Starting phenix.real_space_refine on Thu Aug 6 03:49:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wud_66258/08_2026/9wud_66258.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wud_66258/08_2026/9wud_66258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wud_66258/08_2026/9wud_66258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wud_66258/08_2026/9wud_66258.map" model { file = "/net/cci-nas-00/data/ceres_data/9wud_66258/08_2026/9wud_66258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wud_66258/08_2026/9wud_66258.cif" } resolution = 3.08 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= 0.002 sd= 0.012 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: 6 Type Number sf(0) Gaussians Fe 1 7.16 5 P 6 5.49 5 S 51 5.16 5 C 8143 2.51 5 N 2220 2.21 5 O 2473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12894 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 4504 Classifications: {'peptide': 574} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 548} Chain: "B" Number of atoms: 8178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8178 Classifications: {'peptide': 1024} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 1 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'FAD': 1, 'FMN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 128 Unusual residues: {'FAD': 1, 'FMN': 1, 'HEM': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7763 SG CYS B 404 51.487 27.869 57.763 1.00 35.02 S Time building chain proxies: 1.98, per 1000 atoms: 0.15 Number of scatterers: 12894 At special positions: 0 Unit cell: (85.56, 113.46, 141.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 1 26.01 S 51 16.00 P 6 15.00 O 2473 8.00 N 2220 7.00 C 8143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 446.6 milliseconds 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2956 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 16 sheets defined 46.9% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 508 through 523 Processing helix chain 'A' and resid 534 through 537 removed outlier: 3.890A pdb=" N ILE A 537 " --> pdb=" O ASN A 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 534 through 537' Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 596 through 609 Processing helix chain 'A' and resid 625 through 645 removed outlier: 3.626A pdb=" N TRP A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 671 removed outlier: 3.538A pdb=" N GLY A 670 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER A 671 " --> pdb=" O THR A 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 667 through 671' Processing helix chain 'A' and resid 692 through 696 removed outlier: 3.891A pdb=" N GLY A 696 " --> pdb=" O PRO A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 736 Processing helix chain 'A' and resid 764 through 771 Processing helix chain 'A' and resid 779 through 789 removed outlier: 3.670A pdb=" N PHE A 789 " --> pdb=" O GLU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 Processing helix chain 'A' and resid 806 through 812 removed outlier: 4.341A pdb=" N GLU A 810 " --> pdb=" O GLY A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 832 through 840 Processing helix chain 'A' and resid 883 through 889 Processing helix chain 'A' and resid 922 through 925 Processing helix chain 'A' and resid 926 through 943 removed outlier: 3.760A pdb=" N GLY A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 992 through 1000 removed outlier: 3.805A pdb=" N VAL A 996 " --> pdb=" O TYR A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1011 Processing helix chain 'A' and resid 1023 through 1039 Processing helix chain 'A' and resid 1042 through 1056 Processing helix chain 'B' and resid 13 through 17 Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 26 through 39 removed outlier: 3.742A pdb=" N SER B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 64 Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.725A pdb=" N LYS B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N PHE B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.033A pdb=" N SER B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 106 Processing helix chain 'B' and resid 107 through 113 removed outlier: 3.718A pdb=" N SER B 110 " --> pdb=" O PRO B 107 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN B 111 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG B 112 " --> pdb=" O PHE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 134 removed outlier: 4.697A pdb=" N ASP B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N MET B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 removed outlier: 4.588A pdb=" N LEU B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 removed outlier: 3.588A pdb=" N ARG B 169 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 191 removed outlier: 3.610A pdb=" N THR B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN B 191 " --> pdb=" O MET B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 200 through 227 removed outlier: 3.574A pdb=" N LYS B 204 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 243 removed outlier: 3.579A pdb=" N ARG B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 282 removed outlier: 4.369A pdb=" N GLU B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N THR B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.546A pdb=" N LYS B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 314 through 328 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 399 through 403 Processing helix chain 'B' and resid 406 through 424 Processing helix chain 'B' and resid 508 through 524 Processing helix chain 'B' and resid 561 through 570 Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.501A pdb=" N TYR B 595 " --> pdb=" O ALA B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 610 Processing helix chain 'B' and resid 625 through 645 removed outlier: 3.770A pdb=" N GLN B 629 " --> pdb=" O ASP B 625 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE B 642 " --> pdb=" O TRP B 638 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU B 643 " --> pdb=" O SER B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 654 removed outlier: 4.009A pdb=" N LYS B 654 " --> pdb=" O ASP B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 Processing helix chain 'B' and resid 725 through 737 Processing helix chain 'B' and resid 764 through 771 Processing helix chain 'B' and resid 779 through 789 removed outlier: 3.988A pdb=" N GLU B 785 " --> pdb=" O ALA B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 801 Processing helix chain 'B' and resid 807 through 812 Processing helix chain 'B' and resid 818 through 824 Processing helix chain 'B' and resid 832 through 839 Processing helix chain 'B' and resid 882 through 889 Processing helix chain 'B' and resid 922 through 924 No H-bonds generated for 'chain 'B' and resid 922 through 924' Processing helix chain 'B' and resid 925 through 943 removed outlier: 4.656A pdb=" N PHE B 929 " --> pdb=" O GLY B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 973 removed outlier: 3.662A pdb=" N GLN B 969 " --> pdb=" O LYS B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1000 removed outlier: 3.888A pdb=" N VAL B 996 " --> pdb=" O TYR B 992 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN B1000 " --> pdb=" O VAL B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1011 Processing helix chain 'B' and resid 1023 through 