Starting phenix.real_space_refine on Thu Sep 18 10:17:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vnz_43362/09_2025/8vnz_43362.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vnz_43362/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vnz_43362/09_2025/8vnz_43362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vnz_43362/09_2025/8vnz_43362.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vnz_43362/09_2025/8vnz_43362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vnz_43362/09_2025/8vnz_43362.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 9, 'GLU:plan': 16, 'GLN:plan1': 9, 'ASN:plan1': 9, 'HIS:plan': 1, '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: {'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, '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: {'ASP:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 1} 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: {'ARG:plan': 15, 'GLU:plan': 27, 'TYR:plan': 5, 'GLN:plan1': 10, 'PHE:plan': 6, 'ASP:plan': 15, 'ASN:plan1': 6, 'HIS:plan': 2} 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: {'ARG:plan': 3, 'M3L:plan-1': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2} 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: {'ARG:plan': 2, 'GLU:plan': 5, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLN:plan1': 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: 3.77, per 1000 atoms: 0.26 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: 1.30 Conformation dependent library (CDL) restraints added in 708.3 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.68 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: 2.81 Time building geometry restraints manager: 1.70 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: 4.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.570 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- 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 : 17.04 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG C 741 TYR 0.013 0.001 TYR C 448 PHE 0.024 0.001 PHE L 299 TRP 0.018 0.001 TRP N 301 HIS 0.007 0.001 HIS P 268 Details of bonding type rmsd covalent geometry : bond 0.00287 (15134) covalent geometry : angle 0.64759 (20595) SS BOND : bond 0.00369 ( 1) SS BOND : angle 1.18830 ( 2) hydrogen bonds : bond 0.23937 ( 479) hydrogen bonds : angle 8.93069 ( 1362) *********************** 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 : 0.636 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: 0.1212 time to fit residues: 24.1663 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 : 0.660 ------------------------------------------------------------------------------- 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 98 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.084741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.073804 restraints weight = 97063.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.075175 restraints weight = 59760.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.076056 restraints weight = 42247.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.076721 restraints weight = 32907.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.077081 restraints weight = 27380.699| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15135 Z= 0.202 Angle : 0.665 8.999 20597 Z= 0.347 Chirality : 0.046 0.173 2300 Planarity : 0.005 0.062 2668 Dihedral : 5.289 40.091 2099 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 4.14 % Allowed : 15.81 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.19), residues: 1924 helix: 0.20 (0.25), residues: 451 sheet: -0.65 (0.27), residues: 351 loop : -1.16 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 196 TYR 0.024 0.002 TYR N 32 PHE 0.023 0.002 PHE C 724 TRP 0.016 0.002 TRP N 235 HIS 0.010 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00445 (15134) covalent geometry : angle 0.66468 (20595) SS BOND : bond 0.00597 ( 1) SS BOND : angle 1.78718 ( 2) hydrogen bonds : bond 0.05430 ( 479) hydrogen bonds : angle 6.64964 ( 1362) *********************** 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 181 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 121 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8314 (mmp) cc_final: 0.8090 (mmp) REVERT: N 133 MET cc_start: 0.6662 (tpp) cc_final: 0.5711 (tpp) REVERT: C 47 GLN cc_start: 0.8589 (mm-40) cc_final: 0.7808 (tm-30) REVERT: P 195 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7494 (tt) outliers start: 60 outliers final: 43 residues processed: 172 average time/residue: 0.1090 time to fit residues: 30.1196 Evaluate side-chains 150 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 572 LEU 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 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 252 MET 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 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 51 GLU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 98 LEU 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 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 56 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 44 optimal weight: 0.0370 chunk 50 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.7858 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.086254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.074905 restraints weight = 92533.