Starting phenix.real_space_refine on Sat Feb 7 05:26:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qc8_53006/02_2026/9qc8_53006_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qc8_53006/02_2026/9qc8_53006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qc8_53006/02_2026/9qc8_53006_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qc8_53006/02_2026/9qc8_53006_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qc8_53006/02_2026/9qc8_53006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qc8_53006/02_2026/9qc8_53006.map" } resolution = 2.9 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= -0.008 sd= 1.158 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 19367 2.51 5 N 4945 2.21 5 O 5417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29799 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1253, 9416 Classifications: {'peptide': 1253} Incomplete info: {'truncation_to_alanine': 271} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 1215} Chain breaks: 7 Unresolved non-hydrogen bonds: 941 Unresolved non-hydrogen angles: 1132 Unresolved non-hydrogen dihedrals: 753 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ASN:plan1': 34, 'GLU:plan': 59, 'ARG:plan': 10, 'ASP:plan': 41, 'GLN:plan1': 12, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 566 Chain: "B" Number of atoms: 8883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 8883 Classifications: {'peptide': 1187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 268} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 1150} Chain breaks: 5 Unresolved non-hydrogen bonds: 846 Unresolved non-hydrogen angles: 1059 Unresolved non-hydrogen dihedrals: 638 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'ASN:plan1': 46, 'ASP:plan': 55, 'GLU:plan': 50, 'GLN:plan1': 7, 'ARG:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 548 Chain: "C" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 3710 Classifications: {'peptide': 543} Incomplete info: {'truncation_to_alanine': 211} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 520} Chain breaks: 10 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 718 Unresolved non-hydrogen angles: 911 Unresolved non-hydrogen dihedrals: 556 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'ASP:plan': 14, 'ASN:plan1': 37, 'GLU:plan': 32, 'GLN:plan1': 15, 'ARG:plan': 9, 'PHE:plan': 3, 'HIS:plan': 3, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 454 Chain: "D" Number of atoms: 4008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4008 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 547} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 763 Unresolved non-hydrogen dihedrals: 455 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'ASP:plan': 16, 'ASN:plan1': 37, 'GLU:plan': 28, 'GLN:plan1': 10, 'ARG:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 356 Chain: "E" Number of atoms: 3782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 3782 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 218} Link IDs: {'PTRANS': 21, 'TRANS': 532} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 708 Unresolved non-hydrogen angles: 899 Unresolved non-hydrogen dihedrals: 536 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'ASP:plan': 15, 'ASN:plan1': 40, 'GLU:plan': 25, 'GLN:plan1': 12, 'HIS:plan': 2, 'ARG:plan': 9, 'TYR:plan': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 401 Time building chain proxies: 6.62, per 1000 atoms: 0.22 Number of scatterers: 29799 At special positions: 0 Unit cell: (160.632, 154.008, 220.248, 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 70 16.00 O 5417 8.00 N 4945 7.00 C 19367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS B 583 " - pdb=" SG CYS B 754 " distance=2.03 Simple disulfide: pdb=" SG CYS B 927 " - pdb=" SG CYS B 945 " 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: 2.03 Conformation dependent library (CDL) restraints added in 1.6 seconds 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7842 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 51 sheets defined 24.4% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.540A pdb=" N ASN A 61 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 102 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 224 through 241 removed outlier: 3.561A pdb=" N TYR A 235 " --> pdb=" O HIS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 274 removed outlier: 3.966A pdb=" N LEU A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 307 Processing helix chain 'A' and resid 317 through 330 Processing helix chain 'A' and resid 342 through 356 Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 407 through 414 removed outlier: 3.544A pdb=" N TYR A 410 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLY A 412 " --> pdb=" O GLU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 460 through 464 removed outlier: 3.749A pdb=" N PHE A 464 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.513A pdb=" N LEU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 575 through 584 Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 590 through 606 Processing helix chain 'A' and resid 624 through 630 Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 676 through 709 removed outlier: 5.134A pdb=" N THR A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A 684 " --> pdb=" O ILE A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 742 Processing helix chain 'A' and resid 743 through 750 Processing helix chain 'A' and resid 753 through 788 removed outlier: 3.564A pdb=" N MET A 788 " --> pdb=" O LEU A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 814 removed outlier: 3.695A pdb=" N ALA A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 833 Processing helix chain 'A' and resid 840 through 844 removed outlier: 3.556A pdb=" N ILE A 843 " --> pdb=" O ASP A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 949 Processing helix chain 'A' and resid 1068 through 1081 Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1263 through 1268 removed outlier: 3.508A pdb=" N GLU A1267 " --> pdb=" O TRP A1263 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 91 Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 187 through 193 removed outlier: 3.731A pdb=" N GLU B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 235 removed outlier: 3.927A pdb=" N GLU B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 removed outlier: 3.785A pdb=" N GLY B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 removed outlier: 3.933A pdb=" N PHE B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 276' Processing helix chain 'B' and resid 285 through 306 removed outlier: 4.139A pdb=" N SER B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.605A pdb=" N LYS B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG B 319 " --> pdb=" O ASP B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 333 Processing helix chain 'B' and resid 335 through 344 removed outlier: 4.004A pdb=" N PHE B 339 " --> pdb=" O ASN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 354 through 359 removed outlier: 4.154A pdb=" N PHE B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 390 through 395 removed outlier: 4.100A pdb=" N GLN B 393 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 395 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 removed outlier: 3.527A pdb=" N TYR B 434 " --> pdb=" O TYR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 464 Processing helix chain 'B' and resid 499 through 506 Processing helix chain 'B' and resid 519 through 526 Processing helix chain 'B' and resid 536 through 547 Processing helix chain 'B' and resid 554 through 574 Processing helix chain 'B' and resid 591 through 593 No H-bonds generated for 'chain 'B' and resid 591 through 593' Processing helix chain 'B' and resid 604 through 611 Processing helix chain 'B' and resid 613 through 618 Processing helix chain 'B' and resid 642 through 676 removed outlier: 4.178A pdb=" N GLU B 648 " --> pdb=" O ASN B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 711 removed outlier: 3.533A pdb=" N TYR B 680 " --> pdb=" O TYR B 676 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 711 " --> pdb=" O GLN B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 760 Processing