Starting phenix.real_space_refine on Fri Mar 22 20:46:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hko_0238/03_2024/6hko_0238_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hko_0238/03_2024/6hko_0238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hko_0238/03_2024/6hko_0238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hko_0238/03_2024/6hko_0238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hko_0238/03_2024/6hko_0238_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hko_0238/03_2024/6hko_0238_updated.pdb" } resolution = 3.42 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= 0.011 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 167 5.16 5 C 21594 2.51 5 N 5999 2.21 5 O 6675 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 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 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 TYR 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1176": "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 PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 781": "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 PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "B PHE 1167": "CD1" <-> "CD2" "CE1" <-> "CE2" 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" Residue "N ARG 157": "NH1" <-> "NH2" Residue "M PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34518 Number of models: 1 Model: "" Number of chains: 23 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: 9270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9270 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 59, 'TRANS': 1106} 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: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1751 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} 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: "N" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1110 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 9, 'TRANS': 130} Chain breaks: 2 Chain: "M" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1011 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 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 68.006 53.414 55.211 1.00 74.00 S ATOM 480 SG CYS A 65 71.975 51.423 54.643 1.00 71.20 S ATOM 535 SG CYS A 72 70.921 53.328 57.636 1.00 65.70 S ATOM 781 SG CYS A 102 73.075 103.735 44.141 1.00 86.04 S ATOM 806 SG CYS A 105 75.877 102.219 41.235 1.00 84.96 S ATOM 1597 SG CYS A 233 76.987 104.755 43.724 1.00 90.06 S ATOM 1619 SG CYS A 236 74.511 105.590 40.608 1.00 96.18 S ATOM 20113 SG CYS B1104 83.786 60.894 47.386 1.00 63.28 S ATOM 20139 SG CYS B1107 81.464 64.042 47.458 1.00 63.94 S ATOM 20286 SG CYS B1128 80.119 60.764 47.638 1.00 70.38 S ATOM 20314 SG CYS B1131 82.000 64.245 43.988 1.00 76.84 S ATOM 28740 SG CYS I 10 46.436 130.417 100.974 1.00 95.45 S ATOM 28762 SG CYS I 13 45.071 126.221 100.349 1.00 97.79 S ATOM 28882 SG CYS I 30 45.923 128.780 97.235 1.00102.41 S ATOM 28903 SG CYS I 33 42.671 128.809 100.275 1.00103.05 S ATOM 29217 SG CYS J 7 86.136 42.499 126.430 1.00 45.91 S ATOM 29240 SG CYS J 10 89.493 41.626 127.229 1.00 48.67 S ATOM 29520 SG CYS J 45 89.869 45.223 127.881 1.00 47.13 S ATOM 29526 SG CYS J 46 87.354 42.819 129.878 1.00 47.10 S ATOM 30541 SG CYS L 31 45.745 43.948 108.738 1.00 64.80 S ATOM 30561 SG CYS L 34 43.843 42.481 112.041 1.00 68.55 S ATOM 30665 SG CYS L 48 42.569 41.377 108.561 1.00 76.47 S ATOM 30688 SG CYS L 51 42.262 45.259 110.203 1.00 75.72 S Time building chain proxies: 17.80, per 1000 atoms: 0.52 Number of scatterers: 34518 At special positions: 0 Unit cell: (166.4, 161.2, 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 167 16.00 P 76 15.00 Mg 1 11.99 O 6675 8.00 N 5999 7.00 C 21594 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: 13.13 Conformation dependent library (CDL) restraints added in 5.7 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 65 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 72 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 233 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 236 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1107 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1104 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1128 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1131 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 10 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 33 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 30 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " 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 7 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb=" ZN L3001 " 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 51 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " Number of angles added : 33 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7812 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 141 helices and 38 sheets defined 29.1% alpha, 12.4% beta 22 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 17.07 Creating SS restraints... Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 91 through 98 removed outlier: 3.525A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.042A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 removed outlier: 4.331A pdb=" N ASP A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 198 removed outlier: 3.656A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 227 removed outlier: 3.553A pdb=" N GLU A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 317 through 330 removed outlier: 3.788A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 removed outlier: 3.532A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 5.200A 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 365 through 368 Processing helix chain 'A' and resid 381 through 403 removed outlier: 3.631A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 438 removed outlier: 3.567A pdb=" N VAL A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) 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 518 through 525 Processing helix chain 'A' and resid 551 through 559 removed outlier: 3.650A pdb=" N ALA A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) 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 620 through 624 removed outlier: 3.922A pdb=" N TYR A 624 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 647 removed outlier: 4.067A pdb=" N GLU A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 680 removed outlier: 3.724A pdb=" N GLY A 677 " --> pdb=" O HIS A 673 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 699 removed outlier: 3.712A pdb=" N GLN A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (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 728 through 738 removed outlier: 3.564A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 738 " --> pdb=" O THR A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 800 Processing helix chain 'A' and resid 803 through 819 removed outlier: 3.581A pdb=" N ALA A 807 " --> pdb=" O PRO A 803 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 846 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: 3.556A pdb=" N GLN A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 884 " --> pdb=" O GLN A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 911 removed outlier: 3.610A pdb=" N ILE A 891 " --> pdb=" O ASN A 887 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 930 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 removed outlier: 3.821A pdb=" N PHE A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A1000 " --> pdb=" O TYR A 996 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A1001 " --> pdb=" O PHE A 997 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1027 removed outlier: 4.438A pdb=" N GLY A1017 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR A1018 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A1020 " --> pdb=" O GLY A1017 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A1021 " --> pdb=" O TYR A1018 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A1024 " --> pdb=" O ARG A1021 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS A1025 " --> pdb=" O CYS A1022 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN A1026 " --> pdb=" O LEU A1023 " (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 