Starting phenix.real_space_refine on Fri Mar 22 05:09:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hlr_0240/03_2024/6hlr_0240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hlr_0240/03_2024/6hlr_0240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hlr_0240/03_2024/6hlr_0240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hlr_0240/03_2024/6hlr_0240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hlr_0240/03_2024/6hlr_0240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hlr_0240/03_2024/6hlr_0240_updated.pdb" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 76 5.49 5 Mg 1 5.21 5 S 163 5.16 5 C 20227 2.51 5 N 5638 2.21 5 O 6259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 99": "NH1" <-> "NH2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 834": "NH1" <-> "NH2" Residue "A ARG 878": "NH1" <-> "NH2" Residue "A ARG 884": "NH1" <-> "NH2" Residue "A ARG 985": "NH1" <-> "NH2" Residue "A ARG 1003": "NH1" <-> "NH2" Residue "A ARG 1015": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1176": "NH1" <-> "NH2" Residue "A ARG 1223": "NH1" <-> "NH2" Residue "A TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1494": "NH1" <-> "NH2" Residue "A ARG 1559": "NH1" <-> "NH2" Residue "A ARG 1580": "NH1" <-> "NH2" Residue "A ARG 1640": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "B ARG 429": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B ARG 452": "NH1" <-> "NH2" Residue "B ARG 501": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B ARG 651": "NH1" <-> "NH2" Residue "B ARG 714": "NH1" <-> "NH2" Residue "B ARG 736": "NH1" <-> "NH2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 908": "NH1" <-> "NH2" Residue "B ARG 909": "NH1" <-> "NH2" Residue "B ARG 920": "NH1" <-> "NH2" Residue "B ARG 1023": "NH1" <-> "NH2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "B ARG 1065": "NH1" <-> "NH2" Residue "B ARG 1070": "NH1" <-> "NH2" Residue "B ARG 1129": "NH1" <-> "NH2" Residue "B ARG 1130": "NH1" <-> "NH2" Residue "B ARG 1134": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 295": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "F ARG 119": "NH1" <-> "NH2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "I ARG 61": "NH1" <-> "NH2" Residue "K ARG 77": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32370 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1458, 11513 Classifications: {'peptide': 1458} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1398} Chain breaks: 8 Chain: "B" Number of atoms: 9254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9254 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 59, 'TRANS': 1104} Chain breaks: 3 Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2415 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1740 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 199} Chain breaks: 1 Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1386 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 10, 'TRANS': 165} Chain breaks: 1 Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1052 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 486 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 766 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "R" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "S" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 581 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "T" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 732 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 461 SG CYS A 62 67.801 53.021 56.297 1.00 50.78 S ATOM 480 SG CYS A 65 71.538 51.208 55.864 1.00 50.84 S ATOM 535 SG CYS A 72 70.705 53.247 59.089 1.00 48.46 S ATOM 781 SG CYS A 102 69.856 103.080 45.403 1.00 67.10 S ATOM 806 SG CYS A 105 72.362 102.233 42.704 1.00 67.02 S ATOM 1597 SG CYS A 233 73.571 104.560 45.185 1.00 73.09 S ATOM 1619 SG CYS A 236 70.930 105.579 41.657 1.00 76.35 S ATOM 20097 SG CYS B1104 82.614 61.529 48.510 1.00 46.57 S ATOM 20123 SG CYS B1107 80.436 64.412 48.262 1.00 47.49 S ATOM 20270 SG CYS B1128 79.033 61.182 48.775 1.00 51.02 S ATOM 28713 SG CYS I 10 41.777 128.141 102.488 1.00 72.65 S ATOM 28735 SG CYS I 13 40.843 124.444 101.572 1.00 71.80 S ATOM 28855 SG CYS I 30 41.647 126.408 98.505 1.00 82.07 S ATOM 29190 SG CYS J 7 87.266 42.622 126.948 1.00 36.77 S ATOM 29213 SG CYS J 10 90.633 41.675 127.804 1.00 37.82 S ATOM 29493 SG CYS J 45 90.497 45.869 128.200 1.00 35.42 S ATOM 29499 SG CYS J 46 88.547 43.189 130.297 1.00 35.94 S ATOM 30514 SG CYS L 31 46.342 41.803 110.103 1.00 55.21 S ATOM 30534 SG CYS L 34 44.557 40.432 112.982 1.00 58.44 S ATOM 30638 SG CYS L 48 43.556 38.862 109.822 1.00 69.94 S ATOM 30661 SG CYS L 51 42.636 43.100 111.308 1.00 68.64 S Time building chain proxies: 16.68, per 1000 atoms: 0.52 Number of scatterers: 32370 At special positions: 0 Unit cell: (166.4, 162.24, 169.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 163 16.00 P 76 15.00 Mg 1 11.99 O 6259 8.00 N 5638 7.00 C 20227 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.02 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 65 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 236 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1104 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1107 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1128 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 10 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 30 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 31 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " Number of angles added : 21 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 143 helices and 31 sheets defined 31.1% alpha, 11.9% beta 21 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 14.37 Creating SS restraints... Processing helix chain 'A' and resid 23 through 26 No H-bonds generated for 'chain 'A' and resid 23 through 26' Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 91 through 98 removed outlier: 3.663A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.568A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 198 removed outlier: 3.546A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER A 183 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 227 removed outlier: 3.733A pdb=" N GLU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 330 removed outlier: 3.797A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 removed outlier: 5.480A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 381 through 399 removed outlier: 3.832A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 438 removed outlier: 3.971A pdb=" N ILE A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 459 No H-bonds generated for 'chain 'A' and resid 457 through 459' Processing helix chain 'A' and resid 467 through 470 No H-bonds generated for 'chain 'A' and resid 467 through 470' Processing helix chain 'A' and resid 499 through 504 removed outlier: 3.811A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 525 Processing helix chain 'A' and resid 551 through 559 removed outlier: 3.601A pdb=" N ALA A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 641 through 649 removed outlier: 3.533A pdb=" N GLU A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 657 No H-bonds generated for 'chain 'A' and resid 655 through 657' Processing helix chain 'A' and resid 672 through 680 removed outlier: 3.697A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 697 removed outlier: 3.546A pdb=" N ILE A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 704 No H-bonds generated for 'chain 'A' and resid 702 through 704' Processing helix chain 'A' and resid 729 through 738 Processing helix chain 'A' and resid 794 through 800 removed outlier: 3.552A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 819 removed outlier: 3.506A pdb=" N LEU A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 833 Processing helix chain 'A' and resid 837 through 846 