helix chain 'B' and resid 760 through 786 removed outlier: 4.146A pdb=" N ASN B 773 " --> pdb=" O GLU B 769 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER B 774 " --> pdb=" O GLN B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 801 Processing helix chain 'B' and resid 804 through 809 removed outlier: 3.688A pdb=" N GLU B 809 " --> pdb=" O ILE B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 820 Processing helix chain 'B' and resid 822 through 832 Processing helix chain 'B' and resid 891 through 895 Processing helix chain 'B' and resid 1024 through 1036 removed outlier: 3.639A pdb=" N LEU B1036 " --> pdb=" O TYR B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1190 removed outlier: 3.810A pdb=" N HIS B1190 " --> pdb=" O LYS B1187 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 92 Processing helix chain 'C' and resid 94 through 99 removed outlier: 3.803A pdb=" N ALA C 98 " --> pdb=" O ASN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 4.186A pdb=" N TYR C 168 " --> pdb=" O ASN C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 424 through 426 No H-bonds generated for 'chain 'C' and resid 424 through 426' Processing helix chain 'C' and resid 504 through 508 Processing helix chain 'D' and resid 80 through 92 removed outlier: 3.580A pdb=" N VAL D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 164 through 169 removed outlier: 4.078A pdb=" N TYR D 168 " --> pdb=" O ASN D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 281 Processing helix chain 'D' and resid 398 through 402 removed outlier: 3.502A pdb=" N VAL D 401 " --> pdb=" O PRO D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 426 No H-bonds generated for 'chain 'D' and resid 424 through 426' Processing helix chain 'D' and resid 502 through 507 Processing helix chain 'E' and resid 80 through 90 Processing helix chain 'E' and resid 164 through 168 Processing helix chain 'E' and resid 269 through 282 Processing helix chain 'E' and resid 284 through 289 removed outlier: 3.550A pdb=" N ASN E 287 " --> pdb=" O GLN E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 325 Processing helix chain 'E' and resid 424 through 426 No H-bonds generated for 'chain 'E' and resid 424 through 426' Processing helix chain 'E' and resid 502 through 507 Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.715A pdb=" N GLY A 163 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLU A 49 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 41 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE A 46 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LYS A 39 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N ALA A 37 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 11.070A pdb=" N ARG A 50 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N TYR A 35 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET A 22 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN A 140 " --> pdb=" O GLU A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 removed outlier: 3.557A pdb=" N PHE A 130 " --> pdb=" O VAL A 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222 removed outlier: 7.059A pdb=" N VAL A 201 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL A 203 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 332 through 333 Processing sheet with id=AA8, first strand: chain 'A' and resid 447 through 451 removed outlier: 6.633A pdb=" N LYS A 434 " --> pdb=" O LYS A 529 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE A 531 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLN A 436 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 555 through 557 removed outlier: 6.335A pdb=" N SER A 555 " --> pdb=" O VAL A 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 610 through 611 Processing sheet with id=AB2, first strand: chain 'A' and resid 869 through 871 Processing sheet with id=AB3, first strand: chain 'A' and resid 885 through 888 removed outlier: 7.122A pdb=" N LYS A1044 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE A 954 " --> pdb=" O LYS A1044 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A 965 " --> pdb=" O ILE A 953 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ASN A 955 " --> pdb=" O TRP A 963 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TRP A 963 " --> pdb=" O ASN A 955 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 893 through 894 removed outlier: 3.900A pdb=" N GLU A 893 " --> pdb=" O LYS A 901 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N MET A1057 " --> pdb=" O ARG A 934 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG A 934 " --> pdb=" O MET A1057 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TYR A1059 " --> pdb=" O TRP A 932 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TRP A 932 " --> pdb=" O TYR A1059 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A1015 " --> pdb=" O ASN A1026 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN A1026 " --> pdb=" O ALA A1015 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A1017 " --> pdb=" O GLU A1024 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1100 through 1103 Processing sheet with id=AB6, first strand: chain 'A' and resid 1109 through 1113 Processing sheet with id=AB7, first strand: chain 'A' and resid 1145 through 1150 removed outlier: 4.754A pdb=" N LYS A1145 " --> pdb=" O PHE A1173 " (cutoff:3.500A) removed outlier: 14.680A pdb=" N ILE A1168 " --> pdb=" O THR A1183 " (cutoff:3.500A) removed outlier: 10.731A pdb=" N THR A1183 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU A1170 " --> pdb=" O VAL A1181 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1177 through 1184 current: chain 'A' and resid 1223 through 1227 removed outlier: 7.131A pdb=" N LEU A1224 " --> pdb=" O LEU A1238 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU A1238 " --> pdb=" O LEU A1224 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N PHE A1226 " --> pdb=" O ILE A1236 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 18 through 22 removed outlier: 7.035A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 122 through 125 Processing sheet with id=AC1, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AC2, first strand: chain 'B' and resid 214 through 215 removed outlier: 4.308A pdb=" N SER B 387 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 243 through 248 removed outlier: 5.560A pdb=" N LEU B 260 " --> pdb=" O PRO B 245 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B 247 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 372 through 373 Processing sheet with id=AC5, first strand: chain 'B' and resid 412 through 418 removed outlier: 3.882A pdb=" N MET B 414 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN B 404 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B 495 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 515 through 517 removed outlier: 6.114A pdb=" N SER B 515 " --> pdb=" O VAL B 532 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 576 through 581 Processing sheet with id=AC8, first strand: chain 'B' and resid 835 through 842 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 849 through 852 current: chain 'B' and resid 875 through 879 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 875 through 879 current: chain 'B' and resid 962 through 970 removed outlier: 6.772A pdb=" N ILE B 978 " --> pdb=" O ILE B 985 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 859 through 862 removed outlier: 4.782A pdb=" N LEU B 919 " --> pdb=" O VAL B1005 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE B 931 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLU B 921 " --> pdb=" O TRP B 929 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TRP B 929 " --> pdb=" O GLU B 921 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1055 through 1059 Processing sheet with id=AD2, first strand: chain 'B' and resid 1068 through 1071 Processing sheet with id=AD3, first strand: chain 'B' and resid 1093 through 1097 removed outlier: 15.843A pdb=" N GLY B1111 " --> pdb=" O ILE B1125 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ILE B1125 " --> pdb=" O GLY B1111 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B1113 " --> pdb=" O VAL B1123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1132 