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.076274 restraints weight = 58543.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.077279 restraints weight = 41925.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.077863 restraints weight = 32881.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.078362 restraints weight = 27710.087| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.1398 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= 0.116 Angle : 0.588 10.105 20597 Z= 0.304 Chirality : 0.044 0.153 2300 Planarity : 0.004 0.066 2668 Dihedral : 5.007 39.331 2099 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.59 % Allowed : 16.99 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.19), residues: 1924 helix: 0.30 (0.25), residues: 458 sheet: -0.77 (0.26), residues: 359 loop : -1.14 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 196 TYR 0.021 0.001 TYR L 244 PHE 0.014 0.001 PHE C 290 TRP 0.017 0.001 TRP N 388 HIS 0.010 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00254 (15134) covalent geometry : angle 0.58738 (20595) SS BOND : bond 0.00551 ( 1) SS BOND : angle 1.52746 ( 2) hydrogen bonds : bond 0.04305 ( 479) hydrogen bonds : angle 6.13482 ( 1362) *********************** 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 170 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 118 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.8246 (mmp) cc_final: 0.7975 (mmp) REVERT: N 133 MET cc_start: 0.6514 (tpp) cc_final: 0.5978 (tpp) REVERT: N 253 MET cc_start: 0.5703 (mmt) cc_final: 0.5017 (mmt) REVERT: C 47 GLN cc_start: 0.8491 (mm-40) cc_final: 0.7809 (tm-30) REVERT: C 728 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6950 (t80) REVERT: P 193 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8135 (pp30) REVERT: P 195 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7365 (tt) REVERT: P 271 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7916 (mtmt) outliers start: 52 outliers final: 32 residues processed: 158 average time/residue: 0.1072 time to fit residues: 27.1589 Evaluate side-chains 148 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 250 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 472 SER 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 678 VAL Chi-restraints excluded: chain L residue 116 VAL 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 N residue 37 THR Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 358 ASP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 127 VAL 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 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 193 GLN Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 226 VAL Chi-restraints excluded: chain P residue 271 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 140 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 69 optimal weight: 0.3980 chunk 148 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 59 optimal weight: 0.0870 chunk 135 optimal weight: 20.0000 chunk 68 optimal weight: 0.8980 chunk 153 optimal weight: 0.4980 chunk 21 optimal weight: 5.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 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** P 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.086614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.075264 restraints weight = 92647.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.076652 restraints weight = 58487.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.077632 restraints weight = 42045.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.078317 restraints weight = 32830.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.078725 restraints weight = 27337.921| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15135 Z= 0.111 Angle : 0.582 10.290 20597 Z= 0.299 Chirality : 0.043 0.152 2300 Planarity : 0.004 0.066 2668 Dihedral : 4.780 38.523 2094 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.66 % Allowed : 18.37 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.19), residues: 1924 helix: 0.39 (0.25), residues: 458 sheet: -0.89 (0.27), residues: 353 loop : -1.10 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.022 0.001 TYR L 244 PHE 0.013 0.001 PHE C 290 TRP 0.009 0.001 TRP N 235 HIS 0.010 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00244 (15134) covalent geometry : angle 0.58168 (20595) SS BOND : bond 0.00465 ( 1) SS BOND : angle 1.33945 ( 2) hydrogen bonds : bond 0.03962 ( 479) hydrogen bonds : angle 5.88990 ( 1362) *********************** 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 170 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 117 time to evaluate : 0.604 Fit side-chains revert: symmetry clash REVERT: A 118 MET cc_start: 0.8212 (mmp) cc_final: 0.7944 (mmp) REVERT: N 133 MET cc_start: 0.6744 (tpp) cc_final: 0.6423 (tpp) REVERT: N 253 MET cc_start: 0.5733 (mmt) cc_final: 0.4993 (mmt) REVERT: C 47 GLN cc_start: 0.8470 (mm-40) cc_final: 0.7835 (tm-30) REVERT: C 614 LEU cc_start: 0.8731 (mp) cc_final: 0.8480 (mm) REVERT: C 700 MET cc_start: 0.5186 (ttt) cc_final: 0.4445 (tmm) REVERT: C 728 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6819 (t80) REVERT: P 195 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7325 (tt) REVERT: P 288 MET cc_start: 0.7963 (mmp) cc_final: 0.7758 (mmp) outliers start: 53 outliers final: 36 residues processed: 160 average time/residue: 0.1142 time to fit residues: 28.8758 Evaluate side-chains 148 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 472 SER Chi-restraints excluded: chain A residue 498 SER 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 678 VAL Chi-restraints excluded: chain L residue 116 VAL 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 358 ASP Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 127 VAL 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 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 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 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 110 optimal weight: 6.9990 chunk 11 optimal weight: 30.0000 chunk 153 optimal weight: 0.1980 chunk 88 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 17 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 142 optimal weight: 0.0060 chunk 78 optimal weight: 10.0000 overall best weight: 1.7200 ------------------------------------------------------------------------------- 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 540 GLN ** 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 = 0.4092 r_free = 0.4092 target = 0.085467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.074190 restraints weight = 92970.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.075541 restraints weight = 58847.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.076492 restraints weight = 42361.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.077180 restraints weight = 33301.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.077570 restraints weight = 27785.734| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15135 Z= 0.142 Angle : 0.591 7.685 20597 Z= 0.307 Chirality : 0.044 0.225 2300 Planarity : 0.004 0.065 2668 Dihedral : 4.842 37.213 2094 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.56 % Allowed : 17.47 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.19), residues: 1924 helix: 0.42 (0.25), residues: 458 sheet: -0.81 (0.27), residues: 344 loop : -1.17 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 741 TYR 0.018 0.002 TYR N 32 PHE 0.015 0.001 PHE C 667 TRP 0.016 0.001 TRP N 388 HIS 0.011 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00314 (15134) covalent geometry : angle 0.59042 (20595) SS BOND : bond 0.00464 ( 1) SS BOND : angle 1.49395 ( 2) hydrogen bonds : bond 0.03979 ( 479) hydrogen bonds : angle 5.81296 ( 1362) *********************** 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 179 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 113 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 253 MET cc_start: 0.6049 (mmt) cc_final: 0.4760 (mmt) REVERT: C 47 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7843 (tm-30) REVERT: C 614 LEU cc_start: 0.8795 (mp) cc_final: 0.8522 (mm) REVERT: P 288 MET cc_start: 0.8072 (mmp) cc_final: 0.7689 (mmt) outliers start: 66 outliers final: 47 residues processed: 169 average time/residue: 0.1086 time to fit residues: 29.3232 Evaluate side-chains 158 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 111 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 463 LEU Chi-restraints excluded: chain A residue 498 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 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 51 GLU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 96 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 140 optimal weight: 4.9990 chunk 8 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 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 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 565 GLN ** 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 = 0.4073 r_free = 0.4073 target = 0.084501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.073260 restraints weight = 93200.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.074582 restraints weight = 59091.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.075527 restraints weight = 42576.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.076194 restraints weight = 33643.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.076588 restraints weight = 28162.153| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15135 Z= 0.171 Angle : 0.623 8.548 20597 Z= 0.324 Chirality : 0.044 0.179 2300 Planarity : 0.004 0.064 2668 Dihedral : 5.002 35.989 2094 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.70 % Allowed : 17.96 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.19), residues: 1924 helix: 0.27 (0.25), residues: 464 sheet: -0.80 (0.27), residues: 333 loop : -1.27 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 439 TYR 0.019 0.002 TYR N 32 PHE 0.020 0.002 PHE N 368 TRP 0.012 0.002 TRP N 388 HIS 0.012 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00379 (15134) covalent geometry : angle 0.62243 (20595) SS BOND : bond 0.00483 ( 1) SS BOND : angle 1.56221 ( 2) hydrogen bonds : bond 0.04120 ( 479) hydrogen bonds : angle 5.86275 ( 1362) *********************** 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 