1040 Processing helix chain 'B' and resid 1042 through 1056 Processing sheet with id=AA1, first strand: chain 'A' and resid 528 through 532 removed outlier: 6.619A pdb=" N LEU A 499 " --> pdb=" O GLU A 529 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ALA A 531 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL A 501 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 546 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N PHE A 584 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE A 548 " --> pdb=" O PHE A 584 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N CYS A 586 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR A 550 " --> pdb=" O CYS A 586 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 581 " --> pdb=" O VAL A 612 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 532 removed outlier: 6.619A pdb=" N LEU A 499 " --> pdb=" O GLU A 529 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ALA A 531 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL A 501 " --> pdb=" O ALA A 531 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 546 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N PHE A 584 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE A 548 " --> pdb=" O PHE A 584 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N CYS A 586 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N THR A 550 " --> pdb=" O CYS A 586 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N GLY A 618 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 583 " --> pdb=" O GLY A 618 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLY A 620 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY A 585 " --> pdb=" O GLY A 620 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 660 through 662 Processing sheet with id=AA4, first strand: chain 'A' and resid 860 through 866 removed outlier: 7.261A pdb=" N THR A 699 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N GLU A 689 " --> pdb=" O THR A 699 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS A 701 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN A 687 " --> pdb=" O HIS A 701 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLU A 703 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 683 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 717 through 718 Processing sheet with id=AA6, first strand: chain 'A' and resid 761 through 763 Processing sheet with id=AA7, first strand: chain 'A' and resid 772 through 773 removed outlier: 4.469A pdb=" N HIS A 841 " --> pdb=" O GLU A 773 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 869 through 871 removed outlier: 3.594A pdb=" N GLY A 870 " --> pdb=" O TYR A 879 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 977 through 979 removed outlier: 7.180A pdb=" N ALA A 949 " --> pdb=" O THR A 977 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TYR A 979 " --> pdb=" O ALA A 949 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 951 " --> pdb=" O TYR A 979 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU A1014 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ASP A1062 " --> pdb=" O LEU A1014 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE A1016 " --> pdb=" O ASP A1062 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N TRP A1064 " --> pdb=" O ILE A1016 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY A1018 " --> pdb=" O TRP A1064 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 41 through 45 removed outlier: 7.409A pdb=" N SER B 50 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N THR B 358 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE B 52 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU B 360 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 54 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 334 " --> pdb=" O VAL B 359 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 141 through 142 Processing sheet with id=AB3, first strand: chain 'B' and resid 342 through 344 Processing sheet with id=AB4, first strand: chain 'B' and resid 528 through 532 removed outlier: 3.599A pdb=" N TYR B 503 " --> pdb=" O ALA B 531 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU B 500 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL B 549 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU B 502 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N SER B 551 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY B 504 " --> pdb=" O SER B 551 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL B 546 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE B 584 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE B 548 " --> pdb=" O PHE B 584 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N CYS B 586 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR B 550 " --> pdb=" O CYS B 586 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 581 " --> pdb=" O VAL B 612 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 528 through 532 removed outlier: 3.599A pdb=" N TYR B 503 " --> pdb=" O ALA B 531 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU B 500 " --> pdb=" O LEU B 547 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL B 549 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU B 502 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N SER B 551 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLY B 504 " --> pdb=" O SER B 551 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL B 546 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE B 584 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE B 548 " --> pdb=" O PHE B 584 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N CYS B 586 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR B 550 " --> pdb=" O CYS B 586 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N GLY B 618 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL B 583 " --> pdb=" O GLY B 618 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLY B 620 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY B 585 " --> pdb=" O GLY B 620 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 717 through 720 removed outlier: 6.098A pdb=" N VAL B 684 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N THR B 705 " --> pdb=" O VAL B 684 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 686 " --> pdb=" O GLU B 703 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 688 " --> pdb=" O HIS B 701 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 977 through 979 removed outlier: 6.823A pdb=" N ILE B 917 " --> pdb=" O TYR B 950 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N TYR B 952 " --> pdb=" O ILE B 917 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N MET B 919 " --> pdb=" O TYR B 952 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU B1014 " --> pdb=" O ALA B1060 " (cutoff:3.500A) 545 hydrogen bonds defined for protein. 