through 1135 current: chain 'B' and resid 1152 through 1160 removed outlier: 15.196A pdb=" N LEU B1156 " --> pdb=" O LEU B1167 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N LEU B1167 " --> pdb=" O LEU B1156 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N PHE B1158 " --> pdb=" O LEU B1165 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 39 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 28 through 39 current: chain 'C' and resid 137 through 157 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 137 through 157 current: chain 'C' and resid 355 through 356 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 57 through 64 removed outlier: 3.701A pdb=" N PHE C 293 " --> pdb=" O GLN C 249 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY E 104 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE E 293 " --> pdb=" O GLN E 249 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE D 293 " --> pdb=" O GLN D 249 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 259 through 262 removed outlier: 6.671A pdb=" N TYR C 313 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ASP C 223 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS C 315 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C 217 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU C 216 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C 375 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY C 222 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLU C 369 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 225 through 227 Processing sheet with id=AD8, first strand: chain 'C' and resid 233 through 239 Processing sheet with id=AD9, first strand: chain 'C' and resid 381 through 384 removed outlier: 6.189A pdb=" N ASN C 381 " --> pdb=" O TYR C 407 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU C 409 " --> pdb=" O ASN C 381 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN C 383 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE C 431 " --> pdb=" O ILE C 458 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 393 through 395 removed outlier: 5.434A pdb=" N ALA C 422 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N SER C 468 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N SER C 511 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU C 540 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN C 513 " --> pdb=" O GLU C 540 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 442 through 443 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 442 through 443 current: chain 'E' and resid 138 through 157 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 138 through 157 current: chain 'E' and resid 355 through 356 No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 526 through 529 removed outlier: 3.565A pdb=" N ILE C 618 " --> pdb=" O ARG C 528 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 28 through 39 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 28 through 39 current: chain 'D' and resid 138 through 156 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 138 through 156 current: chain 'D' and resid 355 through 356 No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 215 through 227 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 215 through 227 current: chain 'D' and resid 326 through 335 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 326 through 335 current: chain 'D' and resid 406 through 410 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 406 through 410 current: chain 'D' and resid 454 through 460 No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 233 through 239 Processing sheet with id=AE7, first strand: chain 'D' and resid 392 through 396 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 392 through 396 current: chain 'D' and resid 468 through 474 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 468 through 474 current: chain 'D' and resid 536 through 542 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 536 through 542 current: chain 'D' and resid 580 through 582 No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'D' and resid 525 through 529 Processing sheet with id=AE9, first strand: chain 'D' and resid 552 through 556 Processing sheet with id=AF1, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AF2, first strand: chain 'E' and resid 216 through 227 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 216 through 227 current: chain 'E' and resid 328 through 335 No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 233 through 239 removed outlier: 4.077A pdb=" N CYS E 306 " --> pdb=" O THR E 343 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 381 through 384 removed outlier: 5.093A pdb=" N ASN E 479 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR E 459 " --> pdb=" O ILE E 431 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU E 433 " --> pdb=" O TYR E 457 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N TYR E 457 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 392 through 395 removed outlier: 4.273A pdb=" N ILE E 417 " --> pdb=" O GLU E 500 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ALA E 422 " --> pdb=" O SER E 468 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N SER E 468 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 471 " --> pdb=" O SER E 510 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N SER E 511 " --> pdb=" O SER E 538 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLU E 540 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ASN E 513 " --> pdb=" O GLU E 540 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP E 535 " --> pdb=" O VAL E 610 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU E 568 " --> pdb=" O ILE E 583 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 525 through 529 1093 hydrogen bonds defined for protein. 2955 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: 6.14 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7371 1.33 - 1.45: 7043 1.45 - 1.58: 15925 1.58 - 1.70: 1 1.70 - 1.83: 106 Bond restraints: 30446 Sorted by residual: bond pdb=" CA ASN A 607 " pdb=" C ASN A 607 " ideal model delta sigma weight residual 1.524 1.587 -0.063 1.43e-02 4.89e+03 1.93e+01 bond pdb=" N ILE A 679 " pdb=" CA ILE A 679 " ideal model delta sigma weight residual 1.460 1.486 -0.026 8.60e-03 1.35e+04 9.33e+00 bond pdb=" N MET B 347 " pdb=" CA MET B 347 " ideal model delta sigma weight residual 1.455 1.481 -0.026 9.60e-03 1.09e+04 7.48e+00 bond pdb=" CA TYR C 321 " pdb=" C TYR C 321 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.26e-02 6.30e+03 7.05e+00 bond pdb=" C PRO B 437 " pdb=" O PRO B 437 " ideal model delta sigma weight residual 1.233 1.206 0.027 1.12e-02 7.97e+03 5.88e+00 ... (remaining 30441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 41196 2.21 - 4.42: 365 4.42 - 6.63: 46 6.63 - 8.84: 9 8.84 - 11.05: 5 Bond angle restraints: 41621 Sorted by residual: angle pdb=" N ILE A 679 " pdb=" CA ILE A 679 " pdb=" C ILE A 679 " ideal model delta sigma weight residual 113.71 105.13 8.58 9.50e-01 1.11e+00 8.16e+01 angle pdb=" N ALA A 606 " pdb=" CA ALA A 606 " pdb=" C ALA A 606 " ideal model delta sigma weight residual 110.55 100.63 9.92 1.35e+00 5.49e-01 5.40e+01 angle pdb=" N CYS B 478 " pdb=" CA CYS B 478 " pdb=" C CYS B 478 " ideal model delta sigma weight residual 108.90 119.95 -11.05 1.63e+00 3.76e-01 4.60e+01 angle pdb=" N LYS D 184 " pdb=" CA LYS D 184 " pdb=" C LYS D 184 " ideal model delta sigma weight residual 108.34 119.25 -10.91 1.64e+00 3.72e-01 4.42e+01 angle pdb=" CA PRO B 348 " pdb=" C PRO B 348 " pdb=" O PRO B 348 " ideal model delta sigma weight residual 121.34 114.83 6.51 1.14e+00 7.69e-01 3.26e+01 ... (remaining 41616 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 16166 17.91 - 35.82: 1266 35.82 - 53.74: 262 53.74 - 71.65: 51 71.65 - 89.56: 27 Dihedral angle restraints: 17772 sinusoidal: 5592 harmonic: 12180 Sorted by residual: dihedral pdb=" CB CYS B 927 " pdb=" SG CYS B 927 " pdb=" SG CYS B 945 " pdb=" CB CYS B 945 " ideal model delta sinusoidal sigma weight residual 93.00 137.90 -44.90 1 1.00e+01 1.00e-02 2.80e+01 dihedral pdb=" N ASN A 607 " pdb=" C ASN A 607 " pdb=" CA ASN A 607 " pdb=" CB ASN A 607 " ideal model delta harmonic sigma weight