removed outlier: 3.660A pdb=" N ASP A 845 " --> pdb=" O LYS A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 853 through 861 Processing helix chain 'A' and resid 873 through 884 removed outlier: 3.534A pdb=" N GLN A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 911 removed outlier: 3.579A pdb=" N VAL A 895 " --> pdb=" O ILE A 891 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 930 removed outlier: 3.780A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 944 Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 992 through 1010 Processing helix chain 'A' and resid 1016 through 1026 removed outlier: 3.913A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1052 No H-bonds generated for 'chain 'A' and resid 1050 through 1052' Processing helix chain 'A' and resid 1057 through 1059 No H-bonds generated for 'chain 'A' and resid 1057 through 1059' Processing helix chain 'A' and resid 1066 through 1071 removed outlier: 3.550A pdb=" N ASP A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1080 removed outlier: 4.025A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1085 No H-bonds generated for 'chain 'A' and resid 1083 through 1085' Processing helix chain 'A' and resid 1092 through 1107 removed outlier: 3.860A pdb=" N LYS A1096 " --> pdb=" O GLU A1092 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A1104 " --> pdb=" O LYS A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1115 No H-bonds generated for 'chain 'A' and resid 1113 through 1115' Processing helix chain 'A' and resid 1123 through 1126 No H-bonds generated for 'chain 'A' and resid 1123 through 1126' Processing helix chain 'A' and resid 1138 through 1150 Processing helix chain 'A' and resid 1163 through 1176 removed outlier: 4.037A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1194 removed outlier: 3.984A pdb=" N VAL A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1199 Processing helix chain 'A' and resid 1218 through 1225 removed outlier: 3.539A pdb=" N LEU A1222 " --> pdb=" O ILE A1219 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A1225 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1252 No H-bonds generated for 'chain 'A' and resid 1249 through 1252' Processing helix chain 'A' and resid 1255 through 1258 No H-bonds generated for 'chain 'A' and resid 1255 through 1258' Processing helix chain 'A' and resid 1263 through 1266 removed outlier: 3.537A pdb=" N VAL A1266 " --> pdb=" O LEU A1263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1263 through 1266' Processing helix chain 'A' and resid 1299 through 1305 removed outlier: 3.604A pdb=" N SER A1303 " --> pdb=" O ASN A1299 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1319 removed outlier: 3.517A pdb=" N ASN A1315 " --> pdb=" O GLU A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1336 removed outlier: 3.633A pdb=" N ALA A1327 " --> pdb=" O HIS A1323 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1453 removed outlier: 3.679A pdb=" N ILE A1450 " --> pdb=" O ARG A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1493 Processing helix chain 'A' and resid 1513 through 1515 No H-bonds generated for 'chain 'A' and resid 1513 through 1515' Processing helix chain 'A' and resid 1546 through 1553 Processing helix chain 'A' and resid 1555 through 1567 removed outlier: 3.591A pdb=" N VAL A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1589 Processing helix chain 'A' and resid 1609 through 1615 Processing helix chain 'A' and resid 1618 through 1627 removed outlier: 4.075A pdb=" N THR A1623 " --> pdb=" O CYS A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1643 removed outlier: 3.666A pdb=" N VAL A1643 " --> pdb=" O ALA A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1650 through 1653 removed outlier: 3.516A pdb=" N SER A1653 " --> pdb=" O GLY A1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1650 through 1653' Processing helix chain 'B' and resid 21 through 26 Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.752A pdb=" N ALA B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 removed outlier: 4.205A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 68 removed outlier: 3.538A pdb=" N GLY B 59 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU B 60 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU B 61 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN B 62 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 63 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 65 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP B 67 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.624A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.687A pdb=" N ARG B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 removed outlier: 3.592A pdb=" N ALA B 279 " --> pdb=" O MET B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 292 Processing helix chain 'B' and resid 300 through 316 removed outlier: 3.547A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 309 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 333 removed outlier: 4.077A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 356 removed outlier: 3.668A pdb=" N GLU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.746A pdb=" N ARG B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 406 through 433 removed outlier: 3.556A pdb=" N GLU B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL B 428 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 457 through 467 Processing helix chain 'B' and resid 493 through 499 Processing helix chain 'B' and resid 507 through 510 No H-bonds generated for 'chain 'B' and resid 507 through 510' Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 598 through 613 removed outlier: 3.629A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.718A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N TYR B 671 " --> pdb=" O PHE B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 666 through 671' Processing helix chain 'B' and resid 699 through 703 removed outlier: 3.560A pdb=" N LEU B 703 " --> pdb=" O ILE B 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 699 through 703' Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 712 through 724 removed outlier: 3.556A pdb=" N CYS B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS B 723 " --> pdb=" O CYS B 719 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN B 724 " --> pdb=" O GLN B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 764 No H-bonds generated for 'chain 'B' and resid 762 through 764' Processing helix chain 'B' and resid 791 through 794 No H-bonds generated for 'chain 'B' and resid 791 through 794' Processing helix chain 'B' and resid 834 through 837 removed outlier: 3.643A pdb=" N LEU B 837 " --> pdb=" O LYS B 834 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 834 through 837' Processing helix chain 'B' and resid 933 through 935 No H-bonds generated for 'chain 'B' and resid 933 through 935' Processing helix chain 'B' and resid 951 through 955 removed outlier: 3.642A pdb=" N PHE B 954 " --> pdb=" O PRO B 951 " (cutoff:3.500A) Proline residue: B 955 - end of helix No H-bonds generated for 'chain 'B' and resid 951 through 955' Processing helix chain 'B' and resid 960 through 975 removed outlier: 3.545A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1002 removed outlier: 3.550A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1081 removed outlier: 3.542A pdb=" N ALA B1078 " --> pdb=" O MET B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1092 Processing helix chain 'B' and resid 1180 through 1192 removed outlier: 3.533A pdb=" N SER B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 39 removed outlier: 3.527A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.563A pdb=" N ARG C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 122 through 125 No H-bonds generated for 'chain 'C' and resid 122 through 125' Processing helix chain 'C' and resid 