179 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 111 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 253 MET cc_start: 0.6037 (mmt) cc_final: 0.5095 (mmt) REVERT: C 47 GLN cc_start: 0.8472 (mm-40) cc_final: 0.7849 (tm-30) REVERT: C 614 LEU cc_start: 0.8825 (mp) cc_final: 0.8537 (mm) REVERT: P 193 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8222 (pp30) REVERT: P 288 MET cc_start: 0.8153 (mmp) cc_final: 0.7696 (mmt) outliers start: 68 outliers final: 53 residues processed: 168 average time/residue: 0.1086 time to fit residues: 29.2441 Evaluate side-chains 160 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 106 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 301 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 479 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 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 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 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 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 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 193 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 133 optimal weight: 50.0000 chunk 174 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 58 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 185 optimal weight: 0.7980 chunk 5 optimal weight: 0.0670 chunk 2 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.2522 ------------------------------------------------------------------------------- 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 540 GLN ** C 565 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.085493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.074241 restraints weight = 92626.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.075585 restraints weight = 58702.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.076543 restraints weight = 41943.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.077198 restraints weight = 33019.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.077662 restraints weight = 27767.603| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15135 Z= 0.127 Angle : 0.602 8.675 20597 Z= 0.310 Chirality : 0.044 0.166 2300 Planarity : 0.004 0.065 2668 Dihedral : 4.911 34.987 2094 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.28 % Allowed : 17.89 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.19), residues: 1924 helix: 0.28 (0.25), residues: 463 sheet: -0.85 (0.27), residues: 337 loop : -1.25 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 741 TYR 0.019 0.002 TYR L 244 PHE 0.019 0.001 PHE A 656 TRP 0.014 0.001 TRP N 301 HIS 0.011 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00284 (15134) covalent geometry : angle 0.60135 (20595) SS BOND : bond 0.00383 ( 1) SS BOND : angle 1.63014 ( 2) hydrogen bonds : bond 0.03851 ( 479) hydrogen bonds : angle 5.72319 ( 1362) *********************** 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 179 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 117 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 253 MET cc_start: 0.6008 (mmt) cc_final: 0.5129 (mmt) REVERT: N 369 ILE cc_start: 0.6029 (tt) cc_final: 0.5817 (tt) REVERT: C 47 GLN cc_start: 0.8412 (mm-40) cc_final: 0.7832 (tm-30) REVERT: C 439 MET cc_start: 0.7155 (mtt) cc_final: 0.6919 (mtt) REVERT: C 504 ARG cc_start: 0.8522 (mtt-85) cc_final: 0.8181 (mtt-85) REVERT: C 614 LEU cc_start: 0.8816 (mp) cc_final: 0.8557 (mm) REVERT: C 700 MET cc_start: 0.5974 (ttt) cc_final: 0.5111 (tmm) REVERT: P 193 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: P 288 MET cc_start: 0.8164 (mmp) cc_final: 0.7669 (mmt) outliers start: 62 outliers final: 50 residues processed: 168 average time/residue: 0.1072 time to fit residues: 28.6967 Evaluate side-chains 164 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 113 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 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 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 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 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 96 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 128 LEU 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 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 193 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.0050 chunk 63 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 115 optimal weight: 0.3980 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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** ** 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 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN C 565 GLN ** C 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 607 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 = 0.4118 r_free = 0.4118 target = 0.086634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.075319 restraints weight = 92628.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.076708 restraints weight = 58440.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.077678 restraints weight = 42098.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.078348 restraints weight = 32983.