Processing helix chain 'A' and resid 1073 through 1080 removed outlier: 3.859A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1084 No H-bonds generated for 'chain 'A' and resid 1082 through 1084' Processing helix chain 'A' and resid 1092 through 1107 removed outlier: 3.665A pdb=" N LYS A1096 " --> pdb=" O GLU A1092 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A1102 " --> pdb=" O SER A1098 " (cutoff:3.500A) removed outlier: 3.671A 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 1140 through 1150 removed outlier: 3.505A pdb=" N GLU A1145 " --> pdb=" O GLN A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1176 removed outlier: 3.805A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A1171 " --> pdb=" O ARG A1167 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1199 removed outlier: 3.929A pdb=" N VAL A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) Proline residue: A1196 - end of helix removed outlier: 4.030A pdb=" N GLN A1199 " --> pdb=" O GLU A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1225 removed outlier: 4.048A pdb=" N ARG A1223 " --> pdb=" O PRO A1220 " (cutoff:3.500A) removed outlier: 3.676A 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 1265 No H-bonds generated for 'chain 'A' and resid 1263 through 1265' Processing helix chain 'A' and resid 1299 through 1305 removed outlier: 3.506A pdb=" N SER A1303 " --> pdb=" O ASN A1299 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1319 removed outlier: 3.561A pdb=" N ILE A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1335 removed outlier: 3.594A pdb=" N ALA A1328 " --> pdb=" O LEU A1324 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A1335 " --> pdb=" O LYS A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1441 through 1453 removed outlier: 3.651A pdb=" N ILE A1450 " --> pdb=" O ARG A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1495 removed outlier: 3.538A pdb=" N GLU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1530 Processing helix chain 'A' and resid 1548 through 1552 Processing helix chain 'A' and resid 1554 through 1570 removed outlier: 4.117A pdb=" N ALA A1558 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A1568 " --> pdb=" O ASN A1564 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1589 Processing helix chain 'A' and resid 1609 through 1615 Processing helix chain 'A' and resid 1623 through 1626 No H-bonds generated for 'chain 'A' and resid 1623 through 1626' Processing helix chain 'A' and resid 1639 through 1642 No H-bonds generated for 'chain 'A' and resid 1639 through 1642' Processing helix chain 'A' and resid 1650 through 1652 No H-bonds generated for 'chain 'A' and resid 1650 through 1652' Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.762A pdb=" N SER B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 41 No H-bonds generated for 'chain 'B' and resid 39 through 41' Processing helix chain 'B' and resid 43 through 51 removed outlier: 3.854A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 68 removed outlier: 3.596A pdb=" N GLY B 59 " --> pdb=" O PRO B 56 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU B 60 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU B 61 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU B 63 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 64 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 65 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.629A 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: 3.576A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.607A pdb=" N ASN B 224 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 287 through 292 removed outlier: 3.669A pdb=" N ILE B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 316 removed outlier: 3.577A pdb=" N LEU B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 309 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 335 removed outlier: 3.853A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 356 removed outlier: 3.635A pdb=" N GLU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 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 407 through 433 removed outlier: 3.509A pdb=" N LEU B 413 " --> pdb=" O TYR B 409 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 4.214A 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 removed outlier: 3.639A pdb=" N PHE B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 498 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 562 through 564 No H-bonds generated for 'chain 'B' and resid 562 through 564' Processing helix chain 'B' and resid 598 through 613 removed outlier: 3.892A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 671 removed outlier: 3.926A pdb=" N VAL B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) removed outlier: 5.219A 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: 3.726A 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 721 removed outlier: 3.541A pdb=" N TYR B 717 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN B 718 " --> pdb=" O ARG B 714 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (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 796 removed outlier: 3.851A pdb=" N ARG B 796 " --> pdb=" O SER B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 837 removed outlier: 3.562A 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 Proline residue: B 955 - end of helix Processing helix chain 'B' and resid 960 through 975 removed outlier: 3.654A pdb=" N HIS B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1003 removed outlier: 3.577A pdb=" N LYS B1002 " --> pdb=" O GLU B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1042 No H-bonds generated for 'chain 'B' and resid 1040 through 1042' Processing helix chain 'B' and resid 1073 through 1080 removed outlier: 3.987A 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 1190 Processing helix chain 'C' and resid 33 through 39 removed outlier: 4.003A pdb=" N LYS C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.521A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 102 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: 3.774A pdb=" N SER C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 177 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.960A 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 248 through 250 No H-bonds generated for 'chain 'C' and resid 248 through 250' 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 310 through 330 removed outlier: 3.653A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 40 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 93 removed outlier: 3.817A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 26 removed outlier: 4.510A 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 removed outlier: 3.555A pdb=" N ALA E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 71 removed outlier: 3.555A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 4.112A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 removed outlier: 3.876A pdb=" N VAL E 124 " --> pdb=" O MET E 121 " (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 159 through 167 removed outlier: 3.688A pdb=" N GLU E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 3.840A 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: 3.627A pdb=" N ARG F 65 " --> pdb=" O HIS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 102 removed outlier: 3.558A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 126 removed outlier: 3.691A 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 removed outlier: 3.733A pdb=" N VAL G 61 " --> pdb=" O PRO G 57 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 92 removed outlier: 3.861A 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 'H' and resid 132 through 134 No H-bonds generated for 'chain 'H' and resid 132 through 134' Processing helix chain 'I' and resid 59 through 66 removed outlier: 3.678A pdb=" N LYS I 63 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 59 through 66' Processing helix chain 'J' and resid 15 through 26 removed outlier: 4.091A pdb=" N TRP J 18 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU J 19 " --> pdb=" O ASP J 16 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER J 20 " --> pdb=" O LYS J 17 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU J 22 " --> pdb=" O GLU J 19 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU J 25 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 51 removed outlier: 4.316A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.618A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 127 Processing helix chain 'K' and resid 130 through 141 removed outlier: 3.931A pdb=" N PHE K 135 " --> pdb=" O VAL K 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 96 No H-bonds generated for 'chain 'N' and resid 93 through 96' Processing helix chain 'N' and resid 150 through 153 No H-bonds generated for 'chain 'N' and resid 150 through 153' Processing helix chain 'M' and resid 126 through 128 No H-bonds generated for 'chain 'M' and resid 126 through 128' Processing helix chain 'M' and resid 135 through 141 removed outlier: 3.536A pdb=" N ILE M 141 " --> pdb=" O ALA M 137 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.638A pdb=" N HIS A 378 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 479 through 483 removed outlier: 3.716A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 497 " --> pdb=" O ARG A 606 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 484 through 486 removed outlier: 5.935A pdb=" N LEU A 614 " --> pdb=" O SER A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.943A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 749 through 752 removed outlier: 3.727A pdb=" N CYS A 778 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS A 772 " --> pdb=" O LEU A 776 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU A 776 " --> pdb=" O LYS A 772 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1238 through 1241 removed outlier: 3.526A pdb=" N MET A1238 " --> pdb=" O THR A1521 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1469 through 1475 Processing sheet with id= H, first strand: chain 'B' and resid 108 through 110 Processing sheet with id= I, first strand: chain 'B' and resid 134 through 136 Processing sheet with id= J, first strand: chain 'B' and resid 155 through 157 removed outlier: 3.967A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER B 144 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL B 97 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 194 through 196 Processing sheet with id= L, first strand: chain 'B' and resid 206 through 209 Processing sheet with id= M, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.543A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 625 through 629 removed outlier: 5.588A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 594 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 651 through 655 removed outlier: 3.810A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.671A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 884 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 768 through 772 removed outlier: 3.532A pdb=" N PHE B 769 " --> pdb=" O TYR B1033 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 773 through 775 removed outlier: 6.748A pdb=" N ILE B 947 " --> pdb=" O ALA B 774 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 788 " --> pdb=" O ILE B 948 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 823 through 825 removed outlier: 6.919A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ALA B 860 " --> pdb=" O LYS B 870 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS B 870 " --> pdb=" O ALA B 860 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N PHE B 862 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS B 868 " --> pdb=" O PHE B 862 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id= U, first strand: chain 'B' and resid 1158 through 1160 Processing sheet with id= V, first strand: chain 'C' and resid 225 through 229 removed outlier: 3.729A pdb=" N SER C 226 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 228 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 53 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE C 57 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL C 42 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.521A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 231 through 235 removed outlier: 3.521A pdb=" N GLN C 232 " --> pdb=" O GLY C 292 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 256 through 258 Processing sheet with id= Z, first strand: chain 'E' and resid 78 through 82 removed outlier: 6.859A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.990A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE E 199 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AC, first strand: chain 'G' and resid 38 through 49 removed outlier: 3.721A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP G 125 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL G 81 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 132 through 134 Processing sheet with id= AE, first strand: chain 'G' and resid 144 through 149 Processing sheet with id= AF, first strand: chain 'H' and resid 23 through 29 removed outlier: 3.540A pdb=" N GLU H 126 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 47 through 49 Processing sheet with id= AH, first strand: chain 'L' and resid 29 through 31 Processing sheet with id= AI, first strand: chain 'N' and resid 54 through 57 removed outlier: 6.511A pdb=" N LYS N 135 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LYS N 57 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE N 137 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER N 138 " --> pdb=" O MET N 90 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET N 90 " --> pdb=" O SER N 138 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 110 through 112 Processing sheet with id= AK, first strand: chain 'M' and resid 22 through 25 removed outlier: 8.068A pdb=" N SER M 25 " --> pdb=" O PRO M 94 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU M 96 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE M 51 " --> pdb=" O THR M 66 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL M 52 " --> pdb=" O TYR M 41 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 77 through 81 removed outlier: 3.663A pdb=" N LEU M 80 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN M 89 " --> pdb=" O LEU M 80 " (cutoff:3.500A) 797 hydrogen bonds defined for protein. 2250 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 14.90 Time building geometry restraints manager: 14.24 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: 10198 1.33 - 1.45: 6302 1.45 - 1.58: 18418 1.58 - 1.70: 147 1.70 - 1.82: 267 Bond restraints: 35332 Sorted by residual: bond pdb=" O3B G2P T3000 " pdb=" PG G2P T3000 " ideal model delta sigma weight residual 1.716 1.608 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" O2A G2P T3000 " pdb=" PA G2P T3000 " ideal model delta sigma weight residual 1.513 1.610 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" O2B G2P T3000 " pdb=" PB G2P T3000 " ideal model delta sigma weight residual 1.517 1.610 -0.093 2.00e-02 2.50e+03 2.14e+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 1.81e+01 bond pdb=" C6 G2P T3000 " pdb=" N1 G2P T3000 " ideal model delta sigma weight residual 1.402 1.333 0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 35327 not shown) Histogram of bond angle deviations from ideal: 97.11 - 104.84: 937 104.84 - 112.57: 18036 112.57 - 120.30: 15045 120.30 - 128.03: 13703 128.03 - 135.76: 336 Bond angle restraints: 48057 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 112.96 105.00 7.96 1.00e+00 1.00e+00 6.34e+01 angle pdb=" C SER I 40 " pdb=" N GLN I 41 " pdb=" CA GLN I 41 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C LYS E 103 " pdb=" N ASN E 104 " pdb=" CA ASN E 104 " ideal model delta sigma weight residual 122.46 129.48 -7.02 1.41e+00 5.03e-01 2.48e+01 angle pdb=" C LEU G 49 " pdb=" N ALA G 50 " pdb=" CA ALA G 50 " ideal model delta sigma weight residual 120.97 133.18 -12.21 2.84e+00 1.24e-01 1.85e+01 angle pdb=" N PHE B 954 " pdb=" CA PHE B 954 " pdb=" C PHE B 954 " ideal model delta sigma weight residual 109.81 118.67 -8.86 2.21e+00 2.05e-01 1.61e+01 ... (remaining 48052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 20065 17.47 - 34.93: 950 34.93 - 52.40: 290 52.40 - 69.87: 79 69.87 - 87.33: 18 Dihedral angle restraints: 21402 sinusoidal: 9317 harmonic: 12085 Sorted by residual: dihedral pdb=" CA ASP B 15 " pdb=" C ASP B 15 " pdb=" N PHE B 16 " pdb=" CA PHE B 16 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+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 -152.97 -27.03 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ASP C 273 " pdb=" C ASP C 273 " pdb=" N THR C 274 " pdb=" CA THR C 274 " ideal model delta harmonic sigma weight residual 180.00 153.49 26.51 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 21399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4797 0.090 - 0.179: 543 0.179 - 0.269: 37 0.269 - 0.359: 2 0.359 - 0.449: 1 Chirality restraints: 5380 Sorted by residual: 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 2.20 0.45 2.00e-01 2.50e+01 5.03e+00 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 2.29 0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE A 581 " pdb=" CA ILE A 581 " pdb=" CG1 ILE A 581 " pdb=" CG2 ILE A 581 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 5377 not shown) Planarity restraints: 5944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 150 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO E 151 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B1044 " 0.016 2.00e-02 2.50e+03 2.15e-02 8.10e+00 pdb=" CG PHE B1044 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE B1044 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE B1044 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B1044 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B1044 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B1044 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1033 " -0.025 2.00e-02 2.50e+03 1.95e-02 7.63e+00 pdb=" CG TYR B1033 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B1033 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B1033 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B1033 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B1033 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B1033 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B1033 " -0.004 2.00e-02 2.50e+03 ... (remaining 5941 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 50 2.39 - 3.02: 16941 3.02 - 3.64: 51618 3.64 - 4.27: 80922 4.27 - 4.90: 131674 Nonbonded interactions: 281205 Sorted by model distance: nonbonded pdb=" OD1 ASP A 627 " pdb="MG MG A1701 " model vdw 1.761 2.170 nonbonded pdb=" O3' C R 20 " pdb="MG MG A1701 " model vdw 1.801 2.170 nonbonded pdb=" OG1 THR A 621 " pdb=" O ALA A 626 " model vdw 2.243 2.440 nonbonded pdb=" O VAL A 483 " pdb=" OG1 THR A 613 " model vdw 2.263 2.440 nonbonded pdb=" OD1 ASP A 629 " pdb="MG MG A1701 " model vdw 2.267 2.170 ... (remaining 281200 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.270 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 105.050 Find NCS groups from input model: 0.840 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 : 0.006 0.108 35332 Z= 0.399 Angle : 0.904 12.206 48057 Z= 0.480 Chirality : 0.057 0.449 5380 Planarity : 0.007 0.073 5944 Dihedral : 12.355 87.332 13590 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.14 % Allowed : 3.13 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -4.42 (0.10), residues: 4092 helix: -4.28 (0.06), residues: 1244 sheet: -2.29 (0.18), residues: 628 loop : -2.27 (0.11), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP B 836 HIS 0.016 0.002 HIS E 146 PHE 0.049 0.003 PHE B1044 TYR 0.048 0.003 TYR B1033 ARG 0.020 0.001 ARG B 920 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1139 time to evaluate : 3.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.9132 (mm) cc_final: 0.8823 (mt) REVERT: A 238 MET cc_start: 0.7480 (pmm) cc_final: 0.7177 (ptp) REVERT: A 381 SER cc_start: 0.9217 (p) cc_final: 0.8906 (t) REVERT: A 456 VAL cc_start: 0.9714 (p) cc_final: 0.9475 (t) REVERT: A 925 MET cc_start: 0.9234 (tpp) cc_final: 0.9030 (tpp) REVERT: A 1105 ARG cc_start: 0.6902 (ttt90) cc_final: 0.6605 (ttp-110) REVERT: A 1198 THR cc_start: 0.9030 (m) cc_final: 0.8817 (p) REVERT: A 1300 ASN cc_start: 0.7917 (t0) cc_final: 0.7711 (t0) REVERT: A 1588 MET cc_start: 0.8728 (tpt) cc_final: 0.8359 (tpt) REVERT: B 190 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8612 (pp) REVERT: B 255 ASP cc_start: 0.8337 (t70) cc_final: 0.7910 (t0) REVERT: B 288 ILE cc_start: 0.9518 (mm) cc_final: 0.9234 (mm) REVERT: B 304 ASP cc_start: 0.8332 (m-30) cc_final: 0.7962 (t0) REVERT: B 943 ILE cc_start: 0.8369 (pt) cc_final: 0.8067 (mt) REVERT: C 127 THR cc_start: 0.8862 (p) cc_final: 0.8650 (t) REVERT: D 27 LEU cc_start: 0.8117 (mp) cc_final: 0.7687 (mt) REVERT: D 84 SER cc_start: 0.7710 (p) cc_final: 0.7509 (m) REVERT: E 25 ASP cc_start: 0.8378 (m-30) cc_final: 0.8070 (m-30) REVERT: E 58 MET cc_start: 0.8516 (mtp) cc_final: 0.8274 (mtp) REVERT: E 119 SER cc_start: 0.8734 (m) cc_final: 0.8427 (t) REVERT: E 187 TYR cc_start: 0.8793 (t80) cc_final: 0.8331 (t80) REVERT: F 77 ASP cc_start: 0.8433 (p0) cc_final: 0.8203 (p0) REVERT: G 123 TYR cc_start: 0.8311 (m-10) cc_final: 0.7452 (m-80) REVERT: G 159 LYS cc_start: 0.6920 (tttm) cc_final: 0.6707 (tptp) REVERT: H 9 ILE cc_start: 0.9102 (mp) cc_final: 0.8888 (mm) REVERT: H 14 GLU cc_start: 0.8273 (pp20) cc_final: 0.7471 (pp20) REVERT: H 116 TYR cc_start: 0.8477 (m-10) cc_final: 0.8273 (m-80) REVERT: K 138 LYS cc_start: 0.9101 (mmtt) cc_final: 0.8651 (mmtt) REVERT: N 134 ASP cc_start: 0.5182 (m-30) cc_final: 0.4899 (t70) REVERT: N 135 LYS cc_start: 0.5984 (mttm) cc_final: 0.5398 (tppt) REVERT: M 16 GLN cc_start: 0.7780 (tp-100) cc_final: 0.7558 (tp-100) REVERT: M 53 LEU cc_start: 0.7945 (tp) cc_final: 0.7196 (tp) REVERT: M 60 LEU cc_start: 0.7448 (mt) cc_final: 0.7187 (mt) REVERT: M 135 LYS cc_start: 0.8349 (tptt) cc_final: 0.8106 (mtpt) outliers start: 5 outliers final: 3 residues processed: 1141 average time/residue: 0.5026 time to fit residues: 888.0861 Evaluate side-chains 658 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 654 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 1111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 348 optimal weight: 3.9990 chunk 313 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 323 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 196 optimal weight: 0.4980 chunk 240 optimal weight: 8.9990 chunk 375 optimal weight: 0.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 213 ASN A 559 ASN A 642 ASN A 880 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1141 GLN A1454 HIS A1544 ASN A1647 ASN B 39 GLN B 45 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 456 ASN B 669 GLN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 GLN ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1045 GLN C 172 GLN C 175 GLN C 301 ASN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 GLN D 81 ASN F 61 HIS F 100 GLN G 121 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS G 216 HIS I 41 GLN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35332 Z= 0.240 Angle : 0.630 14.561 48057 Z= 0.332 Chirality : 0.044 0.204 5380 Planarity : 0.005 0.055 5944 Dihedral : 13.249 88.762 5378 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.50 % Allowed : 10.98 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -3.13 (0.11), residues: 4092 helix: -2.67 (0.11), residues: 1252 sheet: -1.85 (0.19), residues: 630 loop : -1.72 (0.12), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 836 HIS 0.006 0.001 HIS G 150 PHE 0.034 0.002 PHE B1044 TYR 0.026 0.001 TYR A 995 ARG 0.006 0.001 ARG B 560 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 719 time to evaluate : 3.