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.671A pdb=" N SER C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 177 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR C 178 " --> pdb=" O GLN C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 173 through 178' Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 246 through 249 No H-bonds generated for 'chain 'C' and resid 246 through 249' Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 310 through 330 removed outlier: 3.564A pdb=" N PHE C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 43 Processing helix chain 'D' and resid 45 through 48 No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 83 through 97 removed outlier: 3.551A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 97 " --> pdb=" O GLN D 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 26 removed outlier: 3.792A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 66 through 71 removed outlier: 3.981A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.644A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 167 removed outlier: 3.543A pdb=" N LEU E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 188 No H-bonds generated for 'chain 'E' and resid 185 through 188' Processing helix chain 'F' and resid 57 through 71 removed outlier: 3.716A pdb=" N LEU F 69 " --> pdb=" O ARG F 65 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 78 No H-bonds generated for 'chain 'F' and resid 76 through 78' Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 117 through 126 removed outlier: 3.646A pdb=" N ALA F 126 " --> pdb=" O MET F 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 53 No H-bonds generated for 'chain 'G' and resid 51 through 53' Processing helix chain 'G' and resid 57 through 65 Processing helix chain 'H' and resid 89 through 92 removed outlier: 3.917A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 89 through 92' Processing helix chain 'I' and resid 62 through 66 removed outlier: 3.694A pdb=" N VAL I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 66' Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 50 removed outlier: 4.097A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.778A pdb=" N LEU J 61 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG J 62 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 81 removed outlier: 3.844A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 130 Processing helix chain 'K' and resid 133 through 141 Processing sheet with id= A, first strand: chain 'A' and resid 479 through 483 removed outlier: 3.875A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 484 through 486 removed outlier: 6.101A pdb=" N LEU A 614 " --> pdb=" O SER A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 506 through 510 removed outlier: 4.072A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 749 through 752 removed outlier: 3.755A pdb=" N CYS A 778 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS A 772 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1238 through 1241 Processing sheet with id= F, first strand: chain 'A' and resid 1459 through 1462 removed outlier: 4.354A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 134 through 136 Processing sheet with id= H, first strand: chain 'B' and resid 155 through 157 removed outlier: 4.098A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER B 144 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL B 97 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 194 through 196 Processing sheet with id= J, first strand: chain 'B' and resid 206 through 209 Processing sheet with id= K, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.471A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 625 through 629 removed outlier: 3.563A pdb=" N GLY B 594 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 651 through 655 removed outlier: 3.580A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.550A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 884 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 769 through 772 Processing sheet with id= P, first strand: chain 'B' and resid 773 through 775 removed outlier: 6.598A pdb=" N ILE B 947 " --> pdb=" O ALA B 774 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'B' and resid 823 through 825 removed outlier: 6.817A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ALA B 860 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LYS B 870 " --> pdb=" O ALA B 860 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id= S, first strand: chain 'B' and resid 1158 through 1160 Processing sheet with id= T, first strand: chain 'C' and resid 51 through 56 removed outlier: 3.536A pdb=" N GLN C 232 " --> pdb=" O GLY C 292 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 10.004A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.368A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 256 through 258 Processing sheet with id= W, first strand: chain 'C' and resid 161 through 163 Processing sheet with id= X, first strand: chain 'E' and resid 78 through 82 removed outlier: 6.887A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.752A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AA, first strand: chain 'G' and resid 38 through 49 removed outlier: 3.551A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TRP G 125 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N VAL G 81 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 232 through 237 removed outlier: 6.556A pdb=" N ASP G 246 " --> pdb=" O ARG G 234 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL G 236 " --> pdb=" O SER G 244 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER G 244 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU G 148 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE G 137 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 23 through 29 removed outlier: 5.432A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'K' and resid 47 through 50 removed outlier: 4.780A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 29 through 31 810 hydrogen bonds defined for protein. 2328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 12.82 Time building geometry restraints manager: 13.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9859 1.33 - 1.46: 6374 1.46 - 1.58: 16507 1.58 - 1.70: 147 1.70 - 1.82: 260 Bond restraints: 33147 Sorted by residual: bond pdb=" O3B G2P T3000 " pdb=" PG G2P T3000 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" O2A G2P T3000 " pdb=" PA G2P T3000 " ideal model delta sigma weight residual 1.513 1.611 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" O2B G2P T3000 " pdb=" PB G2P T3000 " ideal model delta sigma weight residual 1.517 1.609 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C4 G2P T3000 " pdb=" C5 G2P T3000 " ideal model delta sigma weight residual 1.384 1.469 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C6 G2P T3000 " pdb=" N1 G2P T3000 " ideal model delta sigma weight residual 1.402 1.334 0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 33142 not shown) Histogram of bond angle deviations from ideal: 96.55 - 104.44: 792 104.44 - 112.33: 16387 112.33 - 120.23: 14582 120.23 - 128.12: 13037 128.12 - 136.02: 323 Bond angle restraints: 45121 Sorted by residual: angle pdb=" N ILE B 696 " pdb=" CA ILE B 696 " pdb=" C ILE B 696 " ideal model delta sigma weight residual 112.96 105.96 7.00 1.00e+00 1.00e+00 4.91e+01 angle pdb=" C LYS E 103 " pdb=" N ASN E 104 " pdb=" CA ASN E 104 " ideal model delta sigma weight residual 122.46 129.49 -7.03 1.41e+00 5.03e-01 2.48e+01 angle pdb=" N PHE B 954 " pdb=" CA PHE B 954 " pdb=" C PHE B 954 " ideal model delta sigma weight residual 109.81 119.53 -9.72 2.21e+00 2.05e-01 1.93e+01 angle pdb=" C ARG L 42 " pdb=" N THR L 43 " pdb=" CA THR L 43 " ideal model delta sigma weight residual 121.54 129.67 -8.13 1.91e+00 2.74e-01 1.81e+01 angle pdb=" N ARG B 265 " pdb=" CA ARG B 265 " pdb=" C