residual 122.80 133.60 -10.80 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" C ASN A 607 " pdb=" N ASN A 607 " pdb=" CA ASN A 607 " pdb=" CB ASN A 607 " ideal model delta harmonic sigma weight residual -122.60 -133.16 10.56 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 17769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4266 0.077 - 0.154: 559 0.154 - 0.231: 10 0.231 - 0.307: 8 0.307 - 0.384: 10 Chirality restraints: 4853 Sorted by residual: chirality pdb=" CA ASN A 607 " pdb=" N ASN A 607 " pdb=" C ASN A 607 " pdb=" CB ASN A 607 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA ASN D 402 " pdb=" N ASN D 402 " pdb=" C ASN D 402 " pdb=" CB ASN D 402 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA GLU B 370 " pdb=" N GLU B 370 " pdb=" C GLU B 370 " pdb=" CB GLU B 370 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 4850 not shown) Planarity restraints: 5340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 368 " -0.085 5.00e-02 4.00e+02 1.28e-01 2.61e+01 pdb=" N PRO B 369 " 0.221 5.00e-02 4.00e+02 pdb=" CA PRO B 369 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO B 369 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 543 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.25e+00 pdb=" C ILE E 543 " -0.053 2.00e-02 2.50e+03 pdb=" O ILE E 543 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO E 544 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 540 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.86e+00 pdb=" C GLU E 540 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU E 540 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE E 541 " 0.011 2.00e-02 2.50e+03 ... (remaining 5337 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 185 2.57 - 3.15: 24124 3.15 - 3.73: 43500 3.73 - 4.32: 62317 4.32 - 4.90: 106521 Nonbonded interactions: 236647 Sorted by model distance: nonbonded pdb=" O VAL A 586 " pdb=" OH TYR A 742 " model vdw 1.983 3.040 nonbonded pdb=" ND2 ASN D 441 " pdb=" SG CYS D 448 " model vdw 2.015 3.480 nonbonded pdb=" OD2 ASP B 349 " pdb=" OG SER B 822 " model vdw 2.035 3.040 nonbonded pdb=" OG SER A 184 " pdb=" O GLY A 239 " model vdw 2.063 3.040 nonbonded pdb=" N GLU A1235 " pdb=" OE1 GLU A1235 " model vdw 2.071 3.120 ... (remaining 236642 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 22 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 51 or (resid 52 through 54 and (na \ me N or name CA or name C or name O or name CB )) or resid 55 or (resid 56 and ( \ name N or name CA or name C or name O or name CB )) or resid 57 through 61 or (r \ esid 62 and (name N or name CA or name C or name O or name CB )) or resid 63 thr \ ough 65 or (resid 66 through 70 and (name N or name CA or name C or name O or na \ me CB )) or resid 71 through 84 or (resid 85 and (name N or name CA or name C or \ name O or name CB )) or resid 86 through 93 or (resid 94 and (name N or name CA \ or name C or name O or name CB )) or resid 95 through 108 or (resid 109 and (na \ me N or name CA or name C or name O or name CB )) or resid 110 through 133 or (r \ esid 134 through 138 and (name N or name CA or name C or name O or name CB )) or \ resid 139 through 173 or (resid 174 and (name N or name CA or name C or name O \ or name CB )) or resid 175 or (resid 176 through 179 and (name N or name CA or n \ ame C or name O or name CB )) or resid 180 through 185 or (resid 186 through 210 \ and (name N or name CA or name C or name O or name CB )) or resid 211 through 2 \ 29 or (resid 230 through 231 and (name N or name CA or name C or name O or name \ CB )) or resid 232 through 242 or (resid 243 through 244 and (name N or name CA \ or name C or name O or name CB )) or resid 245 through 252 or (resid 253 through \ 255 and (name N or name CA or name C or name O or name CB )) or resid 256 throu \ gh 284 or (resid 285 and (name N or name CA or name C or name O or name CB )) or \ resid 286 or (resid 287 and (name N or name CA or name C or name O or name CB ) \ ) or resid 288 through 289 or (resid 290 and (name N or name CA or name C or nam \ e O or name CB )) or resid 291 through 303 or (resid 304 through 305 and (name N \ or name CA or name C or name O or name CB )) or resid 306 through 345 or (resid \ 352 through 360 and (name N or name CA or name C or name O or name CB )) or res \ id 361 through 370 or (resid 371 and (name N or name CA or name C or name O or n \ ame CB )) or resid 372 or (resid 373 and (name N or name CA or name C or name O \ or name CB )) or resid 374 through 375 or (resid 376 through 377 and (name N or \ name CA or name C or name O or name CB )) or resid 378 through 384 or (resid 385 \ through 392 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 93 through 407 or (resid 408 and (name N or name CA or name C or name O or name \ CB )) or resid 409 through 411 or (resid 412 through 415 and (name N or name CA \ or name C or name O or name CB )) or resid 416 or (resid 417 and (name N or name \ CA or name C or name O or name CB )) or resid 418 through 428 or (resid 429 and \ (name N or name CA or name C or name O or name CB )) or resid 430 through 436 o \ r (resid 437 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 38 through 446 or (resid 447 and (name N or name CA or name C or name O or name \ CB )) or resid 448 through 508 or (resid 509 through 529 and (name N or name CA \ or name C or name O or name CB )) or resid 530 through 531 or (resid 532 through \ 535 and (name N or name CA or name C or name O or name CB )) or resid 536 throu \ gh 537 or (resid 538 and (name N or name CA or name C or name O or name CB )) or \ resid 539 through 571 or resid 578 through 621)) selection = (chain 'D' and ((resid 22 through 24 and (name N or name CA or name C or name O \ or name CB )) or resid 25 through 67 or (resid 68 through 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 84 or (resid 85 and (n \ ame N or name CA or name C or name O or name CB )) or resid 86 through 93 or (re \ sid 94 and (name N or name CA or name C or name O or name CB )) or resid 95 thro \ ugh 98 or (resid 99 through 100 and (name N or name CA or name C or name O or na \ me CB )) or resid 101 through 105 or (resid 106 and (name N or name CA or name C \ or name O or name CB )) or resid 107 through 133 or (resid 134 through 138 and \ (name N or name CA or name C or name O or name CB )) or resid 139 or (resid 140 \ and (name N or name CA or name C or name O or name CB )) or resid 141 through 17 \ 3 or (resid 174 and (name N or name CA or name C or name O or name CB )) or resi \ d 175 or (resid 176 through 179 and (name N or name CA or name C or name O or na \ me CB )) or resid 180 through 181 or (resid 182 and (name N or name CA or name C \ or name O or name CB )) or resid 183 or (resid 184 through 187 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 208 through 210 and (name N o \ r name CA or name C or name O or name CB )) or resid 211 through 212 or (resid 2 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 214 through \ 252 or (resid 253 through 255 and (name N or name CA or name C or name O or nam \ e CB )) or resid 256 or (resid 257 and (name N or name CA or name C or name O or \ name CB )) or resid 258 through 260 or (resid 261 and (name N or name CA or nam \ e C or name O or name CB )) or resid 262 through 269 or (resid 270 through 271 a \ nd (name N or name CA or name C or name O or name CB )) or resid 272 through 278 \ or (resid 279 through 280 and (name N or name CA or name C or name O or name CB \ )) or resid 281 through 296 or (resid 297 through 299 and (name N or name CA or \ name C or name O or name CB )) or resid 300 through 304 or (resid 305 and (name \ N or name CA or name C or name O or name CB )) or resid 306 through 321 or (res \ id 322 through 323 and (name N or name CA or name C or name O or name CB )) or ( \ resid 325 and (name N or name CA or name C or name O or name CB )) or resid 326 \ through 342 or (resid 343 through 345 and (name N or name CA or name C or name O \ or name CB )) or (resid 352 through 360 and (name N or name CA or name C or nam \ e O or name CB )) or resid 361 through 369 or (resid 370 through 371 and (name N \ or name CA or name C or name O or name CB )) or resid 372 or (resid 373 and (na \ me N or name CA or