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8710 (tp) cc_final: 0.8430 (tt) REVERT: A 773 ASP cc_start: 0.7982 (t0) cc_final: 0.7765 (t0) REVERT: A 833 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9024 (pp) REVERT: A 1026 GLN cc_start: 0.8410 (mm110) cc_final: 0.8004 (mp10) REVERT: A 1230 SER cc_start: 0.8972 (m) cc_final: 0.8664 (p) REVERT: A 1300 ASN cc_start: 0.7903 (t0) cc_final: 0.7439 (t0) REVERT: A 1459 LYS cc_start: 0.7497 (ttmt) cc_final: 0.7177 (ttpt) REVERT: A 1474 LEU cc_start: 0.8994 (tt) cc_final: 0.8709 (tt) REVERT: A 1529 MET cc_start: 0.9001 (mmm) cc_final: 0.8538 (mmt) REVERT: B 67 ASP cc_start: 0.8086 (t70) cc_final: 0.7751 (t70) REVERT: B 190 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8629 (pp) REVERT: B 255 ASP cc_start: 0.8424 (t70) cc_final: 0.8217 (t0) REVERT: B 288 ILE cc_start: 0.9558 (mm) cc_final: 0.9340 (mt) REVERT: B 431 ASP cc_start: 0.7307 (m-30) cc_final: 0.7056 (m-30) REVERT: B 456 ASN cc_start: 0.8435 (t0) cc_final: 0.8016 (t0) REVERT: B 561 ILE cc_start: 0.8338 (mp) cc_final: 0.8071 (mt) REVERT: B 943 ILE cc_start: 0.8393 (pt) cc_final: 0.8127 (mt) REVERT: B 1039 MET cc_start: 0.8789 (mtm) cc_final: 0.7985 (mtt) REVERT: D 84 SER cc_start: 0.7552 (p) cc_final: 0.7290 (m) REVERT: D 91 ARG cc_start: 0.7864 (mtt-85) cc_final: 0.7612 (mtt-85) REVERT: E 25 ASP cc_start: 0.8343 (m-30) cc_final: 0.7962 (m-30) REVERT: E 32 GLN cc_start: 0.8414 (tp40) cc_final: 0.6710 (tm-30) REVERT: E 187 TYR cc_start: 0.8859 (t80) cc_final: 0.8301 (t80) REVERT: F 77 ASP cc_start: 0.8386 (p0) cc_final: 0.8126 (p0) REVERT: G 123 TYR cc_start: 0.8085 (m-10) cc_final: 0.7857 (m-80) REVERT: G 159 LYS cc_start: 0.7001 (tttm) cc_final: 0.6734 (tptp) REVERT: H 14 GLU cc_start: 0.7947 (pp20) cc_final: 0.7737 (pp20) REVERT: H 27 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8114 (mt-10) REVERT: H 103 LYS cc_start: 0.9135 (ttpt) cc_final: 0.8712 (ttmm) REVERT: I 32 GLN cc_start: 0.8116 (mt0) cc_final: 0.7805 (mt0) REVERT: J 68 LYS cc_start: 0.8800 (ttpt) cc_final: 0.8570 (ttmt) REVERT: K 68 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7796 (mm-30) REVERT: K 124 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9017 (tp) REVERT: K 138 LYS cc_start: 0.9104 (mmtt) cc_final: 0.8894 (mmtm) REVERT: N 29 PHE cc_start: 0.8106 (m-10) cc_final: 0.7840 (m-80) REVERT: N 79 THR cc_start: 0.8486 (t) cc_final: 0.8167 (m) REVERT: N 80 MET cc_start: 0.7644 (ppp) cc_final: 0.7316 (ppp) REVERT: N 134 ASP cc_start: 0.5402 (m-30) cc_final: 0.4970 (t70) REVERT: M 10 ILE cc_start: 0.7361 (mm) cc_final: 0.7139 (mm) REVERT: M 16 GLN cc_start: 0.7889 (tp-100) cc_final: 0.7502 (tp-100) REVERT: M 48 LYS cc_start: 0.4551 (tptt) cc_final: 0.4341 (tptt) REVERT: M 88 ILE cc_start: 0.8484 (tt) cc_final: 0.8266 (tt) outliers start: 92 outliers final: 46 residues processed: 776 average time/residue: 0.4763 time to fit residues: 598.8600 Evaluate side-chains 650 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 601 time to evaluate : 4.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 312 optimal weight: 3.9990 chunk 255 optimal weight: 8.9990 chunk 103 optimal weight: 0.3980 chunk 375 optimal weight: 1.9990 chunk 405 optimal weight: 20.0000 chunk 334 optimal weight: 0.9990 chunk 372 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 301 optimal weight: 0.0050 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 537 GLN ** A 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN A1036 ASN A1454 HIS A1581 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 368 GLN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 GLN ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1045 GLN C 172 GLN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS G 237 HIS ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 GLN N 106 ASN ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35332 Z= 0.153 Angle : 0.555 12.401 48057 Z= 0.289 Chirality : 0.042 0.215 5380 Planarity : 0.004 0.063 5944 Dihedral : 12.941 81.497 5377 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.45 % Allowed : 13.21 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -2.22 (0.12), residues: 4092 helix: -1.53 (0.13), residues: 1230 sheet: -1.46 (0.19), residues: 647 loop : -1.38 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 836 HIS 0.012 0.001 HIS A1293 PHE 0.028 0.001 PHE B1044 TYR 0.026 0.001 TYR A 995 ARG 0.005 0.000 ARG I 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 661 time to evaluate : 4.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8704 (tp) cc_final: 0.8443 (tt) REVERT: A 213 ASN cc_start: 0.8380 (t0) cc_final: 0.8064 (t0) REVERT: A 773 ASP cc_start: 0.7994 (t0) cc_final: 0.7722 (t0) REVERT: A 833 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9006 (pp) REVERT: A 928 MET cc_start: 0.8853 (ptp) cc_final: 0.8532 (ptp) REVERT: A 1230 SER cc_start: 0.8986 (m) cc_final: 0.8719 (p) REVERT: A 1290 TYR cc_start: 0.8544 (m-80) cc_final: 0.8016 (m-80) REVERT: A 1459 LYS cc_start: 0.7302 (ttmt) cc_final: 0.7050 (ttpt) REVERT: A 1474 LEU cc_start: 0.8930 (tt) cc_final: 0.8630 (tt) REVERT: B 67 ASP cc_start: 0.8089 (t70) cc_final: 0.7814 (t70) REVERT: B 190 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8501 (pp) REVERT: B 288 ILE cc_start: 0.9539 (mm) cc_final: 0.9318 (mt) REVERT: B 456 ASN cc_start: 0.8204 (t0) cc_final: 0.7917 (t0) REVERT: B 561 ILE cc_start: 0.8270 (mp) cc_final: 0.8021 (mt) REVERT: B 943 ILE cc_start: 0.8410 (pt) cc_final: 0.8068 (mt) REVERT: E 25 ASP cc_start: 0.8296 (m-30) cc_final: 0.7964 (m-30) REVERT: E 187 TYR cc_start: 0.8759 (t80) cc_final: 0.8245 (t80) REVERT: F 77 ASP cc_start: 0.8324 (p0) cc_final: 0.8042 (p0) REVERT: F 78 GLN cc_start: 0.8286 (mt0) cc_final: 0.8084 (mt0) REVERT: F 143 PHE cc_start: 0.8807 (p90) cc_final: 0.8526 (p90) REVERT: G 123 TYR cc_start: 0.8137 (m-10) cc_final: 0.7935 (m-80) REVERT: G 159 LYS cc_start: 0.6978 (tttm) cc_final: 0.6755 (tptp) REVERT: H 103 LYS cc_start: 0.9111 (ttpt) cc_final: 0.8604 (ttmm) REVERT: H 105 GLU cc_start: 0.8101 (pt0) cc_final: 0.7339 (pt0) REVERT: H 115 TYR cc_start: 0.8613 (m-80) cc_final: 0.8085 (m-80) REVERT: I 32 GLN cc_start: 0.8191 (mt0) cc_final: 0.7863 (mt0) REVERT: J 68 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8637 (ttmt) REVERT: K 68 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7765 (mm-30) REVERT: K 124 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9118 (tp) REVERT: K 138 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8810 (mmtm) REVERT: N 79 THR cc_start: 0.8653 (t) cc_final: 0.8433 (m) REVERT: N 134 ASP cc_start: 0.5304 (m-30) cc_final: 0.4853 (t70) REVERT: M 11 GLU cc_start: 0.7797 (tp30) cc_final: 0.7007 (mt-10) REVERT: M 16 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7593 (tp-100) REVERT: M 41 TYR cc_start: 0.7095 (m-10) cc_final: 0.6891 (m-80) REVERT: M 88 ILE cc_start: 0.8477 (tt) cc_final: 0.7899 (tt) outliers start: 90 outliers final: 50 residues processed: 713 average time/residue: 0.4684 time to fit residues: 542.6980 Evaluate side-chains 632 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 579 time to evaluate : 4.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 371 optimal weight: 8.9990 chunk 282 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 179 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 377 optimal weight: 8.9990 chunk 399 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 357 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 260 GLN A 378 HIS A 537 GLN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A 880 GLN ** A 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1454 HIS ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 547 HIS B 702 ASN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 923 GLN C 172 GLN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 ASN G 216 HIS ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 35332 Z= 0.496 Angle : 0.700 14.397 48057 Z= 0.363 Chirality : 0.048 0.172 5380 Planarity : 0.005 0.054 5944 Dihedral : 13.128 80.522 5377 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.35 % Allowed : 13.86 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -1.97 (0.13), residues: 4092 helix: -1.11 (0.14), residues: 1240 sheet: -1.43 (0.20), residues: 637 loop : -1.33 (0.13), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 836 HIS 0.008 0.002 HIS C 297 PHE 0.035 0.002 PHE B1044 TYR 0.027 0.002 TYR A 995 ARG 0.014 0.001 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 583 time to evaluate : 3.