ARG B 265 " ideal model delta sigma weight residual 109.96 103.63 6.33 1.58e+00 4.01e-01 1.60e+01 ... (remaining 45116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 18708 17.47 - 34.93: 925 34.93 - 52.40: 298 52.40 - 69.86: 88 69.86 - 87.33: 18 Dihedral angle restraints: 20037 sinusoidal: 8753 harmonic: 11284 Sorted by residual: dihedral pdb=" CA GLN I 41 " pdb=" C GLN I 41 " pdb=" N PHE I 42 " pdb=" CA PHE I 42 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA ASP B 794 " pdb=" C ASP B 794 " pdb=" N GLU B 795 " pdb=" CA GLU B 795 " ideal model delta harmonic sigma weight residual 180.00 152.17 27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA LYS A 463 " pdb=" C LYS A 463 " pdb=" N GLU A 464 " pdb=" CA GLU A 464 " ideal model delta harmonic sigma weight residual -180.00 -152.99 -27.01 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 20034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3947 0.066 - 0.132: 922 0.132 - 0.198: 156 0.198 - 0.265: 19 0.265 - 0.331: 4 Chirality restraints: 5048 Sorted by residual: chirality pdb=" CB ILE B 207 " pdb=" CA ILE B 207 " pdb=" CG1 ILE B 207 " pdb=" CG2 ILE B 207 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB ILE B 203 " pdb=" CA ILE B 203 " pdb=" CG1 ILE B 203 " pdb=" CG2 ILE B 203 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE A1219 " pdb=" CA ILE A1219 " pdb=" CG1 ILE A1219 " pdb=" CG2 ILE A1219 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 5045 not shown) Planarity restraints: 5572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1033 " 0.030 2.00e-02 2.50e+03 2.36e-02 1.11e+01 pdb=" CG TYR B1033 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR B1033 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B1033 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B1033 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B1033 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B1033 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B1033 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 150 " 0.055 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO E 151 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B1044 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" C PHE B1044 " -0.053 2.00e-02 2.50e+03 pdb=" O PHE B1044 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN B1045 " 0.018 2.00e-02 2.50e+03 ... (remaining 5569 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 28 2.37 - 3.00: 15216 3.00 - 3.63: 47659 3.63 - 4.27: 77637 4.27 - 4.90: 126280 Nonbonded interactions: 266820 Sorted by model distance: nonbonded pdb=" OD1 ASP A 627 " pdb="MG MG A1701 " model vdw 1.734 2.170 nonbonded pdb=" O3' C R 20 " pdb="MG MG A1701 " model vdw 2.078 2.170 nonbonded pdb=" OD1 ASP A 629 " pdb="MG MG A1701 " model vdw 2.144 2.170 nonbonded pdb=" OD2 ASP B 843 " pdb=" OH TYR L 29 " model vdw 2.213 2.440 nonbonded pdb=" O PHE B 963 " pdb=" OH TYR B1027 " model vdw 2.228 2.440 ... (remaining 266815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.060 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: 0.030 Extract box with map and model: 5.750 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 92.950 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 0.007 0.106 33147 Z= 0.461 Angle : 0.945 11.777 45121 Z= 0.503 Chirality : 0.059 0.331 5048 Planarity : 0.007 0.083 5572 Dihedral : 12.666 87.329 12749 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.15 % Allowed : 3.55 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.10), residues: 3827 helix: -4.31 (0.06), residues: 1248 sheet: -2.30 (0.19), residues: 547 loop : -2.05 (0.11), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP B 836 HIS 0.016 0.002 HIS E 146 PHE 0.038 0.003 PHE A 637 TYR 0.053 0.003 TYR B1033 ARG 0.024 0.001 ARG B 920 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 980 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 SER cc_start: 0.8707 (t) cc_final: 0.8363 (t) REVERT: A 416 ARG cc_start: 0.6716 (ttt180) cc_final: 0.6377 (ttm110) REVERT: A 1078 LYS cc_start: 0.8543 (mmtp) cc_final: 0.8342 (mmmt) REVERT: A 1170 MET cc_start: 0.8876 (mmp) cc_final: 0.8593 (mmt) REVERT: A 1579 PHE cc_start: 0.8014 (m-80) cc_final: 0.7719 (m-80) REVERT: A 1587 ASP cc_start: 0.8454 (m-30) cc_final: 0.7958 (m-30) REVERT: A 1648 ASN cc_start: 0.8017 (m-40) cc_final: 0.7640 (t0) REVERT: B 108 MET cc_start: 0.8345 (mmt) cc_final: 0.7318 (mmt) REVERT: B 388 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7395 (mt-10) REVERT: B 427 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7663 (tp40) REVERT: B 698 SER cc_start: 0.9006 (p) cc_final: 0.8694 (t) REVERT: B 707 SER cc_start: 0.9267 (t) cc_final: 0.8996 (m) REVERT: B 778 TYR cc_start: 0.8908 (t80) cc_final: 0.7942 (t80) REVERT: B 824 HIS cc_start: 0.8101 (m-70) cc_final: 0.7314 (m-70) REVERT: B 834 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8630 (mmtm) REVERT: B 1061 LYS cc_start: 0.8457 (tttm) cc_final: 0.7960 (tttt) REVERT: B 1065 ARG cc_start: 0.7574 (mtm180) cc_final: 0.7104 (mtp180) REVERT: C 34 GLU cc_start: 0.7917 (mp0) cc_final: 0.7651 (mp0) REVERT: C 128 ASP cc_start: 0.8211 (p0) cc_final: 0.7527 (p0) REVERT: C 226 SER cc_start: 0.8706 (p) cc_final: 0.8384 (m) REVERT: C 319 ARG cc_start: 0.8044 (tpp80) cc_final: 0.7791 (mtt-85) REVERT: D 34 ASP cc_start: 0.7833 (m-30) cc_final: 0.7518 (t70) REVERT: E 8 ASN cc_start: 0.8037 (m-40) cc_final: 0.7543 (m-40) REVERT: E 187 TYR cc_start: 0.8939 (t80) cc_final: 0.8572 (t80) REVERT: F 123 LYS cc_start: 0.8641 (tttt) cc_final: 0.8015 (ttpt) REVERT: G 52 MET cc_start: 0.8271 (ptm) cc_final: 0.8025 (ptm) REVERT: G 236 VAL cc_start: 0.8149 (t) cc_final: 0.7914 (m) REVERT: H 27 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7018 (mt-10) REVERT: H 100 THR cc_start: 0.8801 (m) cc_final: 0.8514 (p) REVERT: H 145 ARG cc_start: 0.8447 (ttm170) cc_final: 0.7956 (ttp-170) REVERT: J 31 ASP cc_start: 0.8317 (p0) cc_final: 0.8072 (p0) REVERT: K 85 ASP cc_start: 0.7853 (t0) cc_final: 0.7392 (t0) REVERT: K 112 THR cc_start: 0.9179 (p) cc_final: 0.8560 (p) REVERT: K 119 LYS cc_start: 0.8360 (tttt) cc_final: 0.8025 (tmtt) REVERT: K 126 ASP cc_start: 0.7765 (m-30) cc_final: 0.7263 (m-30) outliers start: 5 outliers final: 3 residues processed: 984 average time/residue: 0.4959 time to fit residues: 747.9861 Evaluate side-chains 578 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 575 time to evaluate : 3.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 0.9990 chunk 293 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 303 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 225 optimal weight: 6.9990 chunk 351 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 76 GLN A 260 GLN A 489 ASN A 634 ASN ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS A 880 GLN A1062 HIS A1199 GLN A1250 GLN A1453 HIS ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1633 GLN A1647 ASN A1648 ASN B 400 GLN B 473 GLN B 480 GLN ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN B 710 ASN B 718 GLN B 720 GLN B 745 GLN B 921 HIS B 952 HIS B1045 GLN B1199 ASN C 172 GLN C 175 GLN C 207 HIS E 99 HIS E 136 ASN F 78 GLN G 65 HIS ** G 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN H 35 GLN K 106 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33147 Z= 0.236 Angle : 0.614 12.368 45121 Z= 0.326 Chirality : 0.044 0.214 5048 Planarity : 0.005 0.055 5572 Dihedral : 13.404 86.414 5093 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.62 % Allowed : 10.54 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.12), residues: 3827 helix: -2.26 (0.12), residues: 1253 sheet: -1.75 (0.19), residues: 575 loop : -1.48 (0.12), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 836 HIS 0.012 0.001 HIS A1453 PHE 0.025 0.002 PHE B1167 TYR 0.021 0.002 TYR B 655 ARG 0.008 0.001 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 604 time to evaluate : 4.047 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: