Fit side-chains revert: symmetry clash REVERT: N 133 MET cc_start: 0.6681 (mmm) cc_final: 0.3973 (mmm) REVERT: N 253 MET cc_start: 0.5814 (mmt) cc_final: 0.4793 (mmt) REVERT: C 47 GLN cc_start: 0.8516 (mm-40) cc_final: 0.7779 (tm-30) REVERT: C 728 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.7021 (t80) REVERT: P 195 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7410 (tt) outliers start: 63 outliers final: 36 residues processed: 167 average time/residue: 0.2714 time to fit residues: 72.8977 Evaluate side-chains 147 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 308 TYR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 356 PHE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 438 ASP Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 593 HIS Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 728 TYR Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 226 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 181 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.084711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.073829 restraints weight = 98117.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.075202 restraints weight = 60276.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.076135 restraints weight = 42557.624| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15135 Z= 0.175 Angle : 0.632 10.094 20597 Z= 0.328 Chirality : 0.045 0.162 2300 Planarity : 0.004 0.066 2668 Dihedral : 5.103 37.821 2094 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 4.49 % Allowed : 17.27 % Favored : 78.25 % 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: -1.20 (0.19), residues: 1924 helix: 0.26 (0.25), residues: 458 sheet: -0.78 (0.27), residues: 340 loop : -1.26 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 388 HIS 0.012 0.001 HIS C 129 PHE 0.018 0.002 PHE C 724 TYR 0.022 0.002 TYR L 244 ARG 0.003 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 479) hydrogen bonds : angle 6.10966 ( 1362) SS BOND : bond 0.00488 ( 1) SS BOND : angle 1.65913 ( 2) covalent geometry : bond 0.00388 (15134) covalent geometry : angle 0.63158 (20595) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 113 time to evaluate : 1.786 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.8754 (pmm) cc_final: 0.7964 (pmm) REVERT: N 253 MET cc_start: 0.6001 (mmt) cc_final: 0.4940 (mmt) REVERT: C 47 GLN cc_start: 0.8539 (mm-40) cc_final: 0.7836 (tm-30) REVERT: C 439 MET cc_start: 0.7548 (mmt) cc_final: 0.7292 (tpp) outliers start: 65 outliers final: 50 residues processed: 171 average time/residue: 0.2444 time to fit residues: 65.7241 Evaluate side-chains 158 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 108 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 258 HIS Chi-restraints excluded: chain L residue 308 TYR Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 343 ILE Chi-restraints excluded: chain L residue 353 LEU Chi-restraints excluded: chain L residue 356 PHE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 383 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 593 HIS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 278 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 108 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 0.0870 chunk 123 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 49 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** L 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.086023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.074553 restraints weight = 91921.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.075896 restraints weight = 59038.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.076848 restraints weight = 43058.314| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15135 Z= 0.113 Angle : 0.587 7.668 20597 Z= 0.302 Chirality : 0.044 0.152 2300 Planarity : 0.004 0.066 2668 Dihedral : 4.876 36.820 2094 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 4.28 % Allowed : 18.09 % Favored : 77.62 % 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: -1.15 (0.19), residues: 1924 helix: 0.32 (0.25), residues: 464 sheet: -0.88 (0.27), residues: 345 loop : -1.20 (0.18), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 301 HIS 0.011 0.001 HIS C 129 PHE 0.014 0.001 PHE N 368 TYR 0.019 0.001 TYR L 244 ARG 0.003 0.000 ARG C 741 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 479) hydrogen bonds : angle 5.80983 ( 1362) SS BOND : bond 0.00462 ( 1) SS BOND : angle 1.28674 ( 2) covalent geometry : bond 0.00250 (15134) covalent geometry : angle 0.58691 (20595) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 121 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 252 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8400 (pt) REVERT: N 253 MET cc_start: 0.5919 (mmt) cc_final: 0.5144 (mmt) REVERT: C 42 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7290 (m-10) REVERT: C 47 GLN cc_start: 0.8425 (mm-40) cc_final: 0.7831 (tm-30) REVERT: C 565 GLN cc_start: 0.6843 (OUTLIER) cc_final: 0.6532 (pp30) REVERT: C 700 MET cc_start: 0.5452 (ttt) cc_final: 0.4633 (tmm) REVERT: P 193 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8141 (pp30) REVERT: P 195 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7481 (tt) REVERT: P 288 MET cc_start: 0.8065 (mmp) cc_final: 0.7664 (mmt) outliers start: 62 outliers final: 45 residues processed: 172 average time/residue: 0.2287 time to fit residues: 62.8362 Evaluate side-chains 161 