Starting phenix.real_space_refine on Mon Feb 19 16:00:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ay1_11934/02_2024/7ay1_11934_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ay1_11934/02_2024/7ay1_11934.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ay1_11934/02_2024/7ay1_11934_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ay1_11934/02_2024/7ay1_11934_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ay1_11934/02_2024/7ay1_11934_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ay1_11934/02_2024/7ay1_11934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ay1_11934/02_2024/7ay1_11934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ay1_11934/02_2024/7ay1_11934_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ay1_11934/02_2024/7ay1_11934_updated.pdb" } resolution = 3.7 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= -0.002 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 58 5.49 5 S 140 5.16 5 C 16003 2.51 5 N 4124 2.21 5 O 4860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 247": "OE1" <-> "OE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A GLU 428": "OE1" <-> "OE2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A ARG 522": "NH1" <-> "NH2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 787": "OE1" <-> "OE2" Residue "A GLU 837": "OE1" <-> "OE2" Residue "A GLU 910": "OE1" <-> "OE2" Residue "A ARG 954": "NH1" <-> "NH2" Residue "A GLU 1016": "OE1" <-> "OE2" Residue "A TYR 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1065": "OE1" <-> "OE2" Residue "A GLU 1131": "OE1" <-> "OE2" Residue "A GLU 1147": "OE1" <-> "OE2" Residue "A ARG 1178": "NH1" <-> "NH2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "B ARG 404": "NH1" <-> "NH2" Residue "B PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B GLU 498": "OE1" <-> "OE2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B GLU 605": "OE1" <-> "OE2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B GLU 688": "OE1" <-> "OE2" Residue "B ARG 735": "NH1" <-> "NH2" Residue "B GLU 766": "OE1" <-> "OE2" Residue "B GLU 778": "OE1" <-> "OE2" Residue "B ARG 779": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 821": "OE1" <-> "OE2" Residue "B GLU 931": "OE1" <-> "OE2" Residue "B GLU 1054": "OE1" <-> "OE2" Residue "B ARG 1064": "NH1" <-> "NH2" Residue "B GLU 1108": "OE1" <-> "OE2" Residue "B PHE 1128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1143": "OE1" <-> "OE2" Residue "B GLU 1153": "OE1" <-> "OE2" Residue "B ARG 1165": "NH1" <-> "NH2" Residue "B GLU 1191": "OE1" <-> "OE2" Residue "B GLU 1194": "OE1" <-> "OE2" Residue "B GLU 1201": "OE1" <-> "OE2" Residue "B GLU 1202": "OE1" <-> "OE2" Residue "B GLU 1241": "OE1" <-> "OE2" Residue "B GLU 1250": "OE1" <-> "OE2" Residue "B ARG 1273": "NH1" <-> "NH2" Residue "B GLU 1303": "OE1" <-> "OE2" Residue "B PHE 1305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1322": "OE1" <-> "OE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ARG 72": "NH1" <-> "NH2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "D PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D GLU 424": "OE1" <-> "OE2" Residue "D ARG 439": "NH1" <-> "NH2" Residue "D GLU 448": "OE1" <-> "OE2" Residue "D GLU 462": "OE1" <-> "OE2" Residue "D GLU 481": "OE1" <-> "OE2" Residue "D GLU 507": "OE1" <-> "OE2" Residue "D GLU 514": "OE1" <-> "OE2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D GLU 566": "OE1" <-> "OE2" Residue "D GLU 744": "OE1" <-> "OE2" Residue "D GLU 754": "OE1" <-> "OE2" Residue "D GLU 759": "OE1" <-> "OE2" Residue "D TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 26": "OE1" <-> "OE2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E ARG 139": "NH1" <-> "NH2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E ARG 193": "NH1" <-> "NH2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E GLU 472": "OE1" <-> "OE2" Residue "E ARG 476": "NH1" <-> "NH2" Residue "E GLU 598": "OE1" <-> "OE2" Residue "E GLU 636": "OE1" <-> "OE2" Residue "E GLU 637": "OE1" <-> "OE2" Residue "E GLU 640": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25186 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8215 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 33, 'TRANS': 999} Chain breaks: 9 Chain: "B" Number of atoms: 8263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8263 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 35, 'TRANS': 997} Chain breaks: 8 Chain: "C" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 607 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2742 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 327} Chain breaks: 5 Chain: "E" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4720 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 22, 'TRANS': 573} Chain breaks: 4 Chain: "S" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 319 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 87 Chain: "T" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 319 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 