1557 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 5359 1.39 - 1.57: 7723 1.57 - 1.75: 10 1.75 - 1.93: 88 1.93 - 2.11: 3 Bond restraints: 13183 Sorted by residual: bond pdb=" C4 FMN A1101 " pdb=" C4A FMN A1101 " ideal model delta sigma weight residual 1.485 1.387 0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C4 FMN B1103 " pdb=" C4A FMN B1103 " ideal model delta sigma weight residual 1.485 1.388 0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C4A FMN B1103 " pdb=" N5 FMN B1103 " ideal model delta sigma weight residual 1.300 1.376 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" O5' FMN A1101 " pdb=" P FMN A1101 " ideal model delta sigma weight residual 1.676 1.600 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C4A FMN A1101 " pdb=" N5 FMN A1101 " ideal model delta sigma weight residual 1.300 1.375 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 13178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 17412 1.73 - 3.46: 364 3.46 - 5.18: 74 5.18 - 6.91: 22 6.91 - 8.64: 4 Bond angle restraints: 17876 Sorted by residual: angle pdb=" CA GLU B 830 " pdb=" CB GLU B 830 " pdb=" CG GLU B 830 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 angle pdb=" C ASN A1000 " pdb=" N ALA A1001 " pdb=" CA ALA A1001 " ideal model delta sigma weight residual 120.82 125.75 -4.93 1.50e+00 4.44e-01 1.08e+01 angle pdb=" CA GLU B 426 " pdb=" C GLU B 426 " pdb=" O GLU B 426 " ideal model delta sigma weight residual 121.16 117.53 3.63 1.13e+00 7.83e-01 1.03e+01 angle pdb=" C GLU B 426 " pdb=" N PHE B 427 " pdb=" CA PHE B 427 " ideal model delta sigma weight residual 122.99 118.90 4.09 1.41e+00 5.03e-01 8.42e+00 angle pdb=" CB MET B 187 " pdb=" CG MET B 187 " pdb=" SD MET B 187 " ideal model delta sigma weight residual 112.70 104.06 8.64 3.00e+00 1.11e-01 8.29e+00 ... (remaining 17871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.59: 6976 19.59 - 39.17: 756 39.17 - 58.76: 180 58.76 - 78.34: 30 78.34 - 97.93: 22 Dihedral angle restraints: 7964 sinusoidal: 3349 harmonic: 4615 Sorted by residual: dihedral pdb=" C2C HEM B1101 " pdb=" C3C HEM B1101 " pdb=" CAC HEM B1101 " pdb=" CBC HEM B1101 " ideal model delta sinusoidal sigma weight residual 0.00 -49.59 49.59 2 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" O5' FAD A1102 " pdb=" O3P FAD A1102 " pdb=" P FAD A1102 " pdb=" PA FAD A1102 " ideal model delta sinusoidal sigma weight residual -61.77 36.16 -97.93 1 3.00e+01 1.11e-03 1.21e+01 dihedral pdb=" C2D HEM B1101 " pdb=" C3D HEM B1101 " pdb=" CAD HEM B1101 " pdb=" CBD HEM B1101 " ideal model delta sinusoidal sigma weight residual 0.00 89.29 -89.29 2 2.00e+01 2.50e-03 1.20e+01 ... (remaining 7961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1308 0.038 - 0.075: 435 0.075 - 0.113: 142 0.113 - 0.151: 24 0.151 - 0.188: 2 Chirality restraints: 1911 Sorted by residual: chirality pdb=" CG LEU B 152 " pdb=" CB LEU B 152 " pdb=" CD1 LEU B 152 " pdb=" CD2 LEU B 152 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.85e-01 chirality pdb=" CB ILE A 602 " pdb=" CA ILE A 602 " pdb=" CG1 ILE A 602 " pdb=" CG2 ILE A 602 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CB THR B 902 " pdb=" CA THR B 902 " pdb=" OG1 THR B 902 " pdb=" CG2 THR B 902 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 1908 not shown) Planarity restraints: 2317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 591 " -0.026 2.00e-02 2.50e+03 2.30e-02 1.33e+01 pdb=" CG TRP A 591 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 591 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 591 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 591 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 591 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 591 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 591 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 591 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 591 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 921 " -0.046 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO B 922 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 922 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 922 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 960 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C ASP B 960 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP B 960 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE B 961 " 0.011 2.00e-02 2.50e+03 ... (remaining 2314 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4998 2.90 - 3.40: 12850 3.40 - 3.90: 22012 3.90 - 4.40: 25842 4.40 - 4.90: 42724 Nonbonded interactions: 108426 Sorted by model distance: nonbonded pdb=" O ASP B 960 " pdb=" OD1 ASP B 960 " model vdw 2.405 3.040 nonbonded pdb=" C1' FMN B1103 " pdb=" O3' FMN B1103 " model vdw 2.511 2.752 nonbonded pdb=" N ASP B 86 " pdb=" OD1 ASP B 86 " model vdw 2.531 3.120 nonbonded pdb=" O SER B 178 " pdb=" OD1 ASP B 210 " model vdw 2.549 3.040 nonbonded pdb=" N ASN A 560 " pdb=" OD1 ASN A 560 " model vdw 2.556 3.120 ... (remaining 108421 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.700 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 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 : 0.005 0.213 13184 Z= 0.209 Angle : 0.656 8.640 17876 Z= 0.324 Chirality : 0.042 0.188 1911 Planarity : 0.004 0.070 2317 Dihedral : 17.539 97.925 5008 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.74 % Allowed : 20.18 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.50 (0.21), residues: 1592 helix: 0.14 (0.20), residues: 684 sheet: -0.92 (0.32), residues: 268 loop : -0.38 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 99 TYR 0.028 0.001 TYR B 281 PHE 0.015 0.001 PHE B 160 TRP 0.062 0.002 TRP A 591 HIS 0.010 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (13183) covalent geometry : angle 0.65633 / 0.32 (17876) hydrogen bonds : bond 0.14036 / 9.33 ( 536) hydrogen bonds : angle 6.46124 / 4.53 ( 1557) Misc. bond : bond 0.09917 / 5.22 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 0.336 Fit side-chains REVERT: A 575 GLU cc_start: 0.5751 (tp30) cc_final: 0.5011 (tp30) REVERT: A 637 MET cc_start: 0.6387 (tpt) cc_final: 0.5835 (ttp) REVERT: A 697 ARG cc_start: 0.7536 (mtp-110) cc_final: 0.6523 (mtt-85) REVERT: A 725 SER cc_start: 0.7535 (p) cc_final: 0.7303 (t) REVERT: A 742 ASP cc_start: 0.7743 (t0) cc_final: 0.6918 (m-30) REVERT: A 771 SER cc_start: 0.8111 (m) cc_final: 0.7804 (m) REVERT: A 785 GLU cc_start: 0.6284 (mm-30) cc_final: 0.5839 (mp0) REVERT: A 814 LYS cc_start: 0.7848 (mptt) cc_final: 0.7003 (ttmt) REVERT: A 894 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6972 (mt-10) REVERT: A 898 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7086 (ptt) REVERT: A 1048 GLN cc_start: 0.6614 (pt0) cc_final: 0.5973 (tt0) REVERT: B 205 ARG cc_start: 0.7174 (ttt180) cc_final: 0.6473 (ttm170) REVERT: B 212 GLN cc_start: 0.6951 (tp40) cc_final: 0.6289 (pt0) REVERT: B 351 LYS cc_start: 0.6837 (mttt) cc_final: 0.6289 (ttmm) REVERT: B 438 LYS cc_start: 0.7306 (tttt) cc_final: 0.6745 (tptp) REVERT: B 742 ASP cc_start: 0.7170 (t0) cc_final: 0.6942 (t70) REVERT: B 789 PHE cc_start: 0.7572 (m-10) cc_final: 0.6837 (m-10) REVERT: B 798 GLU cc_start: 0.6179 (tp30) cc_final: 0.5562 (pt0) REVERT: B 814 LYS cc_start: 0.8038 (tttm) cc_final: 0.7639 (mtpp) REVERT: B 838 GLU cc_start: 0.6838 (tt0) cc_final: 0.6630 (tt0) REVERT: B 844 LYS cc_start: 0.6437 (mtpt) cc_final: 0.5659 (ptmm) REVERT: B 898 MET cc_start: 0.7450 (pp-130) cc_final: 0.7236 (ptp) REVERT: B 1023 MET cc_start: 0.6674 (tpp) cc_final: 0.6114 (tmm) REVERT: B 1033 ASN cc_start: 0.7885 (m-40) cc_final: 0.7542 (m-40) REVERT: B 1044 GLN cc_start: 0.6764 (tp40) cc_final: 0.6014 (mp10) outliers start: 10 outliers final: 8 residues processed: 182 average time/residue: 0.0880 time to fit residues: 23.6022 Evaluate side-chains 167 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 158 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 