A 187 GLU cc_start: 0.6858 (tm-30) cc_final: 0.6639 (tm-30) REVERT: A 416 ARG cc_start: 0.6714 (ttt180) cc_final: 0.6286 (ttm110) REVERT: A 516 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7961 (pp) REVERT: A 570 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8818 (p) REVERT: A 604 LYS cc_start: 0.8278 (mttt) cc_final: 0.8045 (mtpt) REVERT: A 1078 LYS cc_start: 0.8536 (mmtp) cc_final: 0.8254 (mmmt) REVERT: A 1175 MET cc_start: 0.9150 (ttm) cc_final: 0.8911 (ttp) REVERT: A 1234 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7816 (mttt) REVERT: A 1261 VAL cc_start: 0.8990 (t) cc_final: 0.8763 (m) REVERT: A 1583 ASP cc_start: 0.8106 (m-30) cc_final: 0.7570 (m-30) REVERT: A 1611 MET cc_start: 0.8436 (ttp) cc_final: 0.8196 (ttm) REVERT: A 1648 ASN cc_start: 0.7994 (m110) cc_final: 0.7629 (t0) REVERT: B 205 MET cc_start: 0.8815 (mtm) cc_final: 0.8486 (mtm) REVERT: B 351 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7796 (tp-100) REVERT: B 388 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7378 (mt-10) REVERT: B 397 THR cc_start: 0.9359 (t) cc_final: 0.9066 (m) REVERT: B 698 SER cc_start: 0.9006 (p) cc_final: 0.8692 (t) REVERT: B 707 SER cc_start: 0.9299 (t) cc_final: 0.9085 (m) REVERT: B 785 ASP cc_start: 0.7991 (m-30) cc_final: 0.7761 (m-30) REVERT: B 1065 ARG cc_start: 0.7677 (mtm180) cc_final: 0.7142 (mtp180) REVERT: C 39 ASP cc_start: 0.8213 (m-30) cc_final: 0.7990 (m-30) REVERT: C 128 ASP cc_start: 0.7795 (p0) cc_final: 0.7336 (p0) REVERT: C 174 ARG cc_start: 0.7819 (ptp90) cc_final: 0.7350 (ptp90) REVERT: C 226 SER cc_start: 0.8653 (p) cc_final: 0.8393 (m) REVERT: C 319 ARG cc_start: 0.8247 (tpp80) cc_final: 0.7875 (mtt-85) REVERT: E 45 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7889 (ttpp) REVERT: G 64 GLN cc_start: 0.8855 (mt0) cc_final: 0.8547 (mt0) REVERT: G 234 ARG cc_start: 0.6765 (ttt180) cc_final: 0.6195 (ttp-170) REVERT: H 100 THR cc_start: 0.8866 (m) cc_final: 0.8653 (p) REVERT: H 129 TYR cc_start: 0.8050 (p90) cc_final: 0.7730 (p90) REVERT: K 67 GLU cc_start: 0.8022 (pt0) cc_final: 0.7727 (pt0) REVERT: K 85 ASP cc_start: 0.8100 (t0) cc_final: 0.7503 (t0) REVERT: K 119 LYS cc_start: 0.8348 (tttt) cc_final: 0.8037 (tttm) REVERT: K 122 LYS cc_start: 0.8366 (tptt) cc_final: 0.7908 (tptt) REVERT: K 126 ASP cc_start: 0.7780 (m-30) cc_final: 0.7256 (m-30) REVERT: K 141 SER cc_start: 0.8370 (t) cc_final: 0.8140 (p) REVERT: L 33 GLU cc_start: 0.8811 (tp30) cc_final: 0.8588 (mm-30) outliers start: 90 outliers final: 51 residues processed: 665 average time/residue: 0.4535 time to fit residues: 478.1592 Evaluate side-chains 586 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 531 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 492 THR Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1234 LYS Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1250 GLN Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1448 SER Chi-restraints excluded: chain A residue 1452 SER Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1647 ASN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 292 optimal weight: 5.9990 chunk 239 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 352 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 349 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 282 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A 603 HIS A1250 GLN A1293 HIS A1453 HIS ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1647 ASN ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 HIS B 923 GLN B 975 HIS B1094 ASN E 8 ASN E 99 HIS ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN G 119 HIS J 26 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 33147 Z= 0.412 Angle : 0.665 16.171 45121 Z= 0.347 Chirality : 0.047 0.196 5048 Planarity : 0.005 0.052 5572 Dihedral : 13.280 85.167 5093 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.93 % Allowed : 12.32 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.12), residues: 3827 helix: -1.20 (0.14), residues: 1263 sheet: -1.49 (0.20), residues: 564 loop : -1.15 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 836 HIS 0.018 0.002 HIS E 99 PHE 0.025 0.002 PHE A 637 TYR 0.026 0.002 TYR B1033 ARG 0.011 0.001 ARG A1444 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 525 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8037 (tmm) cc_final: 0.7140 (ttt) REVERT: A 547 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8929 (mp) REVERT: A 604 LYS cc_start: 0.8308 (mttt) cc_final: 0.8088 (mtpt) REVERT: A 1078 LYS cc_start: 0.8563 (mmtp) cc_final: 0.8272 (mmmt) REVERT: A 1175 MET cc_start: 0.9105 (ttm) cc_final: 0.8889 (ttm) REVERT: B 190 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8932 (pp) REVERT: B 205 MET cc_start: 0.8728 (mtm) cc_final: 0.8376 (mtm) REVERT: B 307 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: B 351 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8135 (tp-100) REVERT: B 388 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7579 (mt-10) REVERT: B 397 THR cc_start: 0.9421 (t) cc_final: 0.9084 (m) REVERT: B 785 ASP cc_start: 0.8143 (m-30) cc_final: 0.7855 (m-30) REVERT: B 1065 ARG cc_start: 0.7851 (mtm180) cc_final: 0.7305 (mtp180) REVERT: C 39 ASP cc_start: 0.8242 (m-30) cc_final: 0.8007 (m-30) REVERT: C 89 THR cc_start: 0.8986 (p) cc_final: 0.8780 (m) REVERT: C 128 ASP cc_start: 0.8013 (p0) cc_final: 0.7298 (p0) REVERT: C 174 ARG cc_start: 0.7947 (ptp90) cc_final: 0.7155 (ptp90) REVERT: C 226 SER cc_start: 0.8778 (p) cc_final: 0.8514 (m) REVERT: D 35 GLU cc_start: 0.7765 (mp0) cc_final: 0.7470 (mp0) REVERT: E 45 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8070 (ttpp) REVERT: G 41 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8867 (m) REVERT: G 84 TYR cc_start: 0.9145 (p90) cc_final: 0.8878 (p90) REVERT: G 234 ARG cc_start: 0.6864 (ttt180) cc_final: 0.6334 (ttp-170) REVERT: H 27 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7467 (mt-10) REVERT: H 45 GLU cc_start: 0.7244 (tm-30) cc_final: 0.6896 (tm-30) REVERT: H 100 THR cc_start: 0.8932 (m) cc_final: 0.8693 (p) REVERT: H 123 MET cc_start: 0.9213 (ttp) cc_final: 0.8817 (ttp) REVERT: H 129 TYR cc_start: 0.8131 (p90) cc_final: 0.7782 (p90) REVERT: H 136 LYS cc_start: 0.8679 (mtpp) cc_final: 0.7921 (mtmm) REVERT: H 138 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8024 (pm20) REVERT: I 50 THR cc_start: 0.7825 (m) cc_final: 0.7597 (p) REVERT: K 67 GLU cc_start: 0.8111 (pt0) cc_final: 0.7845 (pt0) REVERT: K 85 ASP cc_start: 0.8199 (t0) cc_final: 0.7529 (t0) REVERT: K 119 LYS cc_start: 0.8383 (tttt) cc_final: 0.8071 (tttm) REVERT: L 40 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8897 (mp) outliers start: 135 outliers final: 97 residues processed: 612 average time/residue: 0.4531 time to fit residues: 445.1714 Evaluate side-chains 598 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 495 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1245 ASP Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1448 SER Chi-restraints excluded: chain A residue 1452 SER Chi-restraints excluded: chain A residue 1456 PHE Chi-restraints excluded: chain A residue 1471 GLU Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1647 ASN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1161 ASP Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain L residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 8.9990 chunk 264 optimal weight: 3.9990 chunk 182 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 353 optimal weight: 4.9990 chunk 374 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 334 optimal weight: 0.0070 chunk 100 optimal weight: 10.0000 overall best weight: 1.