87 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18333 SG CYS D 440 58.673 96.698 38.120 1.00 31.98 S ATOM 18356 SG CYS D 443 60.164 96.542 35.021 1.00 36.96 S ATOM 18740 SG CYS D 506 62.366 95.952 38.023 1.00 29.69 S ATOM 18763 SG CYS D 509 61.198 99.399 37.162 1.00 28.10 S Time building chain proxies: 13.24, per 1000 atoms: 0.53 Number of scatterers: 25186 At special positions: 0 Unit cell: (124.845, 169.505, 171.535, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 140 16.00 P 58 15.00 O 4860 8.00 N 4124 7.00 C 16003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 432 " - pdb=" SG CYS B 469 " distance=2.03 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: 9.29 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 443 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 440 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 509 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 506 " Number of angles added : 6 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5922 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 118 helices and 20 sheets defined 53.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.99 Creating SS restraints... Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.696A pdb=" N MET A 180 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 205 removed outlier: 4.684A pdb=" N SER A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LYS A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 227 through 248 Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.842A pdb=" N HIS A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 292 Processing helix chain 'A' and resid 307 through 318 removed outlier: 3.898A pdb=" N THR A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ARG A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 346 removed outlier: 4.126A pdb=" N LEU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A 346 " --> pdb=" O GLN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 360 through 372 removed outlier: 3.807A pdb=" N LYS A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL A 372 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 Processing helix chain 'A' and resid 410 through 432 Proline residue: A 414 - end of helix removed outlier: 3.966A pdb=" N CYS A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 448 removed outlier: 4.003A pdb=" N LEU A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 Processing helix chain 'A' and resid 470 through 476 removed outlier: 3.549A pdb=" N SER A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 486 Processing helix chain 'A' and resid 493 through 508 Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 512 through 526 Processing helix chain 'A' and resid 532 through 545 removed outlier: 3.995A pdb=" N ALA A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.824A pdb=" N LEU A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 615 removed outlier: 4.575A pdb=" N TYR A 610 " --> pdb=" O TYR A 606 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 633 removed outlier: 4.333A pdb=" N ASN A 621 " --> pdb=" O GLN A 618 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 623 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N MET A 624 " --> pdb=" O ASN A 621 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU A 628 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 631 " --> pdb=" O LEU A 628 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 632 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 698 through 713 removed outlier: 4.096A pdb=" N ASP A 703 " --> pdb=" O TYR A 699 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 704 " --> pdb=" O GLU A 700 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 759 removed outlier: 3.787A pdb=" N LYS A 738 " --> pdb=" O SER A 734 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 743 " --> pdb=" O ASN A 739 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 744 " --> pdb=" O ASN A 740 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL A 746 " --> pdb=" O CYS A 742 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER A 759 " --> pdb=" O GLU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 788 removed outlier: 3.787A pdb=" N LEU A 781 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS A 788 " --> pdb=" O ILE A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 818 removed outlier: 3.659A pdb=" N ALA A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 833 removed outlier: 4.548A pdb=" N GLU A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER A 828 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 831 " --> pdb=" O GLU A 827 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 855 removed outlier: 3.509A pdb=" N ARG A 840 " --> pdb=" O ASN A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 887 removed outlier: 3.533A pdb=" N ASP A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP A 883 " --> pdb=" O ARG A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 921 removed outlier: 3.755A