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.078763 restraints weight = 27614.082| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15135 Z= 0.111 Angle : 0.599 9.047 20597 Z= 0.307 Chirality : 0.044 0.164 2300 Planarity : 0.004 0.066 2668 Dihedral : 4.772 33.993 2094 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.25 % Allowed : 18.99 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.19), residues: 1924 helix: 0.37 (0.25), residues: 462 sheet: -0.89 (0.27), residues: 345 loop : -1.20 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 741 TYR 0.021 0.001 TYR L 244 PHE 0.028 0.001 PHE N 368 TRP 0.016 0.001 TRP N 301 HIS 0.010 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00247 (15134) covalent geometry : angle 0.59890 (20595) SS BOND : bond 0.00358 ( 1) SS BOND : angle 1.26192 ( 2) hydrogen bonds : bond 0.03625 ( 479) hydrogen bonds : angle 5.51838 ( 1362) *********************** 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 168 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 253 MET cc_start: 0.5792 (mmt) cc_final: 0.4872 (mmt) REVERT: N 319 GLU cc_start: 0.8052 (pt0) cc_final: 0.7740 (tm-30) REVERT: C 47 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7879 (tm-30) REVERT: C 439 MET cc_start: 0.7038 (mtt) cc_final: 0.6828 (mtt) REVERT: C 504 ARG cc_start: 0.8580 (mtt-85) cc_final: 0.8212 (mtt-85) REVERT: C 565 GLN cc_start: 0.6896 (OUTLIER) cc_final: 0.6547 (pp30) REVERT: C 614 LEU cc_start: 0.8770 (mp) cc_final: 0.8557 (mm) REVERT: C 700 MET cc_start: 0.5941 (ttt) cc_final: 0.5047 (tmm) REVERT: P 185 ARG cc_start: 0.5450 (mtt90) cc_final: 0.3669 (mmt90) REVERT: P 288 MET cc_start: 0.8099 (mmp) cc_final: 0.7613 (mmt) outliers start: 47 outliers final: 40 residues processed: 159 average time/residue: 0.1072 time to fit residues: 27.0370 Evaluate side-chains 153 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 112 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 463 LEU Chi-restraints excluded: chain A residue 472 SER 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 678 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 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 428 VAL Chi-restraints excluded: chain N residue 37 THR 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 152 ASN Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 565 GLN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 122 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 117 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 67 optimal weight: 0.0070 chunk 189 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- 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** L 160 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 565 GLN ** C 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.086883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.075602 restraints weight = 91967.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.076988 restraints weight = 58248.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.077959 restraints weight = 42076.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.078631 restraints weight = 33056.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.079032 restraints weight = 27602.493| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15135 Z= 0.111 Angle : 0.601 9.210 20597 Z= 0.307 Chirality : 0.044 0.351 2300 Planarity : 0.004 0.065 2668 Dihedral : 4.701 33.293 2094 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.52 % Allowed : 18.92 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.19), residues: 1924 helix: 0.52 (0.25), residues: 456 sheet: -0.79 (0.27), residues: 331 loop : -1.18 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 741 TYR 0.016 0.001 TYR L 244 PHE 0.012 0.001 PHE C 724 TRP 0.022 0.001 TRP C 113 HIS 0.010 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00248 (15134) covalent geometry : angle 0.60121 (20595) SS BOND : bond 0.00378 ( 1) SS BOND : angle 1.16553 ( 2) hydrogen bonds : bond 0.03533 ( 479) hydrogen bonds : angle 5.43342 ( 1362) *********************** 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 166 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 115 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 253 MET cc_start: 0.5786 (mmt) cc_final: 0.4944 (mmt) REVERT: N 319 GLU cc_start: 0.8043 (pt0) cc_final: 0.7716 (tm-30) REVERT: C 47 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7878 (tm-30) REVERT: C 439 MET cc_start: 0.7053 (mtt) cc_final: 0.6845 (mtt) REVERT: C 504 ARG cc_start: 0.8640 (mtt-85) cc_final: 0.8272 (mtt-85) REVERT: C 614 LEU cc_start: 0.8777 (mp) cc_final: 0.8571 (mm) REVERT: P 185 ARG cc_start: 0.5450 (mtt90) cc_final: 0.3743 (mmt90) REVERT: P 195 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7418 (tt) REVERT: P 288 MET cc_start: 0.8118 (mmp) cc_final: 0.7645 (mmt) outliers start: 51 outliers final: 45 residues processed: 157 average time/residue: 0.1025 time to fit residues: 25.6541 Evaluate side-chains 158 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 463 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 514 PHE 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 678 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 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 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 127 VAL