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8566 (tp) REVERT: A 366 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7914 (ttm-80) REVERT: A 439 ASP cc_start: 0.8062 (t0) cc_final: 0.7856 (t0) REVERT: A 635 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8396 (ttt) REVERT: A 747 ILE cc_start: 0.8976 (mp) cc_final: 0.8757 (mp) REVERT: A 773 ASP cc_start: 0.8190 (t0) cc_final: 0.7971 (t0) REVERT: A 833 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.8993 (pp) REVERT: A 1290 TYR cc_start: 0.8665 (m-80) cc_final: 0.8423 (m-80) REVERT: A 1459 LYS cc_start: 0.7537 (ttmt) cc_final: 0.7182 (ttpt) REVERT: A 1474 LEU cc_start: 0.8970 (tt) cc_final: 0.8660 (tt) REVERT: B 67 ASP cc_start: 0.8231 (t70) cc_final: 0.7960 (t70) REVERT: B 561 ILE cc_start: 0.8615 (mp) cc_final: 0.8414 (mt) REVERT: B 1039 MET cc_start: 0.8777 (mtm) cc_final: 0.8062 (mtm) REVERT: D 26 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7773 (tm-30) REVERT: D 38 GLN cc_start: 0.8497 (tt0) cc_final: 0.8139 (tp40) REVERT: E 25 ASP cc_start: 0.8430 (m-30) cc_final: 0.8137 (m-30) REVERT: E 187 TYR cc_start: 0.9041 (t80) cc_final: 0.8605 (t80) REVERT: E 196 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8747 (m) REVERT: F 77 ASP cc_start: 0.8403 (p0) cc_final: 0.8135 (p0) REVERT: F 78 GLN cc_start: 0.8482 (mt0) cc_final: 0.8186 (mt0) REVERT: F 122 MET cc_start: 0.9047 (mtm) cc_final: 0.8688 (mtt) REVERT: H 14 GLU cc_start: 0.8279 (pp20) cc_final: 0.7959 (pp20) REVERT: H 103 LYS cc_start: 0.9222 (ttpt) cc_final: 0.8814 (ttmm) REVERT: H 115 TYR cc_start: 0.8721 (m-80) cc_final: 0.8365 (m-80) REVERT: I 32 GLN cc_start: 0.8327 (mt0) cc_final: 0.7899 (mt0) REVERT: K 68 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7723 (mm-30) REVERT: K 124 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9097 (tp) REVERT: K 138 LYS cc_start: 0.9033 (mmtt) cc_final: 0.8721 (mmtm) REVERT: N 134 ASP cc_start: 0.5501 (m-30) cc_final: 0.5029 (t70) REVERT: M 16 GLN cc_start: 0.7636 (tp-100) cc_final: 0.7358 (tp-100) REVERT: M 41 TYR cc_start: 0.7550 (m-10) cc_final: 0.6996 (m-10) outliers start: 160 outliers final: 99 residues processed: 686 average time/residue: 0.4538 time to fit residues: 508.0687 Evaluate side-chains 640 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 535 time to evaluate : 4.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1484 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1577 VAL Chi-restraints excluded: chain A residue 1611 MET Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 902 SER Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain B residue 1189 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 171 PHE Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 40 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 332 optimal weight: 6.9990 chunk 226 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 297 optimal weight: 9.9990 chunk 164 optimal weight: 0.0770 chunk 340 optimal weight: 20.0000 chunk 275 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 chunk 358 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS A 537 GLN ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN ** A 923 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1108 HIS A1454 HIS B 27 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 ASN G 216 HIS H 35 GLN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS K 99 ASN ** K 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35332 Z= 0.223 Angle : 0.567 12.311 48057 Z= 0.294 Chirality : 0.043 0.157 5380 Planarity : 0.004 0.057 5944 Dihedral : 12.983 82.843 5375 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.02 % Allowed : 15.85 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -1.61 (0.13), residues: 4092 helix: -0.73 (0.14), residues: 1262 sheet: -1.32 (0.20), residues: 647 loop : -1.12 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 836 HIS 0.005 0.001 HIS B 688 PHE 0.028 0.001 PHE B1044 TYR 0.025 0.001 TYR A 995 ARG 0.006 0.000 ARG A1631 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 581 time to evaluate : 3.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7909 (ttm-80) REVERT: A 439 ASP cc_start: 0.7943 (t0) cc_final: 0.7729 (t0) REVERT: A 773 ASP cc_start: 0.8089 (t0) cc_final: 0.7880 (t0) REVERT: A 833 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.8968 (pp) REVERT: A 1290 TYR cc_start: 0.8558 (m-80) cc_final: 0.8063 (m-80) REVERT: A 1459 LYS cc_start: 0.7386 (ttmt) cc_final: 0.7019 (ttpt) REVERT: A 1474 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8618 (tt) REVERT: B 67 ASP cc_start: 0.8189 (t70) cc_final: 0.7950 (t70) REVERT: B 787 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8058 (ptt) REVERT: B 912 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8159 (mm-40) REVERT: B 1039 MET cc_start: 0.8579 (mtm) cc_final: 0.7897 (mtm) REVERT: B 1057 MET cc_start: 0.8339 (mmt) cc_final: 0.8104 (mmt) REVERT: D 26 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7596 (tm-30) REVERT: E 25 ASP cc_start: 0.8356 (m-30) cc_final: 0.8052 (m-30) REVERT: E 187 TYR cc_start: 0.8987 (t80) cc_final: 0.8581 (t80) REVERT: E 196 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8637 (p) REVERT: F 77 ASP cc_start: 0.8326 (p0) cc_final: 0.8075 (p0) REVERT: F 78 GLN cc_start: 0.8419 (mt0) cc_final: 0.8179 (mt0) REVERT: F 122 MET cc_start: 0.9057 (mtm) cc_final: 0.8686 (mtt) REVERT: H 103 LYS cc_start: 0.9181 (ttpt) cc_final: 0.8711 (ttmm) REVERT: H 115 TYR cc_start: 0.8759 (m-80) cc_final: 0.8299 (m-80) REVERT: I 32 GLN cc_start: 0.8265 (mt0) cc_final: 0.7836 (mt0) REVERT: K 68 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7894 (mm-30) REVERT: K 138 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8741 (mmtt) REVERT: N 79 THR cc_start: 0.8430 (t) cc_final: 0.8177 (m) REVERT: N 134 ASP cc_start: 0.5432 (m-30) cc_final: 0.4931 (t70) REVERT: M 16 GLN cc_start: 0.7739 (tp-100) cc_final: 0.7416 (tp-100) REVERT: M 26 PHE cc_start: 0.7702 (m-80) cc_final: 0.7391 (m-80) REVERT: M 41 TYR cc_start: 0.7369 (m-10) cc_final: 0.6818 (m-10) outliers start: 111 outliers final: 68 residues processed: 654 average time/residue: 0.4680 time to fit residues: 503.9990 Evaluate side-chains 619 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 545 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 866 LYS Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain A residue 1647 ASN Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 134 optimal weight: 6.9990 chunk 359 optimal weight: 0.0770 chunk 78 optimal weight: 0.6980 chunk 234 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 399 optimal weight: 3.9990 chunk 331 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 209 optimal weight: 0.8980 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 923 ASN A 926 GLN A1108 HIS A1454 HIS B 27 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN B 339 GLN ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 216 HIS C 323 ASN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS K 99 ASN K 102 ASN ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 35332 Z= 0.162 Angle : 0.532 10.402 48057 Z= 0.277 Chirality : 0.042 0.213 5380 Planarity : 0.004 0.053 5944 Dihedral : 12.832 82.695 5375 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.80 % Allowed : 16.61 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -1.27 (0.13), residues: 4092 helix: -0.36 (0.15), residues: 1267 sheet: -1.15 (0.20), residues: 651 loop : -0.97 (0.14), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 836 HIS 0.008 0.001 HIS B 231 PHE 0.027 0.001 PHE B1044 TYR 0.023 0.001 TYR B1184 ARG 0.007 0.000 ARG B1134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 590 time to evaluate : 3.