920 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0370 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1058 GLN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN B 524 HIS B 605 GLN B 728 ASN B 775 GLN ** B 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.192890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.159578 restraints weight = 13804.232| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 2.23 r_work: 0.3889 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.0767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 13184 Z= 0.115 Angle : 0.534 8.541 17876 Z= 0.269 Chirality : 0.040 0.137 1911 Planarity : 0.004 0.064 2317 Dihedral : 8.646 89.327 1888 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.28 % Allowed : 17.67 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1592 helix: 0.35 (0.20), residues: 693 sheet: -0.81 (0.32), residues: 252 loop : -0.38 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 423 TYR 0.020 0.001 TYR B 167 PHE 0.014 0.001 PHE B 160 TRP 0.016 0.001 TRP A 591 HIS 0.007 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.11 (13183) covalent geometry : angle 0.53360 / 0.27 (17876) hydrogen bonds : bond 0.03560 / 2.38 ( 536) hydrogen bonds : angle 4.85092 / 3.44 ( 1557) Misc. bond : bond 0.01410 / 0.74 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 575 GLU cc_start: 0.5642 (tp30) cc_final: 0.4982 (tp30) REVERT: A 637 MET cc_start: 0.6382 (tpt) cc_final: 0.5840 (ttp) REVERT: A 697 ARG cc_start: 0.7557 (mtp-110) cc_final: 0.6689 (mtt-85) REVERT: A 734 GLN cc_start: 0.7248 (pp30) cc_final: 0.6816 (mm-40) REVERT: A 742 ASP cc_start: 0.6896 (t0) cc_final: 0.6664 (m-30) REVERT: A 771 SER cc_start: 0.7953 (m) cc_final: 0.7696 (m) REVERT: A 785 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6498 (mp0) REVERT: A 814 LYS cc_start: 0.7801 (mptt) cc_final: 0.7134 (ttmt) REVERT: A 894 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7294 (mt-10) REVERT: A 1048 GLN cc_start: 0.6914 (pt0) cc_final: 0.6256 (tt0) REVERT: B 65 ASP cc_start: 0.7353 (t0) cc_final: 0.6729 (p0) REVERT: B 205 ARG cc_start: 0.7158 (ttt180) cc_final: 0.6715 (ttm170) REVERT: B 212 GLN cc_start: 0.7011 (tp40) cc_final: 0.6499 (pt0) REVERT: B 431 LYS cc_start: 0.7087 (ttpt) cc_final: 0.6852 (ttpt) REVERT: B 438 LYS cc_start: 0.7417 (tttt) cc_final: 0.6981 (tptp) REVERT: B 789 PHE cc_start: 0.7391 (m-10) cc_final: 0.7186 (m-10) REVERT: B 798 GLU cc_start: 0.6319 (tp30) cc_final: 0.5863 (pt0) REVERT: B 814 LYS cc_start: 0.8101 (tttm) cc_final: 0.7829 (mtpp) REVERT: B 844 LYS cc_start: 0.6527 (mtpt) cc_final: 0.5876 (ptmm) REVERT: B 1008 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6361 (mm) REVERT: B 1023 MET cc_start: 0.6953 (tpp) cc_final: 0.6433 (tmm) REVERT: B 1031 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7083 (mp) REVERT: B 1033 ASN cc_start: 0.8196 (m-40) cc_final: 0.7785 (m-40) outliers start: 31 outliers final: 13 residues processed: 194 average time/residue: 0.0905 time to fit residues: 25.8088 Evaluate side-chains 169 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1008 LEU Chi-restraints excluded: chain B residue 1031 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 117 optimal weight: 0.2980 chunk 72 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1010 GLN ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 HIS B 811 GLN ** B1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.187249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.153432 restraints weight = 14008.455| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.24 r_work: 0.3835 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13184 Z= 0.158 Angle : 0.562 8.151 17876 Z= 0.281 Chirality : 0.042 0.154 1911 Planarity : 0.004 0.061 2317 Dihedral : 8.624 89.236 1882 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.39 % Allowed : 17.53 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.35 (0.21), residues: 1592 helix: 0.37 (0.20), residues: 696 sheet: -0.89 (0.33), residues: 246 loop : -0.44 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 423 TYR 0.024 0.002 TYR B 167 PHE 0.020 0.002 PHE B 601 TRP 0.016 0.002 TRP B 98 HIS 0.008 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (13183) covalent geometry : angle 0.56178 / 0.28 (17876) hydrogen bonds : bond 0.03521 / 2.36 ( 536) hydrogen bonds : angle 4.65556 / 3.29 ( 1557) Misc. bond : bond 0.01822 / 0.96 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.461 Fit side-chains REVERT: A 575 GLU cc_start: 0.5654 (tp30) cc_final: 0.4995 (tp30) REVERT: A 603 ASP cc_start: 0.5029 (t0) cc_final: 0.4656 (t70) REVERT: A 627 GLU cc_start: 0.5717 (tp30) cc_final: 0.4948 (tp30) REVERT: A 637 MET cc_start: 0.6451 (tpt) cc_final: 0.5931 (ttp) REVERT: A 697 ARG cc_start: 0.7530 (mtp-110) cc_final: 0.6700 (mtt-85) REVERT: A 734 GLN cc_start: 0.7217 (pp30) cc_final: 0.6817 (mm-40) REVERT: A 742 ASP cc_start: 0.6952 (t0) cc_final: 0.6748 (m-30) REVERT: A 767 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6365 (tp) REVERT: A 771 SER cc_start: 0.7962 (m) cc_final: 0.7735 (m) REVERT: A 785 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6544 (mp0) REVERT: A 814 LYS cc_start: 0.7784 (mptt) cc_final: 0.7112 (ttmt) REVERT: A 824 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.5974 (mm-30) REVERT: A 894 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7290 (mt-10) REVERT: A 1000 ASN cc_start: 0.7701 (m-40) cc_final: 0.7400 (m-40) REVERT: A 1048 GLN cc_start: 0.6954 (pt0) cc_final: 0.6423 (tt0) REVERT: A 1062 ASP cc_start: 0.6676 (t70) cc_final: 0.6394 (t0) REVERT: B 65 ASP cc_start: 0.7493 (t0) cc_final: 0.6800 (p0) REVERT: B 205 ARG cc_start: 0.7213 (ttt180) cc_final: 0.6766 (ttm170) REVERT: B 212 GLN cc_start: 0.7053 (tp40) cc_final: 0.6546 (pt0) REVERT: B 423 ARG cc_start: 0.7720 (tpt-90) cc_final: 0.7390 (tpt-90) REVERT: B 438 LYS cc_start: 0.7569 (tttt) cc_final: 0.7094 (tptm) REVERT: B 780 ARG cc_start: 0.6412 (OUTLIER) cc_final: 0.4740 (mtm-85) REVERT: B 798 GLU cc_start: 0.6279 (tp30) cc_final: 0.5839 (pt0) REVERT: B 814 LYS cc_start: 0.8154 (tttm) cc_final: 0.7913 (mtpp) REVERT: B 844 LYS cc_start: 0.6484 (mtpt) cc_final: 0.5807 (ptmm) REVERT: B 898 MET cc_start: 0.7405 (pp-130) cc_final: 0.7199 (pp-130) REVERT: B 1008 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6391 (mm) REVERT: B 1023 MET cc_start: 0.6946 (tpp) cc_final: 0.6482 (tmm) REVERT: B 1033 ASN cc_start: 0.8209 (m-40) cc_final: 0.7749 (m-40) outliers start: 46 outliers final: 21 residues processed: 207 average time/residue: 0.1160 time to fit residues: 34.8280 Evaluate side-chains 181 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 780 ARG Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1008 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 60 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 299 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.187697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.154185 restraints weight = 14011.624| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.22 r_work: 0.3855 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13184 Z= 0.137 Angle : 0.547 9.234 17876 Z= 0.272 Chirality : 0.041 0.149 1911 Planarity : 0.004 0.057 2317 Dihedral : 8.455 89.838 1880 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.87 % Allowed : 18.19 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.21), residues: 