pdb=" N SER A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 932 Processing helix chain 'A' and resid 951 through 970 removed outlier: 3.718A pdb=" N SER A 965 " --> pdb=" O GLN A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 993 Processing helix chain 'A' and resid 1001 through 1014 Processing helix chain 'A' and resid 1022 through 1038 removed outlier: 4.366A pdb=" N SER A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1057 removed outlier: 3.622A pdb=" N ARG A1047 " --> pdb=" O VAL A1043 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP A1052 " --> pdb=" O ASP A1048 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A1055 " --> pdb=" O GLN A1051 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS A1056 " --> pdb=" O ASP A1052 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A1057 " --> pdb=" O ILE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1080 No H-bonds generated for 'chain 'A' and resid 1077 through 1080' Processing helix chain 'A' and resid 1084 through 1109 Processing helix chain 'A' and resid 1129 through 1149 removed outlier: 3.926A pdb=" N THR A1143 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A1144 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1186 removed outlier: 4.302A pdb=" N GLN A1185 " --> pdb=" O LEU A1181 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER A1186 " --> pdb=" O GLN A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1192 through 1204 removed outlier: 3.570A pdb=" N LEU A1197 " --> pdb=" O ASN A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1218 removed outlier: 3.596A pdb=" N TYR A1210 " --> pdb=" O THR A1206 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A1215 " --> pdb=" O SER A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1237 through 1246 Processing helix chain 'A' and resid 1248 through 1270 Processing helix chain 'A' and resid 1292 through 1295 Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 5.266A pdb=" N ALA B 225 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL B 227 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 removed outlier: 4.051A pdb=" N LEU B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER B 251 " --> pdb=" O ASP B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 269 removed outlier: 3.932A pdb=" N ASP B 268 " --> pdb=" O GLN B 264 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 358 through 373 removed outlier: 6.422A pdb=" N ALA B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N SER B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 391 Processing helix chain 'B' and resid 393 through 409 removed outlier: 3.763A pdb=" N LYS B 396 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LYS B 397 " --> pdb=" O GLN B 394 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 399 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 423 Processing helix chain 'B' and resid 425 through 444 removed outlier: 4.668A pdb=" N ASP B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N MET B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER B 434 " --> pdb=" O ASP B 430 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 464 Processing helix chain 'B' and resid 467 through 483 Processing helix chain 'B' and resid 486 through 502 Processing helix chain 'B' and resid 504 through 519 removed outlier: 3.996A pdb=" N MET B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASN B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 511 " --> pdb=" O MET B 507 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE B 513 " --> pdb=" O MET B 509 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU B 518 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP B 519 " --> pdb=" O LYS B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 539 removed outlier: 3.897A pdb=" N ARG B 530 " --> pdb=" O PRO B 526 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 531 " --> pdb=" O GLN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 547 removed outlier: 4.135A pdb=" N ALA B 547 " --> pdb=" O GLN B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 563 removed outlier: 3.877A pdb=" N LEU B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG B 560 " --> pdb=" O HIS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 585 removed outlier: 3.818A pdb=" N ILE B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 620 Processing helix chain 'B' and resid 626 through 641 removed outlier: 4.133A pdb=" N LEU B 630 " --> pdb=" O GLN B 626 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR B 631 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN B 637 " --> pdb=" O ASP B 633 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 663 Processing helix chain 'B' and resid 668 through 670 No H-bonds generated for 'chain 'B' and resid 668 through 670' Processing helix chain 'B' and resid 699 through 705 Processing helix chain 'B' and resid 727 through 744 removed outlier: 4.638A pdb=" N ALA B 731 " --> pdb=" O LEU B 728 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 