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.9167 (tttt) cc_final: 0.8820 (tttm) REVERT: A 366 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7912 (ttm-80) REVERT: A 464 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6910 (tm-30) REVERT: A 773 ASP cc_start: 0.8012 (t0) cc_final: 0.7809 (t0) REVERT: A 833 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.8941 (pp) REVERT: A 1459 LYS cc_start: 0.7339 (ttmt) cc_final: 0.6985 (ttpt) REVERT: A 1474 LEU cc_start: 0.8832 (tt) cc_final: 0.8515 (tt) REVERT: A 1476 LEU cc_start: 0.8453 (mm) cc_final: 0.8162 (mm) REVERT: A 1588 MET cc_start: 0.8729 (tpp) cc_final: 0.8525 (tpt) REVERT: B 778 TYR cc_start: 0.8840 (t80) cc_final: 0.8448 (t80) REVERT: B 787 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.7934 (ptm) REVERT: C 315 PHE cc_start: 0.7937 (t80) cc_final: 0.7490 (t80) REVERT: D 26 GLN cc_start: 0.8421 (tm-30) cc_final: 0.7675 (tm-30) REVERT: D 40 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8461 (mm) REVERT: E 25 ASP cc_start: 0.8308 (m-30) cc_final: 0.8019 (m-30) REVERT: E 110 PHE cc_start: 0.8391 (t80) cc_final: 0.7763 (t80) REVERT: E 187 TYR cc_start: 0.8866 (t80) cc_final: 0.8457 (t80) REVERT: F 77 ASP cc_start: 0.8314 (p0) cc_final: 0.8034 (p0) REVERT: F 78 GLN cc_start: 0.8383 (mt0) cc_final: 0.8177 (mt0) REVERT: F 134 ILE cc_start: 0.9369 (mm) cc_final: 0.9080 (mt) REVERT: F 143 PHE cc_start: 0.8897 (p90) cc_final: 0.8538 (p90) REVERT: H 27 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8158 (mt-10) REVERT: H 103 LYS cc_start: 0.9167 (ttpt) cc_final: 0.8712 (ttmm) REVERT: H 115 TYR cc_start: 0.8782 (m-80) cc_final: 0.8265 (m-80) REVERT: I 32 GLN cc_start: 0.8236 (mt0) cc_final: 0.7814 (mt0) REVERT: K 68 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7874 (mm-30) REVERT: N 79 THR cc_start: 0.8512 (t) cc_final: 0.8252 (m) REVERT: N 134 ASP cc_start: 0.5219 (m-30) cc_final: 0.4810 (t70) REVERT: M 11 GLU cc_start: 0.7948 (tp30) cc_final: 0.7042 (mt-10) REVERT: M 16 GLN cc_start: 0.7724 (tp-100) cc_final: 0.7346 (tp-100) outliers start: 103 outliers final: 70 residues processed: 657 average time/residue: 0.4656 time to fit residues: 503.4399 Evaluate side-chains 614 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 540 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 339 GLN Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain N residue 37 ASN Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 385 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 291 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 336 optimal weight: 7.9990 chunk 223 optimal weight: 9.9990 chunk 398 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1047 GLN A1108 HIS A1454 HIS B 27 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 ASN ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35332 Z= 0.263 Angle : 0.568 10.941 48057 Z= 0.293 Chirality : 0.044 0.190 5380 Planarity : 0.004 0.052 5944 Dihedral : 12.843 82.967 5375 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.18 % Allowed : 16.80 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -1.16 (0.13), residues: 4092 helix: -0.20 (0.15), residues: 1269 sheet: -1.17 (0.20), residues: 669 loop : -0.90 (0.14), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 836 HIS 0.006 0.001 HIS B 231 PHE 0.029 0.001 PHE B1044 TYR 0.027 0.001 TYR A 995 ARG 0.006 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 545 time to evaluate : 3.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.7932 (ttm-80) REVERT: A 635 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8359 (ttt) REVERT: A 773 ASP cc_start: 0.8121 (t0) cc_final: 0.7917 (t0) REVERT: A 833 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.8976 (pp) REVERT: A 1459 LYS cc_start: 0.7373 (ttmt) cc_final: 0.7022 (ttpt) REVERT: A 1474 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8577 (tt) REVERT: B 430 MET cc_start: 0.7630 (tmm) cc_final: 0.7279 (tmm) REVERT: B 778 TYR cc_start: 0.8944 (t80) cc_final: 0.8683 (t80) REVERT: B 787 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8081 (ptt) REVERT: B 815 ARG cc_start: 0.7268 (ptt90) cc_final: 0.7046 (ptt90) REVERT: B 912 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8089 (mm-40) REVERT: C 93 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8811 (pm20) REVERT: D 26 GLN cc_start: 0.8420 (tm-30) cc_final: 0.7821 (tm-30) REVERT: D 38 GLN cc_start: 0.8542 (tt0) cc_final: 0.8163 (tp40) REVERT: E 25 ASP cc_start: 0.8327 (m-30) cc_final: 0.8030 (m-30) REVERT: E 66 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8124 (pp20) REVERT: E 110 PHE cc_start: 0.8430 (t80) cc_final: 0.7793 (t80) REVERT: E 187 TYR cc_start: 0.8941 (t80) cc_final: 0.8555 (t80) REVERT: E 196 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8601 (p) REVERT: F 77 ASP cc_start: 0.8349 (p0) cc_final: 0.8070 (p0) REVERT: F 78 GLN cc_start: 0.8382 (mt0) cc_final: 0.8114 (mt0) REVERT: H 103 LYS cc_start: 0.9180 (ttpt) cc_final: 0.8734 (ttmm) REVERT: H 115 TYR cc_start: 0.8813 (m-80) cc_final: 0.8400 (m-80) REVERT: I 32 GLN cc_start: 0.8320 (mt0) cc_final: 0.7884 (mt0) REVERT: K 68 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7887 (mm-30) REVERT: K 138 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8560 (mmtm) REVERT: N 79 THR cc_start: 0.8538 (t) cc_final: 0.8256 (m) REVERT: M 16 GLN cc_start: 0.7747 (tp-100) cc_final: 0.7342 (tp-100) outliers start: 117 outliers final: 85 residues processed: 618 average time/residue: 0.4612 time to fit residues: 467.1503 Evaluate side-chains 618 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 523 time to evaluate : 4.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 947 ILE Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 138 LYS Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain N residue 37 ASN Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 101 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 246 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 78 optimal weight: 0.0770 chunk 77 optimal weight: 0.7980 chunk 253 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1108 HIS A1454 HIS B 27 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 921 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN D 17 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35332 Z= 0.165 Angle : 0.536 9.685 48057 Z= 0.277 Chirality : 0.042 0.161 5380 Planarity : 0.004 0.056 5944 Dihedral : 12.779 83.390 5375 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.64 % Allowed : 17.89 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -0.95 (0.13), residues: 4092 helix: -0.01 (0.15), residues: 1279 sheet: -1.07 (0.20), residues: 670 loop : -0.77 (0.14), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 836 HIS 0.005 0.001 HIS B 688 PHE 0.026 0.001 PHE B1044 TYR 0.024 0.001 TYR A 995 ARG 0.007 0.000 ARG E 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 573 time to evaluate : 4.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7942 (ttm-80) REVERT: A 833 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.8988 (pp) REVERT: A 1459 LYS cc_start: 0.7318 (ttmt) cc_final: 0.6973 (ttpt) REVERT: A 1474 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8492 (tt) REVERT: B 604 ILE cc_start: 0.8535 (pt) cc_final: 0.8331 (mt) REVERT: B 778 TYR cc_start: 0.8849 (t80) cc_final: 0.8459 (t80) REVERT: B 787 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8004 (ptm) REVERT: B 912 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7996 (mm-40) REVERT: B 1039 MET cc_start: 0.8353 (mtm) cc_final: 0.7909 (mtt) REVERT: D 26 GLN cc_start: 0.8414 (tm-30) cc_final: 0.7811 (tm-30) REVERT: E 25 ASP cc_start: 0.8340 (m-30) cc_final: 0.8067 (m-30) REVERT: E 187 TYR cc_start: 0.8853 (t80) cc_final: 0.8472 (t80) REVERT: F 77 ASP cc_start: 0.8309 (p0) cc_final: 0.8022 (p0) REVERT: F 134 ILE cc_start: 0.9366 (mm) cc_final: 0.9054 (mt) REVERT: F 143 PHE cc_start: 0.8911 (p90) cc_final: 0.8618 (p90) REVERT: H 103 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8701 (ttmm) REVERT: H 115 TYR cc_start: 0.8768 (m-80) cc_final: 0.8365 (m-80) REVERT: I 32 GLN cc_start: 0.8281 (mt0) cc_final: 0.7825 (mt0) REVERT: K 68 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7859 (mm-30) REVERT: K 138 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8461 (mmtm) REVERT: N 79 THR cc_start: 0.8442 (t) cc_final: 0.8239 (m) REVERT: N 134 ASP cc_start: 0.4619 (m-30) cc_final: 0.2911 (t70) REVERT: M 9 GLU cc_start: 0.6454 (tm-30) cc_final: 0.6014 (tm-30) REVERT: M 16 GLN cc_start: 0.7755 (tp-100) cc_final: 0.7412 (tp-100) REVERT: M 41 TYR cc_start: 0.7218 (m-10) cc_final: 0.6893 (m-80) outliers start: 97 outliers final: 73 residues processed: 635 average time/residue: 0.4655 time to fit residues: 484.7754 Evaluate side-chains 619 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 540 time to evaluate : 3.