1592 helix: 0.51 (0.20), residues: 688 sheet: -0.98 (0.32), residues: 255 loop : -0.46 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 956 TYR 0.016 0.001 TYR B 281 PHE 0.028 0.002 PHE A 601 TRP 0.014 0.001 TRP B 98 HIS 0.007 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (13183) covalent geometry : angle 0.54691 / 0.27 (17876) hydrogen bonds : bond 0.03266 / 2.20 ( 536) hydrogen bonds : angle 4.52352 / 3.20 ( 1557) Misc. bond : bond 0.01690 / 0.89 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.368 Fit side-chains REVERT: A 575 GLU cc_start: 0.5753 (tp30) cc_final: 0.5082 (tp30) REVERT: A 603 ASP cc_start: 0.5107 (t0) cc_final: 0.4763 (t70) REVERT: A 627 GLU cc_start: 0.5858 (tp30) cc_final: 0.5538 (mt-10) REVERT: A 637 MET cc_start: 0.6553 (tpt) cc_final: 0.5929 (ttp) REVERT: A 697 ARG cc_start: 0.7548 (mtp-110) cc_final: 0.6700 (mtt-85) REVERT: A 734 GLN cc_start: 0.7457 (pp30) cc_final: 0.6982 (mm-40) REVERT: A 742 ASP cc_start: 0.7231 (t0) cc_final: 0.6845 (m-30) REVERT: A 761 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7228 (tp30) REVERT: A 767 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6455 (tp) REVERT: A 771 SER cc_start: 0.8043 (m) cc_final: 0.7831 (m) REVERT: A 785 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6676 (mp0) REVERT: A 814 LYS cc_start: 0.7890 (mptt) cc_final: 0.7183 (ttmt) REVERT: A 824 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6083 (mt-10) REVERT: A 894 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7462 (mt-10) REVERT: A 898 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7608 (ptt) REVERT: A 1000 ASN cc_start: 0.7638 (m-40) cc_final: 0.7342 (m-40) REVERT: A 1048 GLN cc_start: 0.7057 (pt0) cc_final: 0.6538 (tt0) REVERT: B 65 ASP cc_start: 0.7594 (t0) cc_final: 0.6849 (p0) REVERT: B 205 ARG cc_start: 0.7294 (ttt180) cc_final: 0.6785 (ttm170) REVERT: B 212 GLN cc_start: 0.7278 (tp40) cc_final: 0.6685 (pt0) REVERT: B 351 LYS cc_start: 0.7036 (mtpp) cc_final: 0.6253 (mmtt) REVERT: B 423 ARG cc_start: 0.7764 (tpt-90) cc_final: 0.7459 (tpt-90) REVERT: B 430 TYR cc_start: 0.7337 (p90) cc_final: 0.7072 (p90) REVERT: B 438 LYS cc_start: 0.7714 (tttt) cc_final: 0.7215 (tptm) REVERT: B 780 ARG cc_start: 0.6654 (OUTLIER) cc_final: 0.4985 (mtm-85) REVERT: B 798 GLU cc_start: 0.6290 (tp30) cc_final: 0.5788 (pt0) REVERT: B 814 LYS cc_start: 0.8280 (tttm) cc_final: 0.7982 (mtpp) REVERT: B 838 GLU cc_start: 0.7532 (tt0) cc_final: 0.6996 (tp30) REVERT: B 844 LYS cc_start: 0.6653 (mtpt) cc_final: 0.5918 (ptmm) REVERT: B 950 TYR cc_start: 0.6669 (m-80) cc_final: 0.6435 (m-80) REVERT: B 967 LEU cc_start: 0.5891 (OUTLIER) cc_final: 0.5551 (mt) REVERT: B 1008 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.6472 (mm) REVERT: B 1023 MET cc_start: 0.6975 (tpp) cc_final: 0.6368 (tmm) REVERT: B 1033 ASN cc_start: 0.8238 (m-40) cc_final: 0.7760 (m-40) outliers start: 39 outliers final: 24 residues processed: 199 average time/residue: 0.0967 time to fit residues: 28.0669 Evaluate side-chains 192 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 780 ARG Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1008 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 161 ASN B 299 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 HIS B 589 HIS ** B1039 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.185156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.151639 restraints weight = 14051.693| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 2.24 r_work: 0.3824 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13184 Z= 0.157 Angle : 0.560 8.808 17876 Z= 0.279 Chirality : 0.042 0.161 1911 Planarity : 0.004 0.054 2317 Dihedral : 8.515 89.431 1880 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.39 % Allowed : 18.34 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.21), residues: 1592 helix: 0.48 (0.20), residues: 690 sheet: -1.17 (0.32), residues: 242 loop : -0.48 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 956 TYR 0.024 0.001 TYR B 167 PHE 0.022 0.002 PHE A 601 TRP 0.014 0.001 TRP A 633 HIS 0.006 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (13183) covalent geometry : angle 0.56004 / 0.28 (17876) hydrogen bonds : bond 0.03344 / 2.26 ( 536) hydrogen bonds : angle 4.50484 / 3.18 ( 1557) Misc. bond : bond 0.02003 / 1.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 575 GLU cc_start: 0.5742 (tp30) cc_final: 0.5300 (tp30) REVERT: A 597 ASP cc_start: 0.7337 (t0) cc_final: 0.7126 (t0) REVERT: A 603 ASP cc_start: 0.5190 (t0) cc_final: 0.4876 (t70) REVERT: A 606 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7779 (mp) REVERT: A 637 MET cc_start: 0.6267 (tpt) cc_final: 0.5823 (ttp) REVERT: A 697 ARG cc_start: 0.7497 (mtp-110) cc_final: 0.6699 (mtt-85) REVERT: A 734 GLN cc_start: 0.7213 (pp30) cc_final: 0.6888 (mm110) REVERT: A 761 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6975 (tp30) REVERT: A 767 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6450 (tp) REVERT: A 771 SER cc_start: 0.7975 (m) cc_final: 0.7750 (m) REVERT: A 785 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6509 (mp0) REVERT: A 810 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7344 (pm20) REVERT: A 814 LYS cc_start: 0.7833 (mptt) cc_final: 0.7175 (ttmt) REVERT: A 824 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.5981 (mm-30) REVERT: A 894 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7210 (mt-10) REVERT: A 898 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7374 (ptt) REVERT: A 1000 ASN cc_start: 0.7694 (m-40) cc_final: 0.7396 (m-40) REVERT: A 1048 GLN cc_start: 0.7087 (pt0) cc_final: 0.6730 (tt0) REVERT: B 38 TYR cc_start: 0.6902 (m-10) cc_final: 0.6646 (m-10) REVERT: B 65 ASP cc_start: 0.7522 (t0) cc_final: 0.6814 (p0) REVERT: B 205 ARG cc_start: 0.7153 (ttt180) cc_final: 0.6674 (ttm170) REVERT: B 212 GLN cc_start: 0.7042 (tp40) cc_final: 0.6486 (pt0) REVERT: B 351 LYS cc_start: 0.6947 (mtpp) cc_final: 0.6618 (mtpp) REVERT: B 423 ARG cc_start: 0.7650 (tpt-90) cc_final: 0.7400 (tpt-90) REVERT: B 430 TYR cc_start: 0.7302 (p90) cc_final: 0.6929 (p90) REVERT: B 438 LYS cc_start: 0.7564 (tttt) cc_final: 0.7097 (tptm) REVERT: B 742 ASP cc_start: 0.6858 (t0) cc_final: 0.6443 (m-30) REVERT: B 780 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.4524 (ptt90) REVERT: B 798 GLU cc_start: 0.6171 (tp30) cc_final: 0.5767 (pt0) REVERT: B 844 LYS cc_start: 0.6662 (mtpt) cc_final: 0.5900 (ptmm) REVERT: B 860 ARG cc_start: 0.6722 (ttt90) cc_final: 0.5743 (tpp-160) REVERT: B 967 LEU cc_start: 0.5965 (OUTLIER) cc_final: 0.5737 (mt) REVERT: B 1004 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6259 (mp) REVERT: B 1008 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6407 (mm) REVERT: B 1023 MET cc_start: 0.6917 (tpp) cc_final: 0.6423 (tmm) REVERT: B 1033 ASN cc_start: 0.8199 (m-40) cc_final: 0.7744 (m-40) outliers start: 46 outliers final: 28 residues processed: 208 average time/residue: 0.1044 time to fit residues: 31.4096 Evaluate side-chains 200 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 695 SER Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 780 ARG Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 902 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1008 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 62 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 40 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.8676 > 50:) chunk 100 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 143 optimal weight: 0.0370 chunk 63 optimal weight: 0.1980 chunk 55 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 299 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 HIS B 728 ASN B 775 GLN B 841 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.192273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.163347 restraints weight = 13981.764| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 1.94 r_work: 0.3989 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13184 Z= 0.113 Angle : 0.520 7.852 17876 Z= 0.260 Chirality : 0.040 0.153 1911 Planarity : 0.004 0.053 2317 Dihedral : 8.255 90.000 1877 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.87 % Allowed : 19.15 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.21), residues: 1592 helix: 0.64 (0.20), residues: 690 sheet: -1.05 (0.32), residues: 257 loop : -0.37 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 880 TYR 0.012 0.001 TYR A 736 PHE 0.022 0.001 PHE B 601 TRP 0.013 0.001 TRP B 98 HIS 0.006 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.11 (13183) covalent geometry : angle 0.52020 / 0.26 (17876) hydrogen bonds : bond 0.03078 / 2.09 ( 536) hydrogen bonds : angle 4.33678 / 3.07 ( 1557) Misc. bond : bond 0.01090 / 0.57 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 575 GLU cc_start: 0.5842 (tp30) cc_final: 0.5355 (tp30) REVERT: A 603 ASP cc_start: 0.5086 (t0) cc_final: 0.4751 (t70) REVERT: A 637 MET cc_start: 0.6338 (tpt) cc_final: 0.5733 (ttp) REVERT: A 697 ARG cc_start: 0.7567 (mtp-110) cc_final: 0.6716 (mtt-85) REVERT: A 734 GLN cc_start: 0.7479 (pp30) cc_final: 0.7032 (mm-40) REVERT: A 761 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6977 (tp30) REVERT: A 771 SER cc_start: 0.8000 (m) cc_final: 0.7782 (m) REVERT: A 785 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6615 (mp0) REVERT: A 810 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7479 (pm20) REVERT: A 814 LYS cc_start: 0.7904 (mptt) cc_final: 0.7229 (ttmt) REVERT: A 894 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7388 (mt-10) REVERT: A 898 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7463 (ptt) REVERT: A 1000 ASN cc_start: 0.7691 (m-40) cc_final: 0.7417 (m-40) REVERT: A 1048 GLN cc_start: 0.7003 (pt0) cc_final: 0.6419 (tt0) REVERT: B 65 ASP cc_start: 0.7566 (t0) cc_final: 0.6883 (p0) REVERT: B 187 MET cc_start: 0.6363 (mmm) cc_final: 0.5888 (ttp) REVERT: B 205 ARG cc_start: 0.7136 (ttt180) cc_final: 0.6805 (ttm170) REVERT: B 212 GLN cc_start: 0.7198 (tp40) cc_final: 0.6624 (pt0) REVERT: B 351 LYS cc_start: 0.7059 (mtpp) cc_final: 0.6301 (mmtt) REVERT: B 430 TYR cc_start: 0.7397 (p90) cc_final: 0.6851 (p90) REVERT: B 438 LYS cc_start: 0.7592 (tttt) cc_final: 0.7163 (tptm) REVERT: B 697 ARG cc_start: 0.7076 (mtp85) cc_final: 0.6699 (mtp-110) REVERT: B 780 ARG cc_start: 0.6523 (OUTLIER) cc_final: 0.5019 (mtm-85) REVERT: B 798 GLU cc_start: 0.6120 (tp30) cc_final: 0.5735 (pt0) REVERT: B 844 LYS cc_start: 0.6690 (mtpt) cc_final: 0.5981 (ptmm) REVERT: B 860 ARG cc_start: 0.6652 (ttt90) cc_final: 0.5607 (tpp-160) REVERT: B 898 MET cc_start: 0.7540 (pp-130) cc_final: 0.7322 (ptp) REVERT: B 950 TYR cc_start: 0.6844 (m-80) cc_final: 0.6583 (m-80) REVERT: B 967 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5744 (mt) REVERT: B 1004 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6491 (mp) REVERT: B 1008 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6580 (mm) REVERT: B 1023 MET cc_start: 0.6909 (tpp) cc_final: 0.6378 (tmm) REVERT: B 1033 ASN cc_start: 0.8274 (m-40) cc_final: 0.7826 (m-40) REVERT: B 1053 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6428 (mp) outliers start: 39 outliers final: 24 residues processed: 202 average time/residue: 0.1075 time to fit residues: 31.5240 Evaluate side-chains 185 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 780 ARG Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 902 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1008 LEU Chi-restraints excluded: chain B residue 1053 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 143 optimal weight: 0.0970 chunk 78 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 299 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 HIS B 728 ASN B 775 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.193120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.162423 restraints weight = 14030.656| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.06 r_work: 0.3986 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13184 Z= 0.130 Angle : 0.533 7.623 17876 Z= 0.267 Chirality : 0.041 0.183 1911 Planarity : 0.004 0.052 2317 Dihedral : 8.169 89.907 1877 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.31 % Allowed : 19.07 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.21), residues: 1592 helix: 0.66 (0.20), residues: 690 sheet: -1.12 (0.31), residues: 263 loop : -0.33 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 423 TYR 0.012 0.001 TYR A 736 PHE 0.017 0.001 PHE A 601 TRP 0.055 0.002 TRP A 591 HIS 0.006 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (13183) covalent geometry : angle 0.53254 / 0.27 (17876) hydrogen bonds : bond 0.03114 / 2.11 ( 536) hydrogen bonds : angle 4.34899 / 3.07 ( 1557) Misc. bond : bond 0.01424 / 0.75 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 575 GLU cc_start: 0.5803 (tp30) cc_final: 0.5336 (tp30) REVERT: A 603 ASP cc_start: 0.5175 (t0) cc_final: 0.4820 (t70) REVERT: A 637 MET cc_start: 0.6424 (tpt) cc_final: 0.5792 (ttp) REVERT: A 697 ARG cc_start: 0.7535 (mtp-110) cc_final: 0.6738 (mtt-85) REVERT: A 734 GLN cc_start: 0.7434 (pp30) cc_final: 0.7023 (mm-40) REVERT: A 761 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.7020 (tp30) REVERT: A 771 SER cc_start: 0.8010 (m) cc_final: 0.7792 (m) REVERT: A 785 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6544 (mp0) REVERT: A 810 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7397 (pm20) REVERT: A 814 LYS cc_start: 0.7866 (mptt) cc_final: 0.7223 (ttmt) REVERT: A 824 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6039 (mt-10) REVERT: A 894 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7331 (mt-10) REVERT: A 898 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7533 (ptt) REVERT: A 1000 ASN cc_start: 0.7730 (m-40) cc_final: 0.7449 (m-40) REVERT: A 1004 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7496 (tt) REVERT: A 1048 GLN cc_start: 0.7065 (pt0) cc_final: 0.6476 (tt0) REVERT: B 65 ASP cc_start: 0.7554 (t0) cc_final: 0.6893 (p0) REVERT: B 187 MET cc_start: 0.6429 (mmm) cc_final: 0.6172 (ttp) REVERT: B 205 ARG cc_start: 0.7127 (ttt180) cc_final: 0.6778 (ttm170) REVERT: B 212 GLN cc_start: 0.7154 (tp40) cc_final: 0.6620 (pt0) REVERT: B 351 LYS cc_start: 0.7132 (mtpp) cc_final: 0.6330 (mmtt) REVERT: B 438 LYS cc_start: 0.7663 (tttt) cc_final: 0.7223 (tptm) REVERT: B 697 ARG cc_start: 0.7077 (mtp85) cc_final: 0.6716 (mtp-110) REVERT: B 780 ARG cc_start: 0.6655 (OUTLIER) cc_final: 0.5110 (mtm-85) REVERT: B 798 GLU cc_start: 0.6156 (tp30) cc_final: 0.5792 (pt0) REVERT: B 844 LYS cc_start: 0.6682 (mtpt) cc_final: 0.5952 (ptmm) REVERT: B 860 ARG cc_start: 0.6744 (ttt90) cc_final: 0.5633 (tpp-160) REVERT: B 898 MET cc_start: 0.7576 (pp-130) cc_final: 0.7370 (ptp) REVERT: B 950 TYR cc_start: 0.6798 (m-80) cc_final: 0.6574 (m-80) REVERT: B 967 