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN ** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 HIS ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1648 ASN ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 ASN C 161 HIS C 172 GLN E 8 ASN E 99 HIS ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33147 Z= 0.190 Angle : 0.545 14.451 45121 Z= 0.286 Chirality : 0.042 0.144 5048 Planarity : 0.004 0.050 5572 Dihedral : 13.058 80.501 5090 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.38 % Allowed : 13.54 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3827 helix: -0.51 (0.14), residues: 1258 sheet: -1.32 (0.20), residues: 581 loop : -0.89 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 836 HIS 0.008 0.001 HIS A1453 PHE 0.030 0.001 PHE G 138 TYR 0.017 0.001 TYR A1097 ARG 0.005 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 533 time to evaluate : 3.445 Fit side-chains revert: symmetry clash REVERT: A 604 LYS cc_start: 0.8239 (mttt) cc_final: 0.8025 (mtpt) REVERT: A 1078 LYS cc_start: 0.8479 (mmtp) cc_final: 0.8272 (mmmt) REVERT: B 164 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8561 (ptp) REVERT: B 190 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8852 (pp) REVERT: B 205 MET cc_start: 0.8615 (mtm) cc_final: 0.8302 (mtm) REVERT: B 307 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7783 (tt0) REVERT: B 397 THR cc_start: 0.9336 (t) cc_final: 0.8998 (m) REVERT: B 698 SER cc_start: 0.9130 (p) cc_final: 0.8736 (t) REVERT: B 785 ASP cc_start: 0.8023 (m-30) cc_final: 0.7771 (m-30) REVERT: B 944 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8218 (mt0) REVERT: C 39 ASP cc_start: 0.8148 (m-30) cc_final: 0.7930 (m-30) REVERT: C 128 ASP cc_start: 0.7887 (p0) cc_final: 0.7386 (p0) REVERT: C 174 ARG cc_start: 0.8173 (ptp90) cc_final: 0.7202 (ptp90) REVERT: C 226 SER cc_start: 0.8693 (p) cc_final: 0.8473 (m) REVERT: C 319 ARG cc_start: 0.8192 (tpp80) cc_final: 0.7778 (mtt-85) REVERT: D 35 GLU cc_start: 0.7807 (mp0) cc_final: 0.7528 (mp0) REVERT: E 45 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8203 (ttpp) REVERT: H 27 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7429 (mt-10) REVERT: H 45 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6729 (tm-30) REVERT: H 136 LYS cc_start: 0.8654 (mtpp) cc_final: 0.7981 (mttp) REVERT: H 138 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: K 67 GLU cc_start: 0.8100 (pt0) cc_final: 0.7823 (pt0) REVERT: K 85 ASP cc_start: 0.8157 (t0) cc_final: 0.7691 (t0) REVERT: K 119 LYS cc_start: 0.8333 (tttt) cc_final: 0.8054 (tttm) REVERT: L 40 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8934 (mp) outliers start: 116 outliers final: 74 residues processed: 606 average time/residue: 0.4271 time to fit residues: 417.1860 Evaluate side-chains 582 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 502 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1452 SER Chi-restraints excluded: chain A residue 1456 PHE Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1155 ASP Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 137 GLN Chi-restraints excluded: chain H residue 138 GLU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 154 optimal weight: 8.9990 chunk 319 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 335 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A1214 ASN A1453 HIS ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN D 17 ASN E 8 ASN E 99 HIS E 101 GLN F 78 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 33147 Z= 0.491 Angle : 0.680 13.655 45121 Z= 0.353 Chirality : 0.049 0.201 5048 Planarity : 0.005 0.056 5572 Dihedral : 13.167 83.485 5090 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.37 % Allowed : 14.04 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3827 helix: -0.41 (0.14), residues: 1259 sheet: -1.28 (0.21), residues: 563 loop : -0.82 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 836 HIS 0.017 0.002 HIS E 99 PHE 0.029 0.002 PHE B1167 TYR 0.022 0.002 TYR B1033 ARG 0.007 0.001 ARG A1221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 472 time to evaluate : 3.632 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7795 (tmm) cc_final: 0.6912 (ttt) REVERT: A 63 SER cc_start: 0.8666 (m) cc_final: 0.8428 (p) REVERT: A 246 ASP cc_start: 0.4977 (t70) cc_final: 0.4604 (t0) REVERT: A 329 ARG cc_start: 0.8262 (ttm110) cc_final: 0.8009 (ttp80) REVERT: B 164 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8731 (ptp) REVERT: B 190 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8934 (pp) REVERT: B 388 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7569 (mt-10) REVERT: B 515 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7669 (t) REVERT: B 785 ASP cc_start: 0.8269 (m-30) cc_final: 0.7977 (m-30) REVERT: B 944 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8140 (mt0) REVERT: B 1065 ARG cc_start: 0.7920 (mtp180) cc_final: 0.7604 (mtp180) REVERT: C 226 SER cc_start: 0.8855 (p) cc_final: 0.8623 (m) REVERT: C 319 ARG cc_start: 0.8248 (tpp80) cc_final: 0.7854 (mtt-85) REVERT: D 35 GLU cc_start: 0.7886 (mp0) cc_final: 0.7626 (mp0) REVERT: E 45 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8071 (ttpp) REVERT: E 122 LYS cc_start: 0.7801 (mmtp) cc_final: 0.6629 (pttm) REVERT: G 138 PHE cc_start: 0.6854 (t80) cc_final: 0.6636 (t80) REVERT: G 234 ARG cc_start: 0.7117 (ttt180) cc_final: 0.6591 (ttp-170) REVERT: H 27 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7633 (mt-10) REVERT: H 45 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7137 (tm-30) REVERT: K 67 GLU cc_start: 0.8127 (pt0) cc_final: 0.7831 (pt0) REVERT: K 85 ASP cc_start: 0.8212 (t0) cc_final: 0.7522 (t0) REVERT: K 119 LYS cc_start: 0.8462 (tttt) cc_final: 0.8093 (tttm) REVERT: L 40 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8958 (mp) outliers start: 150 outliers final: 107 residues processed: 576 average time/residue: 0.4360 time to fit residues: 402.2106 Evaluate side-chains 569 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 457 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1214 ASN Chi-restraints excluded: chain A residue 1235 THR Chi-restraints excluded: chain A residue 1245 ASP Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1452 SER Chi-restraints excluded: chain A residue 1456 PHE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 172 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 37 SER Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 80 ILE Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 8.9990 chunk 336 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 219 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 chunk 374 optimal weight: 0.8980 chunk 310 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 196 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS A1214 ASN A1250 GLN A1453 HIS ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN B 896 GLN C 172 GLN E 8 ASN E 99 HIS ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33147 Z= 0.237 Angle : 0.560 12.315 45121 Z= 0.294 Chirality : 0.043 0.155 5048 Planarity : 0.004 0.054 5572 Dihedral : 13.041 80.213 5090 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.90 % Allowed : 14.88 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.13), residues: 3827 helix: -0.01 (0.15), residues: 1259 sheet: -1.19 (0.21), residues: 550 loop : -0.71 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 836 HIS 0.008 0.001 HIS A1453 PHE 0.021 0.001 PHE B1167 TYR 0.015 0.001 TYR H 95 ARG 0.004 0.000 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 485 time to evaluate : 3.819 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7984 (tmm) cc_final: 0.6848 (ttt) REVERT: A 63 SER cc_start: 0.8622 (m) cc_final: 0.8355 (p) REVERT: A 246 ASP cc_start: 0.4855 (t70) cc_final: 0.4478 (t70) REVERT: A 393 SER cc_start: 0.8937 (m) cc_final: 0.8414 (p) REVERT: A 1004 GLU cc_start: 0.7728 (tp30) cc_final: 0.7341 (tp30) REVERT: B 164 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8707 (ptp) REVERT: B 190 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8862 (pp) REVERT: B 515 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7651 (t) REVERT: B 784 