name C or name O or name CB )) or resid 374 through 375 or (r \ esid 376 through 377 and (name N or name CA or name C or name O or name CB )) or \ resid 378 or (resid 379 through 392 and (name N or name CA or name C or name O \ or name CB )) or resid 393 through 398 or resid 402 through 407 or (resid 408 an \ d (name N or name CA or name C or name O or name CB )) or resid 409 through 411 \ or (resid 412 through 415 and (name N or name CA or name C or name O or name CB \ )) or resid 416 or (resid 417 and (name N or name CA or name C or name O or name \ CB )) or resid 418 through 419 or (resid 420 through 424 and (name N or name CA \ or name C or name O or name CB )) or resid 425 through 427 or (resid 428 throug \ h 429 and (name N or name CA or name C or name O or name CB )) or resid 430 or ( \ resid 431 and (name N or name CA or name C or name O or name CB )) or resid 432 \ through 436 or (resid 437 and (name N or name CA or name C or name O or name CB \ )) or resid 438 or (resid 439 and (name N or name CA or name C or name O or name \ CB )) or resid 440 through 442 or (resid 443 through 444 and (name N or name CA \ or name C or name O or name CB )) or (resid 445 through 447 and (name N or name \ CA or name C or name O or name CB )) or resid 448 through 451 or (resid 452 and \ (name N or name CA or name C or name O or name CB )) or resid 453 through 460 o \ r (resid 461 through 462 and (name N or name CA or name C or name O or name CB ) \ ) or resid 464 through 474 or (resid 475 through 478 and (name N or name CA or n \ ame C or name O or name CB )) or resid 479 through 482 or (resid 483 through 484 \ and (name N or name CA or name C or name O or name CB )) or resid 485 through 4 \ 86 or (resid 489 through 496 and (name N or name CA or name C or name O or name \ CB )) or resid 497 through 498 or (resid 499 through 501 and (name N or name CA \ or name C or name O or name CB )) or (resid 502 through 515 and (name N or name \ CA or name C or name O or name CB )) or (resid 524 through 529 and (name N or na \ me CA or name C or name O or name CB )) or resid 530 through 532 or (resid 533 t \ hrough 535 and (name N or name CA or name C or name O or name CB )) or resid 536 \ or (resid 537 through 538 and (name N or name CA or name C or name O or name CB \ )) or resid 539 through 540 or (resid 541 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 555 through 557 and (name N or name CA or name C o \ r name O or name CB )) or resid 558 through 559 or (resid 560 through 563 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 567 through 571 and \ (name N or name CA or name C or name O or name CB )) or resid 578 through 600 o \ r (resid 603 through 615 and (name N or name CA or name C or name O or name CB ) \ ) or resid 616 or (resid 617 through 621 and (name N or name CA or name C or nam \ e O or name CB )))) selection = (chain 'E' and (resid 22 through 26 or (resid 27 and (name N or name CA or name \ C or name O or name CB )) or resid 28 through 51 or (resid 52 through 54 and (na \ me N or name CA or name C or name O or name CB )) or resid 55 or (resid 56 and ( \ name N or name CA or name C or name O or name CB )) or resid 57 through 61 or (r \ esid 62 and (name N or name CA or name C or name O or name CB )) or resid 63 thr \ ough 80 or (resid 81 through 82 and (name N or name CA or name C or name O or na \ me CB )) or resid 83 through 105 or (resid 106 and (name N or name CA or name C \ or name O or name CB )) or resid 107 through 108 or (resid 109 and (name N or na \ me CA or name C or name O or name CB )) or resid 110 through 139 or (resid 140 a \ nd (name N or name CA or name C or name O or name CB )) or resid 141 through 163 \ or (resid 164 through 166 and (name N or name CA or name C or name O or name CB \ )) or resid 167 through 208 or (resid 209 through 210 and (name N or name CA or \ name C or name O or name CB )) or resid 211 through 212 or (resid 213 and (name \ N or name CA or name C or name O or name CB )) or resid 214 through 230 or (res \ id 231 and (name N or name CA or name C or name O or name CB )) or resid 232 thr \ ough 242 or (resid 243 through 244 and (name N or name CA or name C or name O or \ name CB )) or resid 245 through 260 or (resid 261 and (name N or name CA or nam \ e C or name O or name CB )) or resid 262 through 263 or (resid 264 through 267 a \ nd (name N or name CA or name C or name O or name CB )) or resid 268 through 269 \ or (resid 270 through 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 277 or (resid 278 through 280 and (name N or name CA or \ name C or name O or name CB )) or resid 281 through 283 or (resid 284 through 2 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 286 or (res \ id 287 and (name N or name CA or name C or name O or name CB )) or resid 288 thr \ ough 289 or (resid 290 and (name N or name CA or name C or name O or name CB )) \ or resid 291 through 303 or (resid 304 through 305 and (name N or name CA or nam \ e C or name O or name CB )) or resid 306 through 323 or resid 325 through 340 or \ (resid 341 and (name N or name CA or name C or name O or name CB )) or resid 34 \ 2 through 419 or (resid 420 through 424 and (name N or name CA or name C or name \ O or name CB )) or resid 425 through 442 or (resid 443 through 444 and (name N \ or name CA or name C or name O or name CB )) or resid 445 through 460 or (resid \ 461 through 462 and (name N or name CA or name C or name O or name CB )) or resi \ d 464 through 474 or (resid 475 through 478 and (name N or name CA or name C or \ name O or name CB )) or resid 479 through 482 or (resid 483 through 484 and (nam \ e N or name CA or name C or name O or name CB )) or resid 485 through 486 or res \ id 489 through 512 or (resid 513 through 529 and (name N or name CA or name C or \ name O or name CB )) or resid 530 through 531 or (resid 532 through 535 and (na \ me N or name CA or name C or name O or name CB )) or resid 536 or (resid 537 thr \ ough 538 and (name N or name CA or name C or name O or name CB )) or resid 539 t \ hrough 543 or resid 556 through 559 or (resid 560 through 563 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 567 through 600 and (name N or \ name CA or name C or name O or name CB )) or (resid 603 through 615 and (name N \ or name CA or name C or name O or name CB )) or resid 616 through 620 or (resid \ 621 and (name N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 25.870 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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 0.075 30449 Z= 0.159 Angle : 0.550 11.051 41627 Z= 0.333 Chirality : 0.050 0.384 4853 Planarity : 0.003 0.128 5340 Dihedral : 14.366 89.562 9921 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.34 % Allowed : 17.24 % Favored : 82.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.92 % 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 are not related in a simple way. whole: 0.12 (0.14), residues: 4027 helix: 2.23 (0.19), residues: 849 sheet: 0.04 (0.15), residues: 1104 loop : -0.81 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 253 TYR 0.019 0.001 TYR E 310 PHE 0.011 0.001 PHE D 497 TRP 0.007 0.001 TRP B 561 HIS 0.005 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00318 (30446) covalent geometry : angle 0.54963 (41621) SS BOND : bond 0.00298 ( 3) SS BOND : angle 0.78054 ( 6) hydrogen bonds : bond 0.15830 ( 1093) hydrogen bonds : angle 6.46131 ( 2955) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 1.243 Fit side-chains REVERT: A 88 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8596 (mp) outliers start: 9 outliers final: 5 residues processed: 118 average time/residue: 0.6025 time to fit residues: 86.1258 Evaluate side-chains 97 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain B residue 186 TYR Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain C residue 96 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 ASN A 773 ASN A 944 GLN A1014 ASN B 314 ASN B 353 ASN B 502 ASN B 652 ASN C 66 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN D 172 ASN D 322 GLN E 44 ASN E 425 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.057519 restraints weight = 79506.777| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.95 r_work: 0.2729 