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 575 HIS Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 734 CYS Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 787 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 912 GLN Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 131 ASN Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 138 LYS Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 362 optimal weight: 0.0970 chunk 381 optimal weight: 0.0000 chunk 347 optimal weight: 3.9990 chunk 370 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 chunk 291 optimal weight: 0.5980 chunk 113 optimal weight: 0.0670 chunk 335 optimal weight: 9.9990 chunk 350 optimal weight: 0.0020 chunk 369 optimal weight: 0.9990 overall best weight: 0.1528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1108 HIS A1454 HIS A1592 GLN B 27 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 HIS ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN K 70 HIS L 53 HIS ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 35332 Z= 0.136 Angle : 0.530 8.771 48057 Z= 0.272 Chirality : 0.042 0.214 5380 Planarity : 0.004 0.061 5944 Dihedral : 12.679 83.814 5375 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.23 % Allowed : 18.56 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -0.72 (0.13), residues: 4092 helix: 0.22 (0.15), residues: 1276 sheet: -0.89 (0.20), residues: 660 loop : -0.69 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 836 HIS 0.005 0.001 HIS B 231 PHE 0.036 0.001 PHE A 239 TYR 0.024 0.001 TYR A 995 ARG 0.009 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 615 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7999 (ttm-80) REVERT: A 833 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9013 (pp) REVERT: A 1049 MET cc_start: 0.8676 (ttm) cc_final: 0.8459 (tpp) REVERT: A 1121 ASP cc_start: 0.7958 (t0) cc_final: 0.7756 (t70) REVERT: A 1200 MET cc_start: 0.5434 (mpp) cc_final: 0.2757 (tpt) REVERT: A 1459 LYS cc_start: 0.7174 (ttmt) cc_final: 0.6859 (ttpt) REVERT: A 1474 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8370 (tt) REVERT: A 1476 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8157 (mm) REVERT: A 1529 MET cc_start: 0.9052 (mmm) cc_final: 0.8713 (mmp) REVERT: B 650 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8944 (mt) REVERT: B 778 TYR cc_start: 0.8775 (t80) cc_final: 0.8405 (t80) REVERT: D 26 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7839 (tm-30) REVERT: D 38 GLN cc_start: 0.8499 (tt0) cc_final: 0.8238 (tp40) REVERT: D 41 GLU cc_start: 0.8443 (pt0) cc_final: 0.8201 (pt0) REVERT: E 66 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8126 (pp20) REVERT: E 187 TYR cc_start: 0.8807 (t80) cc_final: 0.8468 (t80) REVERT: G 106 LYS cc_start: 0.9025 (ttpt) cc_final: 0.8641 (ttpt) REVERT: H 103 LYS cc_start: 0.9033 (ttpt) cc_final: 0.8786 (ttmt) REVERT: H 115 TYR cc_start: 0.8714 (m-80) cc_final: 0.8280 (m-80) REVERT: K 68 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7697 (mt-10) REVERT: K 138 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8431 (mmtm) REVERT: N 134 ASP cc_start: 0.4295 (m-30) cc_final: 0.2766 (t70) REVERT: M 16 GLN cc_start: 0.7713 (tp-100) cc_final: 0.6605 (tp-100) REVERT: M 41 TYR cc_start: 0.7240 (m-10) cc_final: 0.6969 (m-80) outliers start: 82 outliers final: 57 residues processed: 665 average time/residue: 0.4605 time to fit residues: 505.5364 Evaluate side-chains 614 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 550 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1476 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 85 GLU Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain K residue 138 LYS Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 243 optimal weight: 4.9990 chunk 392 optimal weight: 20.0000 chunk 239 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 272 optimal weight: 1.9990 chunk 411 optimal weight: 1.9990 chunk 378 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1047 GLN A1108 HIS A1250 GLN A1454 HIS B 27 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN K 70 HIS ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35332 Z= 0.262 Angle : 0.578 9.822 48057 Z= 0.296 Chirality : 0.044 0.183 5380 Planarity : 0.004 0.067 5944 Dihedral : 12.748 83.803 5375 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.50 % Allowed : 19.03 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -0.72 (0.13), residues: 4092 helix: 0.23 (0.15), residues: 1287 sheet: -0.95 (0.20), residues: 659 loop : -0.68 (0.14), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 836 HIS 0.006 0.001 HIS B 231 PHE 0.027 0.002 PHE B1044 TYR 0.025 0.001 TYR A 995 ARG 0.008 0.001 ARG I 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8184 Ramachandran restraints generated. 4092 Oldfield, 0 Emsley, 4092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 546 time to evaluate : 4.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7921 (ttm-80) REVERT: A 589 MET cc_start: 0.8349 (mmm) cc_final: 0.7602 (mmm) REVERT: A 833 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.8990 (pp) REVERT: A 1459 LYS cc_start: 0.7367 (ttmt) cc_final: 0.7044 (ttpt) REVERT: A 1474 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8520 (tt) REVERT: A 1529 MET cc_start: 0.9141 (mmm) cc_final: 0.8854 (mmp) REVERT: B 650 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8951 (mt) REVERT: B 778 TYR cc_start: 0.8921 (t80) cc_final: 0.8621 (t80) REVERT: B 1039 MET cc_start: 0.8590 (mtm) cc_final: 0.7950 (mtt) REVERT: D 26 GLN cc_start: 0.8445 (tm-30) cc_final: 0.7748 (tm-30) REVERT: D 38 GLN cc_start: 0.8542 (tt0) cc_final: 0.8288 (tp40) REVERT: D 41 GLU cc_start: 0.8479 (pt0) cc_final: 0.8238 (pt0) REVERT: E 66 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8054 (pp20) REVERT: E 187 TYR cc_start: 0.8935 (t80) cc_final: 0.8623 (t80) REVERT: H 14 GLU cc_start: 0.8106 (pp20) cc_final: 0.7293 (pp20) REVERT: H 27 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8182 (mp0) REVERT: H 103 LYS cc_start: 0.9123 (ttpt) cc_final: 0.8712 (ttmm) REVERT: H 115 TYR cc_start: 0.8792 (m-80) cc_final: 0.8449 (m-80) REVERT: I 32 GLN cc_start: 0.8236 (mt0) cc_final: 0.7787 (mt0) REVERT: K 68 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7803 (mt-10) REVERT: K 138 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8409 (mmtm) REVERT: M 16 GLN cc_start: 0.7554 (tp-100) cc_final: 0.7291 (tp-100) REVERT: M 41 TYR cc_start: 0.7288 (m-10) cc_final: 0.6849 (m-10) outliers start: 92 outliers final: 70 residues processed: 609 average time/residue: 0.4570 time to fit residues: 454.4144 Evaluate side-chains 608 residues out of total 3679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 532 time to evaluate : 3.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 1272 VAL Chi-restraints excluded: chain A residue 1294 MET Chi-restraints excluded: chain A residue 1474 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 943 ILE Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1033 TYR Chi-restraints excluded: chain B residue 1074 MET Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 34 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 134 ASN Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain K residue 138 LYS Chi-restraints excluded: chain L residue 37 LYS Chi-restraints excluded: chain L residue 40 LEU Chi-restraints excluded: chain N residue 37 ASN Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain M residue 128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 260 optimal weight: 3.9990 chunk 349 optimal weight: 10.0000 chunk 100 optimal weight: 0.0980 chunk 302 optimal weight: 10.0000 chunk 48 optimal weight: 0.0980 chunk 91 optimal weight: 0.8980 chunk 328 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 336 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN A1047 GLN A1108 HIS A1250 GLN A1293 HIS A1454 HIS B 27 ASN ** B 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.123239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.094030 restraints weight = 61131.955| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.16 r_work: 0.3014 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35332 Z= 0.157 Angle : 0.552 11.328 48057 Z= 0.282 Chirality : 0.042 0.202 5380 Planarity : 0.004 0.065 5944 Dihedral : 12.727 84.198 5375 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.98 % Allowed : 19.73 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % 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: -0.62 (0.13), residues: 4092 helix: 0.32 (0.15), residues: 1286 sheet: -0.88 (0.20), residues: 665 loop : -0.63 (0.14), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 836 HIS 0.005 0.001 HIS B 688 PHE 0.024 0.001 PHE B1044 TYR 0.026 0.001 TYR A 995 ARG 0.007 0.000 ARG B1134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10024.11 seconds wall clock time: 179 minutes 11.97 seconds (10751.97 seconds total)