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: B 785 ASP cc_start: 0.8138 (m-30) cc_final: 0.7886 (m-30) REVERT: B 944 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8236 (mt0) REVERT: B 1065 ARG cc_start: 0.7890 (mtp180) cc_final: 0.7673 (mtp180) REVERT: C 128 ASP cc_start: 0.8082 (p0) cc_final: 0.7808 (p0) REVERT: C 226 SER cc_start: 0.8748 (p) cc_final: 0.8548 (m) REVERT: C 319 ARG cc_start: 0.8229 (tpp80) cc_final: 0.7836 (mtt-85) REVERT: D 35 GLU cc_start: 0.7891 (mp0) cc_final: 0.7665 (mp0) REVERT: E 45 LYS cc_start: 0.8418 (ttmt) cc_final: 0.8165 (ttpp) REVERT: E 122 LYS cc_start: 0.7776 (mmtp) cc_final: 0.6746 (pttm) REVERT: G 138 PHE cc_start: 0.6884 (t80) cc_final: 0.6643 (t80) REVERT: H 27 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7550 (mt-10) REVERT: H 45 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6996 (tm-30) REVERT: I 63 LYS cc_start: 0.8373 (mmtt) cc_final: 0.7670 (mtmt) REVERT: J 25 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.8893 (mp) REVERT: K 85 ASP cc_start: 0.8134 (t0) cc_final: 0.7528 (t0) REVERT: K 119 LYS cc_start: 0.8427 (tttt) cc_final: 0.8098 (tmtt) REVERT: L 40 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8966 (mp) outliers start: 134 outliers final: 103 residues processed: 573 average time/residue: 0.4320 time to fit residues: 399.4312 Evaluate side-chains 569 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 459 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1214 ASN Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1250 GLN Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1452 SER Chi-restraints excluded: chain A residue 1456 PHE Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1647 ASN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 784 ASP Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1161 ASP Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 361 optimal weight: 0.0060 chunk 42 optimal weight: 0.9980 chunk 213 optimal weight: 4.9990 chunk 273 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 315 optimal weight: 8.9990 chunk 209 optimal weight: 0.8980 chunk 373 optimal weight: 1.9990 chunk 233 optimal weight: 0.2980 chunk 227 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS A1214 ASN A1453 HIS ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1662 ASN ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1163 GLN C 172 GLN E 99 HIS ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33147 Z= 0.152 Angle : 0.527 12.055 45121 Z= 0.276 Chirality : 0.042 0.232 5048 Planarity : 0.004 0.053 5572 Dihedral : 12.932 79.145 5090 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.41 % Allowed : 15.58 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3827 helix: 0.35 (0.15), residues: 1259 sheet: -1.06 (0.21), residues: 567 loop : -0.57 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 836 HIS 0.008 0.001 HIS A1453 PHE 0.019 0.001 PHE B1167 TYR 0.014 0.001 TYR B 655 ARG 0.007 0.000 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 500 time to evaluate : 3.530 Fit side-chains revert: symmetry clash REVERT: A 63 SER cc_start: 0.8594 (m) cc_final: 0.8353 (p) REVERT: A 188 TYR cc_start: 0.8885 (t80) cc_final: 0.8606 (t80) REVERT: A 393 SER cc_start: 0.8917 (m) cc_final: 0.8353 (p) REVERT: A 490 ILE cc_start: 0.8519 (mm) cc_final: 0.8203 (mt) REVERT: A 1004 GLU cc_start: 0.7669 (tp30) cc_final: 0.7340 (tp30) REVERT: A 1261 VAL cc_start: 0.9088 (t) cc_final: 0.8835 (m) REVERT: B 65 VAL cc_start: 0.8460 (OUTLIER) cc_final: 0.8050 (m) REVERT: B 190 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8832 (pp) REVERT: B 515 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7558 (t) REVERT: B 785 ASP cc_start: 0.8046 (m-30) cc_final: 0.7813 (m-30) REVERT: B 944 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8252 (mt0) REVERT: B 1033 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: C 128 ASP cc_start: 0.8010 (p0) cc_final: 0.7778 (p0) REVERT: C 319 ARG cc_start: 0.8233 (tpp80) cc_final: 0.7863 (mtt-85) REVERT: E 45 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8201 (ttpp) REVERT: E 122 LYS cc_start: 0.7775 (mmtp) cc_final: 0.6755 (pttm) REVERT: G 138 PHE cc_start: 0.6890 (t80) cc_final: 0.6672 (t80) REVERT: H 27 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7530 (mt-10) REVERT: H 45 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6937 (tm-30) REVERT: I 63 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7664 (mtmt) REVERT: J 25 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8878 (mp) REVERT: K 81 MET cc_start: 0.9282 (mmm) cc_final: 0.9024 (tpt) REVERT: K 85 ASP cc_start: 0.8118 (t0) cc_final: 0.7729 (t0) REVERT: K 119 LYS cc_start: 0.8391 (tttt) cc_final: 0.8097 (tmtt) REVERT: L 40 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8927 (mp) outliers start: 117 outliers final: 86 residues processed: 580 average time/residue: 0.4392 time to fit residues: 411.5405 Evaluate side-chains 564 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 471 time to evaluate : 3.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1214 ASN Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1456 PHE Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1555 VAL Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1647 ASN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 230 optimal weight: 0.0060 chunk 148 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 237 optimal weight: 0.0170 chunk 254 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 293 optimal weight: 0.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN A1214 ASN A1250 GLN A1447 GLN ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 33147 Z= 0.138 Angle : 0.516 11.713 45121 Z= 0.269 Chirality : 0.042 0.218 5048 Planarity : 0.003 0.053 5572 Dihedral : 12.845 79.112 5090 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.20 % Allowed : 15.96 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3827 helix: 0.58 (0.15), residues: 1259 sheet: -0.96 (0.21), residues: 569 loop : -0.47 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 836 HIS 0.009 0.001 HIS E 99 PHE 0.014 0.001 PHE B1167 TYR 0.016 0.001 TYR H 98 ARG 0.007 0.000 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 505 time to evaluate : 3.606 Fit side-chains revert: symmetry clash REVERT: A 393 SER cc_start: 0.8944 (m) cc_final: 0.8412 (p) REVERT: A 490 ILE cc_start: 0.8346 (mm) cc_final: 0.8016 (mt) REVERT: A 1004 GLU cc_start: 0.7682 (tp30) cc_final: 0.7362 (tp30) REVERT: A 1261 VAL cc_start: 0.9070 (t) cc_final: 0.8866 (m) REVERT: B 65 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8090 (m) REVERT: B 698 SER cc_start: 0.9075 (p) cc_final: 0.8689 (t) REVERT: B 783 MET cc_start: 0.7952 (mtt) cc_final: 0.7367 (mtt) REVERT: B 785 ASP cc_start: 0.7993 (m-30) cc_final: 0.7771 (m-30) REVERT: B 944 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8254 (mt0) REVERT: B 1033 TYR cc_start: 0.8949 (OUTLIER) cc_final: 0.8356 (m-80) REVERT: C 128 ASP cc_start: 0.7892 (p0) cc_final: 0.7690 (p0) REVERT: C 319 ARG cc_start: 0.8230 (tpp80) cc_final: 0.7813 (mtt-85) REVERT: E 122 LYS cc_start: 0.7802 (mmtp) cc_final: 0.6802 (pttm) REVERT: G 138 PHE cc_start: 0.6913 (t80) cc_final: 0.6705 (t80) REVERT: H 27 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7525 (mt-10) REVERT: H 45 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6980 (tm-30) REVERT: H 146 ARG cc_start: 0.5517 (mtm180) cc_final: 0.5163 (mtm180) REVERT: J 25 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8895 (mp) REVERT: K 81 MET cc_start: 0.9260 (mmm) cc_final: 0.9019 (tpt) REVERT: K 85 ASP cc_start: 0.8082 (t0) cc_final: 0.7722 (t0) REVERT: K 97 SER cc_start: 0.8817 (m) cc_final: 0.8581 (m) REVERT: K 119 LYS cc_start: 0.8363 (tttt) cc_final: 0.8092 (tmtt) REVERT: L 40 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8899 (mp) outliers start: 110 outliers final: 87 residues processed: 579 average time/residue: 0.4360 time to fit residues: 404.9748 Evaluate side-chains 567 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 475 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1214 ASN Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1300 ASN Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1555 VAL Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain A residue 1647 ASN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 99 HIS Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 339 optimal weight: 0.3980 chunk 357 optimal weight: 0.3980 chunk 326 optimal weight: 6.9990 chunk 347 optimal weight: 10.0000 chunk 209 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 272 optimal weight: 0.0270 chunk 106 optimal weight: 8.9990 chunk 314 optimal weight: 2.9990 chunk 328 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 overall best weight: 1.