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 30449 Z= 0.310 Angle : 0.583 8.470 41627 Z= 0.317 Chirality : 0.049 0.297 4853 Planarity : 0.004 0.082 5340 Dihedral : 4.444 49.457 4439 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.25 % Allowed : 15.64 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 are not related in a simple way. whole: -0.07 (0.13), residues: 4027 helix: 1.89 (0.18), residues: 853 sheet: -0.10 (0.15), residues: 1114 loop : -0.82 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 253 TYR 0.029 0.002 TYR B 368 PHE 0.018 0.002 PHE D 497 TRP 0.011 0.001 TRP A1089 HIS 0.011 0.002 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00730 (30446) covalent geometry : angle 0.58298 (41621) SS BOND : bond 0.00216 ( 3) SS BOND : angle 1.20130 ( 6) hydrogen bonds : bond 0.05185 ( 1093) hydrogen bonds : angle 5.23897 ( 2955) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 93 time to evaluate : 1.321 Fit side-chains REVERT: A 1094 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8595 (mtt) REVERT: B 195 MET cc_start: 0.8563 (mmt) cc_final: 0.8326 (mmt) REVERT: E 320 ASP cc_start: 0.8824 (t0) cc_final: 0.8607 (t0) outliers start: 59 outliers final: 17 residues processed: 145 average time/residue: 0.5592 time to fit residues: 99.6081 Evaluate side-chains 103 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 759 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 321 TYR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain E residue 292 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 205 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 316 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 398 optimal weight: 10.0000 chunk 405 optimal weight: 1.9990 chunk 369 optimal weight: 8.9990 chunk 362 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 ASN A1069 GLN C 44 ASN C 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.074223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.058966 restraints weight = 78908.871| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.95 r_work: 0.2764 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30449 Z= 0.144 Angle : 0.463 8.588 41627 Z= 0.255 Chirality : 0.045 0.188 4853 Planarity : 0.003 0.071 5340 Dihedral : 4.008 22.016 4429 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.68 % Allowed : 16.32 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 are not related in a simple way. whole: 0.17 (0.13), residues: 4027 helix: 2.19 (0.18), residues: 854 sheet: 0.04 (0.15), residues: 1111 loop : -0.71 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 141 TYR 0.026 0.001 TYR B 368 PHE 0.017 0.001 PHE E 442 TRP 0.010 0.001 TRP A 974 HIS 0.005 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00331 (30446) covalent geometry : angle 0.46282 (41621) SS BOND : bond 0.00345 ( 3) SS BOND : angle 0.57397 ( 6) hydrogen bonds : bond 0.04161 ( 1093) hydrogen bonds : angle 4.87499 ( 2955) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 92 time to evaluate : 1.232 Fit side-chains REVERT: A 974 TRP cc_start: 0.9554 (OUTLIER) cc_final: 0.9253 (t-100) REVERT: A 1194 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9048 (mm) REVERT: B 195 MET cc_start: 0.8655 (mmt) cc_final: 0.8422 (mmt) REVERT: E 314 GLU cc_start: 0.8710 (tt0) cc_final: 0.8437 (mt-10) outliers start: 44 outliers final: 16 residues processed: 132 average time/residue: 0.5346 time to fit residues: 87.4280 Evaluate side-chains 105 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 974 TRP Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 186 TYR Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 292 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 266 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 379 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 64 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 344 optimal weight: 9.9990 chunk 292 optimal weight: 50.0000 chunk 321 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1014 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.073467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.058321 restraints weight = 78537.534| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.91 r_work: 0.2747 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30449 Z= 0.181 Angle : 0.471 8.851 41627 Z= 0.257 Chirality : 0.045 0.190 4853 Planarity : 0.003 0.064 5340 Dihedral : 3.959 21.332 4429 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.25 % Allowed : 16.13 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 are not related in a simple way. whole: 0.25 (0.13), residues: 4027 helix: 2.24 (0.18), residues: 855 sheet: 0.11 (0.15), residues: 1103 loop : -0.67 (0.14), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 141 TYR 0.024 0.001 TYR B 368 PHE 0.015 0.001 PHE E 442 TRP 0.012 0.001 TRP A 974 HIS 0.007 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00426 (30446) covalent geometry : angle 0.47048 (41621) SS BOND : bond 0.00281 ( 3) SS BOND : angle 0.65970 ( 6) hydrogen bonds : bond 0.04021 ( 1093) hydrogen bonds : angle 4.75178 ( 2955) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 92 time to evaluate : 1.098 Fit side-chains REVERT: A 974 TRP cc_start: 0.9552 (OUTLIER) cc_final: 0.9246 (t-100) REVERT: A 1235 GLU cc_start: 0.8395 (mp0) cc_final: 0.8181 (mp0) REVERT: E 314 GLU cc_start: 0.8732 (tt0) cc_final: 0.8466 (mt-10) REVERT: E 320 ASP cc_start: 0.8870 (t0) cc_final: 0.8657 (t0) outliers start: 59 outliers final: 27 residues processed: 147 average time/residue: 0.4924 time to fit residues: 90.5629 Evaluate side-chains 117 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 974 TRP Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain B residue 186 TYR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 759 ASN Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 442 PHE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 246 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 156 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 363 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 773 ASN A1014 ASN B 502 ASN C 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.057512 restraints weight = 81206.474| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.88 r_work: 0.2738 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 30449 Z= 0.290 Angle : 0.533 8.823 41627 Z= 0.289 Chirality : 0.047 0.226 4853 Planarity : 0.003 0.059 5340 Dihedral : 4.244 21.908 4429 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.56 % Allowed : 16.51 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 are not related in a simple way. whole: 0.08 (0.13), residues: 4027 helix: 2.04 (0.18), residues: 859 sheet: 0.03 (0.15), residues: 1098 loop : -0.77 (0.14), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 253 TYR 0.026 0.001 TYR B 368 PHE 0.016 0.002 PHE B 275 TRP 0.008 0.001 TRP B 282 HIS 0.009 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00690 (30446) covalent geometry : angle 0.53270 (41621) SS BOND : bond 0.00361 ( 3) SS BOND : angle 0.89117 ( 6) hydrogen bonds : bond 0.04567 ( 1093) hydrogen bonds : angle 4.94890 ( 2955) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 89 time to evaluate : 1.255 Fit side-chains REVERT: A 1094 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8517 (mtm) REVERT: A 1194 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9157 (mm) REVERT: A 1235 GLU cc_start: 0.8484 (mp0) cc_final: 0.8275 (mp0) REVERT: B 195 MET cc_start: 0.8688 (mmt) cc_final: 0.8295 (mmp) REVERT: B 973 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8470 (mtp85) REVERT: B 1170 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8124 (tmm-80) REVERT: E 251 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.7932 (mtt180) REVERT: E 314 GLU cc_start: 0.8760 (tt0) cc_final: 0.8473 (mt-10) REVERT: E 320 ASP cc_start: 0.8885 (t0) cc_final: 0.8683 (t0) REVERT: E 621 HIS cc_start: 0.7689 (m-70) cc_final: 0.7180 (m-70) outliers start: 67 outliers final: 33 residues processed: 150 average time/residue: 0.5433 time to fit residues: 100.8781 Evaluate side-chains 126 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 88 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 PHE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 186 