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 111 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 308 TYR Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 343 ILE Chi-restraints excluded: chain L residue 356 PHE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 383 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 565 GLN Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 593 HIS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 193 GLN Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 226 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 41 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS L 104 HIS ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 ASN ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 415 GLN ** N 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 250 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.080412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.069400 restraints weight = 96721.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.070687 restraints weight = 61725.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.071536 restraints weight = 44646.455| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 15135 Z= 0.363 Angle : 0.860 8.361 20597 Z= 0.453 Chirality : 0.051 0.327 2300 Planarity : 0.006 0.068 2668 Dihedral : 6.337 59.098 2094 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 29.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 5.46 % Allowed : 18.65 % Favored : 75.90 % 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: -1.91 (0.18), residues: 1924 helix: -0.45 (0.23), residues: 453 sheet: -1.01 (0.27), residues: 322 loop : -1.73 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP N 388 HIS 0.014 0.002 HIS C 129 PHE 0.029 0.003 PHE A 656 TYR 0.029 0.004 TYR C 447 ARG 0.006 0.001 ARG L 439 Details of bonding type rmsd hydrogen bonds : bond 0.05606 ( 479) hydrogen bonds : angle 6.78530 ( 1362) SS BOND : bond 0.00746 ( 1) SS BOND : angle 2.57373 ( 2) covalent geometry : bond 0.00791 (15134) covalent geometry : angle 0.85953 (20595) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 103 time to evaluate : 1.749 Fit side-chains revert: symmetry clash REVERT: A 659 HIS cc_start: 0.7505 (OUTLIER) cc_final: 0.6778 (t-90) REVERT: L 358 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.5104 (p90) REVERT: N 133 MET cc_start: 0.6604 (mmm) cc_final: 0.5089 (tmm) REVERT: N 253 MET cc_start: 0.6014 (mmt) cc_final: 0.5065 (mmt) REVERT: C 47 GLN cc_start: 0.8595 (mm-40) cc_final: 0.7838 (tm-30) REVERT: C 134 MET cc_start: 0.5236 (ppp) cc_final: 0.5023 (ppp) REVERT: P 190 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.4732 (t80) outliers start: 79 outliers final: 56 residues processed: 172 average time/residue: 0.2251 time to fit residues: 62.8079 Evaluate side-chains 160 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 101 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 172 ILE Chi-restraints excluded: chain L residue 204 ASN Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 258 HIS Chi-restraints excluded: chain L residue 308 TYR Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 343 ILE Chi-restraints excluded: chain L residue 353 LEU Chi-restraints excluded: chain L residue 356 PHE Chi-restraints excluded: chain L residue 358 TYR Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 383 VAL Chi-restraints excluded: chain L residue 404 LEU Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain L residue 438 ASP Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 593 HIS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 225 THR Chi-restraints excluded: chain P residue 270 SER Chi-restraints excluded: chain P residue 278 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 66 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 30.0000 chunk 142 optimal weight: 0.6980 chunk 10 optimal weight: 20.0000 chunk 158 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.083845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.072719 restraints weight = 94014.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.074072 restraints weight = 59003.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.074993 restraints weight = 42080.788| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15135 Z= 0.143 Angle : 0.653 8.760 20597 Z= 0.338 Chirality : 0.045 0.154 2300 Planarity : 0.004 0.068 2668 Dihedral : 5.613 52.511 2094 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.94 % Allowed : 20.51 % Favored : 75.55 % 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: -1.47 (0.19), residues: 1924 helix: 0.07 (0.25), residues: 454 sheet: -0.97 (0.26), residues: 343 loop : -1.44 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 591 HIS 0.013 0.001 HIS C 129 PHE 0.045 0.002 PHE A 132 TYR 0.020 0.002 TYR L 244 ARG 0.006 0.000 ARG C 578 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 479) hydrogen bonds : angle 6.07810 ( 1362) SS BOND : bond 0.00246 ( 1) SS BOND : angle 1.53368 ( 2) covalent geometry : bond 0.00317 (15134) covalent geometry : angle 0.65249 (20595) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 108 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 659 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.6741 (t-90) REVERT: L 308 TYR cc_start: 0.6678 (OUTLIER) cc_final: 0.6468 (p90) REVERT: N 253 MET cc_start: 0.6096 (mmt) cc_final: 0.4961 (mmt) REVERT: C 47 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7843 (tm-30) REVERT: P 185 ARG cc_start: 0.5533 (mtt90) cc_final: 0.3483 (mmt90) outliers start: 57 outliers final: 44 residues processed: 156 average time/residue: 0.2241 time to fit residues: 55.7875 Evaluate side-chains 149 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 258 HIS Chi-restraints excluded: chain L residue 308 TYR Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 343 ILE Chi-restraints excluded: chain L residue 353 LEU Chi-restraints excluded: chain L residue 356 PHE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 383 VAL Chi-restraints excluded: chain L residue 404 LEU Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 593 HIS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 278 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 86 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 192 optimal weight: 0.0470 chunk 118 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 overall best weight: 0.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.084989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.073827 restraints weight = 91769.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.075205 restraints weight = 57542.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.076157 restraints weight = 41125.818| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15135 Z= 0.124 Angle : 0.627 7.646 20597 Z= 0.324 Chirality : 0.044 0.152 2300 Planarity : 0.004 0.065 2668 Dihedral : 5.303 52.041 2094 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.87 % Allowed : 20.10 % Favored : 76.04 % 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: -1.40 (0.19), residues: 1924 helix: 0.20 (0.25), residues: 456 sheet: -1.07 (0.27), residues: 337 loop : -1.38 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 301 HIS 0.013 0.001 HIS C 129 PHE 0.036 0.001 PHE A 132 TYR 0.021 0.001 TYR L 244 ARG 0.005 0.000 ARG C 741 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 479) hydrogen bonds : angle 5.80248 ( 1362) SS BOND : bond 0.00401 ( 1) SS BOND : angle 1.21724 ( 2) covalent geometry : bond 0.00276 (15134) covalent geometry : angle 0.62668 (20595) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 114 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.6539 (t-90) REVERT: L 308 TYR cc_start: 0.6614 (OUTLIER) cc_final: 0.6390 (p90) REVERT: N 253 MET cc_start: 0.6032 (mmt) cc_final: 0.5018 (mmt) REVERT: N 369 ILE cc_start: 0.6111 (tt) cc_final: 0.5892 (tt) REVERT: C 42 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7490 (m-10) REVERT: C 47 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7860 (tm-30) REVERT: P 185 ARG cc_start: 0.5621 (mtt90) cc_final: 0.3638 (mmt90) outliers start: 56 outliers final: 46 residues processed: 161 average time/residue: 0.2469 time to fit residues: 63.6011 Evaluate side-chains 155 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 106 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 258 HIS Chi-restraints excluded: chain L residue 308 TYR Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 343 ILE Chi-restraints excluded: chain L residue 353 LEU Chi-restraints excluded: chain L residue 356 PHE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 383 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 295 PHE Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 593 HIS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 278 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 181 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 153 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 329 ASN ** N 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.085744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.074977 restraints weight = 96155.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.076367 restraints weight = 58663.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.077295 restraints weight = 41229.464| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15135 Z= 0.126 Angle : 0.631 9.495 20597 Z= 0.324 Chirality : 0.044 0.153 2300 Planarity : 0.004 0.065 2668 Dihedral : 5.196 50.478 2094 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.87 % Allowed : 20.23 % Favored : 75.90 % 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: -1.30 (0.19), residues: 1924 helix: 0.33 (0.25), residues: 455 sheet: -0.97 (0.27), residues: 329 loop : -1.34 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP N 388 HIS 0.013 0.001 HIS C 129 PHE 0.034 0.002 PHE A 132 TYR 0.020 0.001 TYR L 244 ARG 0.007 0.000 ARG C 741 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 479) hydrogen bonds : angle 5.66323 ( 1362) SS BOND : bond 0.00393 ( 1) SS BOND : angle 1.11121 ( 2) covalent geometry : bond 0.00284 (15134) covalent geometry : angle 0.63141 (20595) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 113 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 HIS cc_start: 0.6917 (OUTLIER) cc_final: 0.6540 (t-90) REVERT: L 308 TYR cc_start: 0.6559 (OUTLIER) cc_final: 0.6336 (p90) REVERT: N 253 MET cc_start: 0.5964 (mmt) cc_final: 0.4917 (mmt) REVERT: N 319 GLU cc_start: 0.8013 (pt0) cc_final: 0.7801 (tm-30) REVERT: C 42 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7449 (m-10) REVERT: C 47 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7864 (tm-30) REVERT: P 185 ARG cc_start: 0.5655 (mtt90) cc_final: 0.3768 (mmt90) outliers start: 56 outliers final: 52 residues processed: 160 average time/residue: 0.2620 time to fit residues: 67.2266 Evaluate side-chains 164 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 109 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 258 HIS Chi-restraints excluded: chain L residue 308 TYR Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 343 ILE Chi-restraints excluded: chain L residue 353 LEU Chi-restraints excluded: chain L residue 356 PHE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 383 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 593 HIS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 225 THR Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 159 optimal weight: 0.0870 chunk 143 optimal weight: 20.0000 chunk 133 optimal weight: 50.0000 chunk 141 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 71 optimal weight: 0.0980 chunk 10 optimal weight: 6.