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN A1214 ASN ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 ASN C 172 GLN ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 33147 Z= 0.178 Angle : 0.526 11.853 45121 Z= 0.273 Chirality : 0.042 0.214 5048 Planarity : 0.003 0.056 5572 Dihedral : 12.801 79.819 5090 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.94 % Allowed : 16.57 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3827 helix: 0.69 (0.15), residues: 1264 sheet: -0.92 (0.21), residues: 568 loop : -0.42 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 836 HIS 0.007 0.001 HIS A1453 PHE 0.015 0.001 PHE B1167 TYR 0.018 0.001 TYR H 141 ARG 0.008 0.000 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 472 time to evaluate : 3.777 Fit side-chains revert: symmetry clash REVERT: A 393 SER cc_start: 0.8944 (m) cc_final: 0.8413 (p) REVERT: A 490 ILE cc_start: 0.8326 (mm) cc_final: 0.8024 (mm) REVERT: A 1004 GLU cc_start: 0.7694 (tp30) cc_final: 0.7376 (tp30) REVERT: A 1261 VAL cc_start: 0.9071 (t) cc_final: 0.8864 (m) REVERT: B 698 SER cc_start: 0.9105 (p) cc_final: 0.8700 (t) REVERT: B 783 MET cc_start: 0.8027 (mtt) cc_final: 0.7430 (mtt) REVERT: B 785 ASP cc_start: 0.8029 (m-30) cc_final: 0.7786 (m-30) REVERT: B 944 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8248 (mt0) REVERT: C 128 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7595 (p0) REVERT: C 319 ARG cc_start: 0.8172 (tpp80) cc_final: 0.7796 (mtt-85) REVERT: E 122 LYS cc_start: 0.7797 (mmtp) cc_final: 0.6812 (pttm) REVERT: H 27 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7546 (mt-10) REVERT: H 45 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7060 (tm-30) REVERT: J 25 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8889 (mp) REVERT: J 31 ASP cc_start: 0.8388 (p0) cc_final: 0.8083 (p0) REVERT: K 81 MET cc_start: 0.9279 (mmm) cc_final: 0.9039 (tpt) REVERT: K 97 SER cc_start: 0.8831 (m) cc_final: 0.8593 (m) REVERT: L 40 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8911 (mp) outliers start: 101 outliers final: 89 residues processed: 537 average time/residue: 0.4416 time to fit residues: 381.9342 Evaluate side-chains 549 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 456 time to evaluate : 3.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1300 ASN Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1456 PHE Chi-restraints excluded: chain A residue 1555 VAL Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 228 optimal weight: 0.7980 chunk 367 optimal weight: 0.8980 chunk 224 optimal weight: 4.9990 chunk 174 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 385 optimal weight: 7.9990 chunk 354 optimal weight: 6.9990 chunk 307 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1447 GLN ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 GLN B1165 ASN ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33147 Z= 0.214 Angle : 0.543 11.899 45121 Z= 0.281 Chirality : 0.043 0.210 5048 Planarity : 0.004 0.055 5572 Dihedral : 12.790 80.603 5090 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.80 % Allowed : 17.01 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3827 helix: 0.74 (0.15), residues: 1266 sheet: -0.94 (0.21), residues: 563 loop : -0.41 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 836 HIS 0.007 0.001 HIS A1453 PHE 0.017 0.001 PHE B1167 TYR 0.017 0.001 TYR H 95 ARG 0.012 0.000 ARG H 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7654 Ramachandran restraints generated. 3827 Oldfield, 0 Emsley, 3827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 461 time to evaluate : 3.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 393 SER cc_start: 0.8924 (m) cc_final: 0.8386 (p) REVERT: A 490 ILE cc_start: 0.8372 (mm) cc_final: 0.8046 (mm) REVERT: A 1004 GLU cc_start: 0.7729 (tp30) cc_final: 0.7392 (tp30) REVERT: A 1261 VAL cc_start: 0.9055 (t) cc_final: 0.8812 (m) REVERT: B 515 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7591 (t) REVERT: B 698 SER cc_start: 0.9104 (p) cc_final: 0.8681 (t) REVERT: B 783 MET cc_start: 0.8115 (mtt) cc_final: 0.7487 (mtt) REVERT: B 785 ASP cc_start: 0.8083 (m-30) cc_final: 0.7858 (m-30) REVERT: B 944 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8241 (mt0) REVERT: B 1057 MET cc_start: 0.9178 (mmp) cc_final: 0.8908 (mmt) REVERT: C 128 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7648 (p0) REVERT: C 319 ARG cc_start: 0.8184 (tpp80) cc_final: 0.7799 (mtt-85) REVERT: E 122 LYS cc_start: 0.7777 (mmtp) cc_final: 0.6900 (pttm) REVERT: H 27 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7580 (mt-10) REVERT: H 45 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7175 (tm-30) REVERT: J 25 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.8870 (mp) REVERT: J 31 ASP cc_start: 0.8428 (p0) cc_final: 0.8108 (p0) REVERT: K 97 SER cc_start: 0.8828 (m) cc_final: 0.8596 (m) REVERT: L 40 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8904 (mp) outliers start: 96 outliers final: 88 residues processed: 526 average time/residue: 0.4601 time to fit residues: 391.2388 Evaluate side-chains 551 residues out of total 3434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 458 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 898 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 973 GLU Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1169 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1246 VAL Chi-restraints excluded: chain A residue 1300 ASN Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1456 PHE Chi-restraints excluded: chain A residue 1480 THR Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1555 VAL Chi-restraints excluded: chain A residue 1569 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 584 CYS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 837 LEU Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1055 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1199 ASN Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 243 optimal weight: 2.9990 chunk 327 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 283 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 307 optimal weight: 0.0010 chunk 128 optimal weight: 10.0000 chunk 315 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.099020 restraints weight = 46410.730| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.78 r_work: 0.3008 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33147 Z= 0.197 Angle : 0.535 11.890 45121 Z= 0.277 Chirality : 0.043 0.207 5048 Planarity : 0.004 0.057 5572 Dihedral : 12.763 80.426 5090 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.88 % Allowed : 16.77 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3827 helix: 0.81 (0.15), residues: 1268 sheet: -0.91 (0.21), residues: 564 loop : -0.38 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 836 HIS 0.007 0.001 HIS A1453 PHE 0.017 0.001 PHE B1167 TYR 0.015 0.001 TYR H 95 ARG 0.008 0.000 ARG B 434 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8760.00 seconds wall clock time: 157 minutes 28.45 seconds (9448.45 seconds total)