Chi-restraints excluded: chain C residue 128 LEU 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 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 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 191 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 174 optimal weight: 0.0570 chunk 7 optimal weight: 10.0000 chunk 176 optimal weight: 0.4980 chunk 13 optimal weight: 5.9990 overall best weight: 2.5102 ------------------------------------------------------------------------------- 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** ** 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 540 GLN ** 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 = 0.4070 r_free = 0.4070 target = 0.084297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.073047 restraints weight = 93425.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.074379 restraints weight = 59219.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.075310 restraints weight = 42916.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.075970 restraints weight = 33812.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.076407 restraints weight = 28431.214| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15135 Z= 0.187 Angle : 0.677 9.750 20597 Z= 0.351 Chirality : 0.046 0.351 2300 Planarity : 0.004 0.062 2668 Dihedral : 5.113 31.787 2094 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.31 % Allowed : 19.41 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.19), residues: 1924 helix: 0.28 (0.24), residues: 464 sheet: -0.86 (0.27), residues: 333 loop : -1.32 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 741 TYR 0.019 0.002 TYR N 32 PHE 0.038 0.002 PHE N 368 TRP 0.024 0.002 TRP C 113 HIS 0.012 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00415 (15134) covalent geometry : angle 0.67691 (20595) SS BOND : bond 0.00412 ( 1) SS BOND : angle 1.71080 ( 2) hydrogen bonds : bond 0.04099 ( 479) hydrogen bonds : angle 5.68570 ( 1362) ********************** 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 163 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 115 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 133 MET cc_start: 0.6999 (mmm) cc_final: 0.4260 (mmm) REVERT: N 253 MET cc_start: 0.5817 (mmt) cc_final: 0.4988 (mmt) REVERT: N 319 GLU cc_start: 0.8141 (pt0) cc_final: 0.7745 (tm-30) REVERT: C 47 GLN cc_start: 0.8458 (mm-40) cc_final: 0.7870 (tm-30) REVERT: C 447 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.6617 (m-80) REVERT: C 504 ARG cc_start: 0.8661 (mtt-85) cc_final: 0.8297 (mtt-85) REVERT: C 614 LEU cc_start: 0.8872 (mp) cc_final: 0.8654 (mm) REVERT: P 288 MET cc_start: 0.8267 (mmp) cc_final: 0.7715 (mmt) outliers start: 48 outliers final: 41 residues processed: 154 average time/residue: 0.1013 time to fit residues: 24.7444 Evaluate side-chains 153 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 498 SER Chi-restraints excluded: chain A residue 678 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 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 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 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 152 ASN Chi-restraints excluded: chain C residue 447 TYR Chi-restraints excluded: chain C residue 451 PHE 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 193 GLN Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 225 THR Chi-restraints excluded: chain P residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 96 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 131 optimal weight: 0.0270 chunk 111 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 35 optimal weight: 0.0980 chunk 57 optimal weight: 0.7980 chunk 88 optimal weight: 0.0030 chunk 108 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 overall best weight: 0.3448 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.087218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.075974 restraints weight = 91278.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.077382 restraints weight = 58018.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.078324 restraints weight = 41597.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.078980 restraints weight = 32754.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.079447 restraints weight = 27439.661| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15135 Z= 0.113 Angle : 0.636 10.588 20597 Z= 0.324 Chirality : 0.045 0.356 2300 Planarity : 0.004 0.067 2668 Dihedral : 4.837 30.833 2094 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.42 % Allowed : 20.51 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.19), residues: 1924 helix: 0.47 (0.25), residues: 460 sheet: -0.78 (0.28), residues: 329 loop : -1.20 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 741 TYR 0.021 0.001 TYR L 244 PHE 0.038 0.001 PHE A 132 TRP 0.019 0.002 TRP C 113 HIS 0.010 0.001 HIS C 129 Details of bonding type rmsd covalent geometry : bond 0.00249 (15134) covalent geometry : angle 0.63584 (20595) SS BOND : bond 0.00312 ( 1) SS BOND : angle 0.99147 ( 2) hydrogen bonds : bond 0.03607 ( 479) hydrogen bonds : angle 5.41398 ( 1362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2518.16 seconds wall clock time: 44 minutes 48.27 seconds (2688.27 seconds total)