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** L 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.085985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.075272 restraints weight = 97106.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.076648 restraints weight = 58928.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.077564 restraints weight = 41222.491| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15135 Z= 0.124 Angle : 0.634 11.173 20597 Z= 0.325 Chirality : 0.045 0.355 2300 Planarity : 0.004 0.065 2668 Dihedral : 5.079 48.286 2094 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.94 % Allowed : 20.30 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 1924 helix: 0.48 (0.25), residues: 445 sheet: -0.99 (0.27), residues: 340 loop : -1.28 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 388 HIS 0.012 0.001 HIS C 129 PHE 0.034 0.001 PHE A 132 TYR 0.019 0.001 TYR L 244 ARG 0.007 0.000 ARG C 741 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 479) hydrogen bonds : angle 5.57884 ( 1362) SS BOND : bond 0.00382 ( 1) SS BOND : angle 1.07037 ( 2) covalent geometry : bond 0.00277 (15134) covalent geometry : angle 0.63381 (20595) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3848 Ramachandran restraints generated. 1924 Oldfield, 0 Emsley, 1924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 112 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 632 MET cc_start: 0.7114 (mtp) cc_final: 0.6660 (mmt) REVERT: L 308 TYR cc_start: 0.6614 (OUTLIER) cc_final: 0.6384 (p90) REVERT: N 253 MET cc_start: 0.5955 (mmt) cc_final: 0.4890 (mmt) REVERT: N 319 GLU cc_start: 0.8005 (pt0) cc_final: 0.7797 (tm-30) REVERT: N 399 MET cc_start: 0.5360 (tpp) cc_final: 0.5137 (ttt) REVERT: C 42 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7468 (m-10) REVERT: C 47 GLN cc_start: 0.8384 (mm-40) cc_final: 0.7885 (tm-30) REVERT: P 185 ARG cc_start: 0.5610 (mtt90) cc_final: 0.3731 (mmt90) REVERT: P 190 PHE cc_start: 0.6253 (OUTLIER) cc_final: 0.5343 (t80) outliers start: 57 outliers final: 50 residues processed: 161 average time/residue: 0.2363 time to fit residues: 60.0671 Evaluate side-chains 163 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 110 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 PHE Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 659 HIS Chi-restraints excluded: chain A residue 664 HIS Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 195 GLU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 258 HIS Chi-restraints excluded: chain L residue 308 TYR Chi-restraints excluded: chain L residue 324 CYS Chi-restraints excluded: chain L residue 343 ILE Chi-restraints excluded: chain L residue 353 LEU Chi-restraints excluded: chain L residue 356 PHE Chi-restraints excluded: chain L residue 377 LEU Chi-restraints excluded: chain L residue 383 VAL Chi-restraints excluded: chain L residue 428 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 149 VAL Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 286 CYS Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 593 HIS Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain P residue 190 PHE Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 220 VAL Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 278 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 114 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 HIS ** N 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.083850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.072764 restraints weight = 93914.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.074102 restraints weight = 59190.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.075012 restraints weight = 42352.725| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15135 Z= 0.184 Angle : 0.674 9.302 20597 Z= 0.349 Chirality : 0.046 0.359 2300 Planarity : 0.004 0.062 2668 Dihedral : 5.292 45.067 2094 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 4.07 % Allowed : 19.89 % Favored : 76.04 % 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: -1.34 (0.19), residues: 1924 helix: 0.37 (0.25), residues: 448 sheet: -1.00 (0.27), residues: 342 loop : -1.40 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 388 HIS 0.013 0.001 HIS C 129 PHE 0.037 0.002 PHE A 132 TYR 0.019 0.002 TYR L 244 ARG 0.007 0.000 ARG C 741 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 479) hydrogen bonds : angle 5.75725 ( 1362) SS BOND : bond 0.00420 ( 1) SS BOND : angle 1.40760 ( 2) covalent geometry : bond 0.00410 (15134) covalent geometry : angle 0.67383 (20595) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5365.67 seconds wall clock time: 97 minutes 43.95 seconds (5863.95 seconds total)