TYR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 759 ASN Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 973 ARG Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1170 ARG Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 442 PHE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain E residue 292 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 266 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 385 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 323 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.075277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.060074 restraints weight = 79161.767| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.87 r_work: 0.2798 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30449 Z= 0.105 Angle : 0.442 8.567 41627 Z= 0.241 Chirality : 0.044 0.184 4853 Planarity : 0.003 0.062 5340 Dihedral : 3.906 20.995 4429 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.56 % Allowed : 17.66 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 are not related in a simple way. whole: 0.29 (0.13), residues: 4027 helix: 2.24 (0.18), residues: 864 sheet: 0.11 (0.15), residues: 1119 loop : -0.63 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 253 TYR 0.024 0.001 TYR B 368 PHE 0.015 0.001 PHE E 442 TRP 0.010 0.001 TRP A 974 HIS 0.004 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00237 (30446) covalent geometry : angle 0.44205 (41621) SS BOND : bond 0.00310 ( 3) SS BOND : angle 0.37218 ( 6) hydrogen bonds : bond 0.03614 ( 1093) hydrogen bonds : angle 4.61382 ( 2955) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 104 time to evaluate : 1.043 Fit side-chains REVERT: A 1094 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8508 (mtm) REVERT: A 1194 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9144 (mm) REVERT: A 1235 GLU cc_start: 0.8459 (mp0) cc_final: 0.8161 (mp0) REVERT: B 195 MET cc_start: 0.8758 (mmt) cc_final: 0.7780 (mmp) REVERT: B 973 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8427 (mtp85) REVERT: B 1170 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8018 (tmm-80) REVERT: C 364 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: E 251 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8076 (mtt180) REVERT: E 314 GLU cc_start: 0.8659 (tt0) cc_final: 0.8404 (mt-10) REVERT: E 320 ASP cc_start: 0.8899 (t0) cc_final: 0.8686 (t0) outliers start: 41 outliers final: 22 residues processed: 140 average time/residue: 0.5463 time to fit residues: 94.0392 Evaluate side-chains 119 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 PHE Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 186 TYR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 759 ASN Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 973 ARG Chi-restraints excluded: chain B residue 1170 ARG Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain C residue 442 PHE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 251 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 172 optimal weight: 9.9990 chunk 185 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 308 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 394 optimal weight: 4.9990 chunk 395 optimal weight: 0.0970 chunk 174 optimal weight: 0.5980 chunk 208 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 overall best weight: 2.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 773 ASN ** 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 = 0.3241 r_free = 0.3241 target = 0.073506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.058628 restraints weight = 79589.754| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.84 r_work: 0.2770 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 30449 Z= 0.190 Angle : 0.473 8.386 41627 Z= 0.257 Chirality : 0.045 0.219 4853 Planarity : 0.003 0.059 5340 Dihedral : 3.970 20.887 4429 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.77 % Favored : 96.20 % Rotamer: Outliers : 1.87 % Allowed : 17.51 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 are not related in a simple way. whole: 0.28 (0.13), residues: 4027 helix: 2.25 (0.18), residues: 861 sheet: 0.07 (0.15), residues: 1129 loop : -0.63 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 253 TYR 0.021 0.001 TYR B 368 PHE 0.014 0.001 PHE A1004 TRP 0.008 0.001 TRP A 974 HIS 0.007 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00447 (30446) covalent geometry : angle 0.47335 (41621) SS BOND : bond 0.00305 ( 3) SS BOND : angle 0.62862 ( 6) hydrogen bonds : bond 0.03961 ( 1093) hydrogen bonds : angle 4.68080 ( 2955) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 92 time to evaluate : 1.290 Fit side-chains REVERT: A 1094 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8537 (mtm) REVERT: A 1194 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9141 (mm) REVERT: A 1235 GLU cc_start: 0.8487 (mp0) cc_final: 0.8168 (mp0) REVERT: B 210 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9084 (tttt) REVERT: B 973 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8388 (mtp85) REVERT: B 1170 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8092 (tmm-80) REVERT: E 251 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7934 (mtt180) REVERT: E 314 GLU cc_start: 0.8706 (tt0) cc_final: 0.8490 (mt-10) REVERT: E 320 ASP cc_start: 0.8896 (t0) cc_final: 0.8667 (t0) REVERT: E 621 HIS cc_start: 0.7633 (m-70) cc_final: 0.7045 (m-70) outliers start: 49 outliers final: 31 residues processed: 137 average time/residue: 0.5956 time to fit residues: 100.1473 Evaluate side-chains 128 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 91 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 PHE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 186 TYR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 759 ASN Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 973 ARG Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1170 ARG Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 442 PHE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain E residue 292 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 377 optimal weight: 0.6980 chunk 294 optimal weight: 0.3980 chunk 120 optimal weight: 4.9990 chunk 329 optimal weight: 0.9990 chunk 363 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 335 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 ASN C 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.077449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.062440 restraints weight = 80639.670| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.80 r_work: 0.2811 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30449 Z= 0.103 Angle : 0.435 8.144 41627 Z= 0.237 Chirality : 0.044 0.178 4853 Planarity : 0.003 0.059 5340 Dihedral : 3.781 20.282 4429 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 1.75 % Allowed : 17.58 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 are not related in a simple way. whole: 0.44 (0.14), residues: 4027 helix: 2.42 (0.18), residues: 858 sheet: 0.21 (0.15), residues: 1129 loop : -0.57 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 253 TYR 0.021 0.001 TYR B 368 PHE 0.014 0.001 PHE E 442 TRP 0.009 0.001 TRP A 974 HIS 0.004 0.000 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00235 (30446) covalent geometry : angle 0.43490 (41621) SS BOND : bond 0.00288 ( 3) SS BOND : angle 0.37049 ( 6) hydrogen bonds : bond 0.03438 ( 1093) hydrogen bonds : angle 4.49610 ( 2955) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 102 time to evaluate : 1.066 Fit side-chains REVERT: A 1094 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8507 (mtm) REVERT: A 1194 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9176 (mm) REVERT: A 1235 GLU cc_start: 0.8449 (mp0) cc_final: 0.8070 (mp0) REVERT: B 195 MET cc_start: 0.8632 (mmt) cc_final: 0.8155 (mmp) REVERT: B 973 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8363 (mtp85) REVERT: C 364 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: E 251 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8036 (mtt180) REVERT: E 314 GLU cc_start: 0.8653 (tt0) cc_final: 0.8442 (mt-10) REVERT: E 320 ASP cc_start: 0.8913 (t0) cc_final: 0.8672 (t0) outliers start: 46 outliers final: 25 residues processed: 143 average time/residue: 0.5907 