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5775 (mt) REVERT: B 1004 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6534 (mp) REVERT: B 1008 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6567 (mm) REVERT: B 1023 MET cc_start: 0.6926 (tpp) cc_final: 0.6393 (tmm) REVERT: B 1033 ASN cc_start: 0.8287 (m-40) cc_final: 0.7845 (m-40) REVERT: B 1053 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6419 (mp) outliers start: 45 outliers final: 26 residues processed: 199 average time/residue: 0.1230 time to fit residues: 35.5412 Evaluate side-chains 192 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 824 GLU Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 780 ARG Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 902 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1008 LEU Chi-restraints excluded: chain B residue 1053 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 83 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 127 optimal weight: 0.2980 chunk 122 optimal weight: 0.1980 chunk 108 optimal weight: 0.3980 chunk 79 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 97 optimal weight: 0.0010 chunk 10 optimal weight: 0.5980 overall best weight: 0.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 590 ASN B 299 GLN B 322 ASN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 HIS B 728 ASN B 775 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.197440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.166613 restraints weight = 14059.002| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 2.07 r_work: 0.4021 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3877 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13184 Z= 0.102 Angle : 0.518 8.097 17876 Z= 0.261 Chirality : 0.040 0.251 1911 Planarity : 0.004 0.050 2317 Dihedral : 7.906 89.745 1877 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.72 % Allowed : 19.81 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1592 helix: 0.78 (0.20), residues: 688 sheet: -1.04 (0.32), residues: 253 loop : -0.30 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 TYR 0.019 0.001 TYR B 167 PHE 0.027 0.001 PHE B 601 TRP 0.091 0.002 TRP A 591 HIS 0.005 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 (13183) covalent geometry : angle 0.51827 / 0.26 (17876) hydrogen bonds : bond 0.02934 / 2.00 ( 536) hydrogen bonds : angle 4.26701 / 3.02 ( 1557) Misc. bond : bond 0.01102 / 0.58 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 575 GLU cc_start: 0.5801 (tp30) cc_final: 0.5341 (tp30) REVERT: A 603 ASP cc_start: 0.5096 (t0) cc_final: 0.4700 (t70) REVERT: A 637 MET cc_start: 0.6384 (tpt) cc_final: 0.5665 (ttp) REVERT: A 697 ARG cc_start: 0.7496 (mtp-110) cc_final: 0.6705 (mtt-85) REVERT: A 734 GLN cc_start: 0.7459 (pp30) cc_final: 0.7025 (mm-40) REVERT: A 742 ASP cc_start: 0.6749 (m-30) cc_final: 0.6526 (m-30) REVERT: A 761 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6926 (tp30) REVERT: A 771 SER cc_start: 0.7979 (m) cc_final: 0.7754 (m) REVERT: A 785 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6541 (mp0) REVERT: A 810 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7408 (pm20) REVERT: A 814 LYS cc_start: 0.7807 (mptt) cc_final: 0.7181 (ttmt) REVERT: A 894 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 898 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7400 (ptt) REVERT: A 1000 ASN cc_start: 0.7683 (m-40) cc_final: 0.7340 (m-40) REVERT: A 1048 GLN cc_start: 0.7076 (pt0) cc_final: 0.6497 (tt0) REVERT: B 65 ASP cc_start: 0.7453 (t0) cc_final: 0.6904 (p0) REVERT: B 205 ARG cc_start: 0.7121 (ttt180) cc_final: 0.6744 (ttm170) REVERT: B 212 GLN cc_start: 0.7150 (tp40) cc_final: 0.6670 (pt0) REVERT: B 351 LYS cc_start: 0.7117 (mtpp) cc_final: 0.6304 (mmtt) REVERT: B 697 ARG cc_start: 0.7085 (mtp85) cc_final: 0.6712 (mtp-110) REVERT: B 780 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.5053 (mtm-85) REVERT: B 808 TYR cc_start: 0.6509 (t80) cc_final: 0.6300 (t80) REVERT: B 830 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6529 (mt-10) REVERT: B 844 LYS cc_start: 0.6596 (mtpt) cc_final: 0.5940 (ptmm) REVERT: B 859 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6085 (tt0) REVERT: B 860 ARG cc_start: 0.6580 (ttt90) cc_final: 0.5480 (tpp-160) REVERT: B 898 MET cc_start: 0.7575 (pp-130) cc_final: 0.7364 (ptp) REVERT: B 950 TYR cc_start: 0.6791 (m-80) cc_final: 0.6557 (m-80) REVERT: B 956 ARG cc_start: 0.5090 (mtm-85) cc_final: 0.4882 (mtm180) REVERT: B 967 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5694 (mt) REVERT: B 1023 MET cc_start: 0.6898 (tpp) cc_final: 0.6368 (tmm) REVERT: B 1033 ASN cc_start: 0.8301 (m-40) cc_final: 0.7862 (m-40) REVERT: B 1053 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6361 (mp) outliers start: 37 outliers final: 25 residues processed: 196 average time/residue: 0.1110 time to fit residues: 31.8244 Evaluate side-chains 184 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 442 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 780 ARG Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 859 GLU Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1053 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 35 optimal weight: 0.0670 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 139 optimal weight: 0.3980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 299 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 HIS B 728 ASN B 775 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.195948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.164383 restraints weight = 14233.200| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.14 r_work: 0.3984 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13184 Z= 0.122 Angle : 0.536 8.125 17876 Z= 0.271 Chirality : 0.041 0.259 1911 Planarity : 0.004 0.050 2317 Dihedral : 7.809 88.682 1877 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.87 % Allowed : 20.18 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.21), residues: 1592 helix: 0.77 (0.20), residues: 687 sheet: -1.03 (0.32), residues: 253 loop : -0.35 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 TYR 0.025 0.001 TYR B 167 PHE 0.017 0.001 PHE A 601 TRP 0.073 0.002 TRP A 591 HIS 0.006 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.12 (13183) covalent geometry : angle 0.53637 / 0.27 (17876) hydrogen bonds : bond 0.03077 / 2.09 ( 536) hydrogen bonds : angle 4.30070 / 3.05 ( 1557) Misc. bond : bond 0.01288 / 0.68 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 575 GLU cc_start: 0.5887 (tp30) cc_final: 0.5418 (tp30) REVERT: A 603 ASP cc_start: 0.5226 (t0) cc_final: 0.4870 (t70) REVERT: A 637 MET cc_start: 0.6442 (tpt) cc_final: 0.5696 (ttp) REVERT: A 697 ARG cc_start: 0.7411 (mtp-110) cc_final: 0.6632 (mtt-85) REVERT: A 734 GLN cc_start: 0.7466 (pp30) cc_final: 0.6933 (mm-40) REVERT: A 742 ASP cc_start: 0.6936 (m-30) cc_final: 0.6707 (m-30) REVERT: A 761 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6978 (tp30) REVERT: A 771 SER cc_start: 0.8019 (m) cc_final: 0.7789 (m) REVERT: A 785 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6487 (mp0) REVERT: A 810 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7471 (pm20) REVERT: A 814 LYS cc_start: 0.7844 (mptt) cc_final: 0.7156 (ttmt) REVERT: A 894 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7411 (mt-10) REVERT: A 898 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7509 (ptt) REVERT: A 1000 ASN cc_start: 0.7652 (m-40) cc_final: 0.7407 (m-40) REVERT: A 1004 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7518 (tt) REVERT: A 1048 GLN cc_start: 0.7046 (pt0) cc_final: 0.6458 (tt0) REVERT: B 65 ASP cc_start: 0.7508 (t0) cc_final: 0.6917 (p0) REVERT: B 205 ARG cc_start: 0.7132 (ttt180) cc_final: 0.6706 (ttm170) REVERT: B 212 GLN cc_start: 0.7258 (tp40) cc_final: 0.6642 (pt0) REVERT: B 351 LYS cc_start: 0.7116 (mtpp) cc_final: 0.6270 (mmtt) REVERT: B 540 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5705 (mp) REVERT: B 697 ARG cc_start: 0.7121 (mtp85) cc_final: 0.6731 (mtp-110) REVERT: B 780 ARG cc_start: 0.6645 (OUTLIER) cc_final: 0.5032 (mtm-85) REVERT: B 830 GLU cc_start: 0.7298 (tm-30) cc_final: 0.6597 (mt-10) REVERT: B 844 LYS cc_start: 0.6644 (mtpt) cc_final: 0.5926 (ptmm) REVERT: B 859 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6050 (tt0) REVERT: B 860 ARG cc_start: 0.6618 (ttt90) cc_final: 0.5483 (tpp-160) REVERT: B 956 ARG cc_start: 0.5085 (mtm-85) cc_final: 0.4877 (mtm180) REVERT: B 967 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.5680 (mt) REVERT: B 1008 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6499 (mm) REVERT: B 1023 MET cc_start: 0.6878 (tpp) cc_final: 0.6303 (tmm) REVERT: B 1033 ASN cc_start: 0.8231 (m-40) cc_final: 0.7782 (m-40) REVERT: B 1053 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6348 (mp) outliers start: 39 outliers final: 25 residues processed: 186 average time/residue: 0.1243 time to fit residues: 34.5189 Evaluate side-chains 185 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 780 ARG Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 849 SER Chi-restraints excluded: chain B residue 859 GLU Chi-restraints excluded: chain B residue 902 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1008 LEU Chi-restraints excluded: chain B residue 1053 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 158 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 299 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.193937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.163347 restraints weight = 14064.842| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.07 r_work: 0.3983 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3840 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13184 Z= 0.126 Angle : 0.548 8.398 17876 Z= 0.274 Chirality : 0.041 0.318 1911 Planarity : 0.004 0.051 2317 Dihedral : 7.740 88.004 1877 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.80 % Allowed : 20.18 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.21), residues: 1592 helix: 0.73 (0.20), residues: 688 sheet: -1.04 (0.32), residues: 252 loop : -0.35 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 TYR 0.023 0.001 TYR B 167 PHE 0.033 0.001 PHE B 601 TRP 0.069 0.002 TRP A 591 HIS 0.006 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (13183) covalent geometry : angle 0.54846 / 0.27 (17876) hydrogen bonds : bond 0.03094 / 2.10 ( 536) hydrogen bonds : angle 4.34818 / 3.08 ( 1557) Misc. bond : bond 0.01490 / 0.78 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3184 Ramachandran restraints generated. 1592 Oldfield, 0 Emsley, 1592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 575 GLU cc_start: 0.5824 (tp30) cc_final: 0.5384 (tp30) REVERT: A 603 ASP cc_start: 0.5173 (t0) cc_final: 0.4842 (t70) REVERT: A 637 MET cc_start: 0.6480 (tpt) cc_final: 0.5768 (ttp) REVERT: A 697 ARG cc_start: 0.7371 (mtp-110) cc_final: 0.6648 (mtt-85) REVERT: A 734 GLN cc_start: 0.7461 (pp30) cc_final: 0.6963 (mm-40) REVERT: A 742 ASP cc_start: 0.7091 (m-30) cc_final: 0.6835 (m-30) REVERT: A 761 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6966 (tp30) REVERT: A 771 SER cc_start: 0.7972 (m) cc_final: 0.7748 (m) REVERT: A 785 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6524 (mp0) REVERT: A 810 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7458 (pm20) REVERT: A 814 LYS cc_start: 0.7800 (mptt) cc_final: 0.7170 (ttmt) REVERT: A 894 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7366 (mt-10) REVERT: A 898 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7492 (ptt) REVERT: A 1000 ASN cc_start: 0.7668 (m-40) cc_final: 0.7432 (m-40) REVERT: A 1004 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7509 (tt) REVERT: B 65 ASP cc_start: 0.7476 (t0) cc_final: 0.6915 (p0) REVERT: B 205 ARG cc_start: 0.7118 (ttt180) cc_final: 0.6716 (ttm170) REVERT: B 212 GLN cc_start: 0.7165 (tp40) cc_final: 0.6676 (pt0) REVERT: B 351 LYS cc_start: 0.7092 (mtpp) cc_final: 0.6289 (mmtt) REVERT: B 540 LEU cc_start: 0.5979 (OUTLIER) cc_final: 0.5726 (mp) REVERT: B 697 ARG cc_start: 0.7116 (mtp85) cc_final: 0.6729 (mtp-110) REVERT: B 780 ARG cc_start: 0.6395 (OUTLIER) cc_final: 0.4849 (mtm-85) REVERT: B 844 LYS cc_start: 0.6625 (mtpt) cc_final: 0.5906 (ptmm) REVERT: B 859 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6028 (tt0) REVERT: B 860 ARG cc_start: 0.6635 (ttt90) cc_final: 0.5537 (tpp-160) REVERT: B 956 ARG cc_start: 0.5149 (mtm-85) cc_final: 0.4764 (mtm-85) REVERT: B 967 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5756 (mt) REVERT: B 1008 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6438 (mm) REVERT: B 1023 MET cc_start: 0.6800 (tpp) cc_final: 0.6286 (tmm) REVERT: B 1033 ASN cc_start: 0.8285 (m-40) cc_final: 0.7858 (m-40) REVERT: B 1053 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6448 (mp) outliers start: 38 outliers final: 24 residues processed: 184 average time/residue: 0.1264 time to fit residues: 33.7729 Evaluate side-chains 183 residues out of total 1358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 942 GLU Chi-restraints excluded: chain A residue 976 MET Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 597 ASP Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 780 ARG Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 859 GLU Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1007 ILE Chi-restraints excluded: chain B residue 1008 LEU Chi-restraints excluded: chain B residue 1053 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 9 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 299 GLN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 524 HIS B 728 ASN B 775 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.193425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.162910 restraints weight = 13980.262| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 2.05 r_work: 0.3982 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13184 Z= 0.132 Angle : 0.554 8.507 17876 Z= 0.276 Chirality : 0.042 0.308 1911 Planarity : 0.004 0.051 2317 Dihedral : 7.747 87.471 1877 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.65 % Allowed : 20.54 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1592 helix: 0.71 (0.20), residues: 688 sheet: -1.03 (0.32), residues: 259 loop : -0.33 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 423 TYR 0.020 0.001 TYR B 167 PHE 0.029 0.002 PHE B 425 TRP 0.065 0.002 TRP A 591 HIS 0.006 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.13 (13183) covalent geometry : angle 0.55380 / 0.28 (17876) hydrogen bonds : bond 0.03143 / 2.13 ( 536) hydrogen bonds : angle 4.34070 / 3.07 ( 1557) Misc. bond : bond 0.01539 / 0.81 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2920.42 seconds wall clock time: 50 minutes 53.95 seconds (3053.95 seconds total)