time to fit residues: 103.8493 Evaluate side-chains 123 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 PHE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 186 TYR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 973 ARG Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 442 PHE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain E residue 292 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 53 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 333 optimal weight: 4.9990 chunk 386 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 181 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.059324 restraints weight = 79997.990| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.87 r_work: 0.2781 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30449 Z= 0.172 Angle : 0.463 8.261 41627 Z= 0.252 Chirality : 0.045 0.238 4853 Planarity : 0.003 0.059 5340 Dihedral : 3.863 20.267 4429 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.60 % Favored : 96.37 % Rotamer: Outliers : 1.68 % Allowed : 17.70 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 are not related in a simple way. whole: 0.39 (0.14), residues: 4027 helix: 2.34 (0.18), residues: 864 sheet: 0.18 (0.15), residues: 1135 loop : -0.59 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 253 TYR 0.020 0.001 TYR B 368 PHE 0.018 0.001 PHE E 442 TRP 0.008 0.001 TRP A 974 HIS 0.006 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00405 (30446) covalent geometry : angle 0.46334 (41621) SS BOND : bond 0.00281 ( 3) SS BOND : angle 0.55824 ( 6) hydrogen bonds : bond 0.03771 ( 1093) hydrogen bonds : angle 4.58120 ( 2955) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 94 time to evaluate : 1.241 Fit side-chains REVERT: A 1094 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8532 (mtm) REVERT: A 1194 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9173 (mm) REVERT: A 1235 GLU cc_start: 0.8474 (mp0) cc_final: 0.8077 (mp0) REVERT: B 195 MET cc_start: 0.8646 (mmt) cc_final: 0.8202 (mmp) REVERT: B 973 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8354 (mtp85) REVERT: B 1170 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8048 (tmm-80) REVERT: C 364 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: E 81 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8699 (tp30) REVERT: E 251 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.7940 (mtt180) REVERT: E 314 GLU cc_start: 0.8706 (tt0) cc_final: 0.8458 (mt-10) REVERT: E 320 ASP cc_start: 0.8893 (t0) cc_final: 0.8646 (t0) REVERT: E 621 HIS cc_start: 0.7646 (m-70) cc_final: 0.7042 (m-70) outliers start: 44 outliers final: 28 residues processed: 133 average time/residue: 0.5451 time to fit residues: 89.0716 Evaluate side-chains 126 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 PHE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 186 TYR Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 759 ASN Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 973 ARG Chi-restraints excluded: chain B residue 1170 ARG Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 442 PHE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 251 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 164 optimal weight: 0.0010 chunk 237 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 373 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 289 optimal weight: 30.0000 chunk 301 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 773 ASN ** 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 = 0.3245 r_free = 0.3245 target = 0.073710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.058906 restraints weight = 78872.453| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.82 r_work: 0.2778 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30449 Z= 0.178 Angle : 0.471 8.497 41627 Z= 0.256 Chirality : 0.045 0.234 4853 Planarity : 0.003 0.058 5340 Dihedral : 3.921 20.521 4429 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.30 % Favored : 96.65 % Rotamer: Outliers : 1.49 % Allowed : 17.93 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 are not related in a simple way. whole: 0.36 (0.13), residues: 4027 helix: 2.32 (0.18), residues: 861 sheet: 0.15 (0.16), residues: 1115 loop : -0.59 (0.14), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 253 TYR 0.021 0.001 TYR B 368 PHE 0.019 0.001 PHE E 442 TRP 0.008 0.001 TRP A 974 HIS 0.006 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00419 (30446) covalent geometry : angle 0.47100 (41621) SS BOND : bond 0.00301 ( 3) SS BOND : angle 0.60054 ( 6) hydrogen bonds : bond 0.03853 ( 1093) hydrogen bonds : angle 4.61523 ( 2955) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8054 Ramachandran restraints generated. 4027 Oldfield, 0 Emsley, 4027 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 1.241 Fit side-chains REVERT: A 1094 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8529 (mtm) REVERT: A 1194 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9160 (mm) REVERT: A 1235 GLU cc_start: 0.8452 (mp0) cc_final: 0.8016 (mp0) REVERT: B 195 MET cc_start: 0.8657 (mmt) cc_final: 0.8222 (mmp) REVERT: B 210 LYS cc_start: 0.9551 (OUTLIER) cc_final: 0.9127 (tttt) REVERT: B 973 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8359 (mtp85) REVERT: B 1170 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8071 (tmm-80) REVERT: C 364 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8232 (tt0) REVERT: E 251 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.7935 (mtt180) REVERT: E 314 GLU cc_start: 0.8717 (tt0) cc_final: 0.8465 (mt-10) REVERT: E 320 ASP cc_start: 0.8894 (t0) cc_final: 0.8650 (t0) REVERT: E 621 HIS cc_start: 0.7685 (m-70) cc_final: 0.7122 (m-70) outliers start: 39 outliers final: 28 residues processed: 130 average time/residue: 0.5911 time to fit residues: 93.4598 Evaluate side-chains 126 residues out of total 3781 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 PHE Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1194 LEU Chi-restraints excluded: chain A residue 1260 ILE Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 186 TYR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 400 GLU Chi-restraints excluded: chain B residue 478 CYS Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 759 ASN Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 973 ARG Chi-restraints excluded: chain B residue 1170 ARG Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 364 GLN Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 442 PHE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 538 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 251 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 406 optimal weight: 1.9990 chunk 366 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 330 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 291 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 773 ASN ** 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 = 0.3262 r_free = 0.3262 target = 0.076978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.061934 restraints weight = 81059.910| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.86 r_work: 0.2795 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30449 Z= 0.122 Angle : 0.448 8.441 41627 Z= 0.243 Chirality : 0.044 0.205 4853 Planarity : 0.003 0.059 5340 Dihedral : 3.814 19.923 4429 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.23 % Favored : 96.72 % Rotamer: Outliers : 1.49 % Allowed : 18.00 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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 are not related in a simple way. whole: 0.47 (0.14), residues: 4027 helix: 2.44 (0.18), residues: 856 sheet: 0.26 (0.16), residues: 1110 loop : -0.55 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 253 TYR 0.020 0.001 TYR B 368 PHE 0.020 0.001 PHE E 442 TRP 0.008 0.001 TRP A 974 HIS 0.005 0.001 HIS B1190 Details of bonding type rmsd covalent geometry : bond 0.00283 (30446) covalent geometry : angle 0.44757 (41621) SS BOND : bond 0.00276 ( 3) SS BOND : angle 0.42019 ( 6) hydrogen bonds : bond 0.03574 ( 1093) hydrogen bonds : angle 4.51815 ( 2955) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7367.59 seconds wall clock time: 126 minutes 46.52 seconds (7606.52 seconds total)