777 through 799 removed outlier: 3.699A pdb=" N ASN B 798 " --> pdb=" O ARG B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 832 removed outlier: 4.342A pdb=" N GLU B 827 " --> pdb=" O GLN B 823 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS B 828 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR B 829 " --> pdb=" O ILE B 825 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 832 " --> pdb=" O LYS B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 937 removed outlier: 3.583A pdb=" N HIS B 937 " --> pdb=" O SER B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 979 removed outlier: 3.689A pdb=" N SER B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1019 removed outlier: 3.585A pdb=" N LEU B1019 " --> pdb=" O CYS B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1037 removed outlier: 4.009A pdb=" N ASN B1025 " --> pdb=" O THR B1021 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS B1026 " --> pdb=" O PRO B1022 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B1037 " --> pdb=" O TYR B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1052 through 1072 removed outlier: 3.709A pdb=" N SER B1060 " --> pdb=" O HIS B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1079 Processing helix chain 'B' and resid 1081 through 1097 removed outlier: 3.524A pdb=" N GLN B1084 " --> pdb=" O PRO B1081 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASN B1085 " --> pdb=" O GLU B1082 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B1096 " --> pdb=" O VAL B1093 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG B1097 " --> pdb=" O LEU B1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 1107 through 1123 removed outlier: 3.584A pdb=" N ASN B1120 " --> pdb=" O HIS B1116 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE B1121 " --> pdb=" O TYR B1117 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N HIS B1122 " --> pdb=" O LEU B1118 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLN B1123 " --> pdb=" O GLN B1119 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1144 removed outlier: 3.533A pdb=" N GLU B1143 " --> pdb=" O MET B1139 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS B1144 " --> pdb=" O VAL B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1164 removed outlier: 3.823A pdb=" N ALA B1156 " --> pdb=" O LYS B1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1192 removed outlier: 3.501A pdb=" N HIS B1183 " --> pdb=" O ASN B1179 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA B1184 " --> pdb=" O ASP B1180 " (cutoff:3.500A) Processing helix chain 'B' and resid 1196 through 1212 removed outlier: 3.835A pdb=" N VAL B1208 " --> pdb=" O ALA B1204 " (cutoff:3.500A) Proline residue: B1209 - end of helix Processing helix chain 'B' and resid 1231 through 1247 Processing helix chain 'B' and resid 1258 through 1282 removed outlier: 4.239A pdb=" N LEU B1281 " --> pdb=" O ILE B1277 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE B1282 " --> pdb=" O LEU B1278 " (cutoff:3.500A) Processing helix chain 'B' and resid 1288 through 1309 removed outlier: 4.041A pdb=" N ARG B1299 " --> pdb=" O LEU B1295 " (cutoff:3.500A) Processing helix chain 'B' and resid 1311 through 1317 removed outlier: 3.772A pdb=" N SER B1316 " --> pdb=" O LEU B1312 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE B1317 " --> pdb=" O LEU B1313 " (cutoff:3.500A) Processing helix chain 'B' and resid 1322 through 1347 removed outlier: 3.627A pdb=" N SER B1326 " --> pdb=" O GLU B1322 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP B1334 " --> pdb=" O THR B1330 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B1346 " --> pdb=" O CYS B1342 " (cutoff:3.500A) Processing helix chain 'B' and resid 1351 through 1377 removed outlier: 5.305A pdb=" N HIS B1356 " --> pdb=" O ARG B1352 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL B1357 " --> pdb=" O LEU B1353 " (cutoff:3.500A) Proline residue: B1358 - end of helix removed outlier: 4.219A pdb=" N LEU B1367 " --> pdb=" O THR B1363 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL B1368 " --> pdb=" O LEU B1364 " (cutoff:3.500A) Processing helix chain 'B' and resid 1381 through 1383 No H-bonds generated for 'chain 'B' and resid 1381 through 1383' Processing helix chain 'C' and resid 23 through 34 Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'D' and resid 91 through 100 removed outlier: 3.531A pdb=" N ILE D 95 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 122 removed outlier: 3.672A pdb=" N LYS D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE D 113 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 143 No H-bonds generated for 'chain 'D' and resid 141 through 143' Processing helix chain 'D' and resid 145 through 165 removed outlier: 4.152A pdb=" N GLN D 150 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 188 Processing helix chain 'D' and resid 190 through 192 No H-bonds generated for 'chain 'D' and resid 190 through 192' Processing helix chain 'D' and resid 200 through 224 Processing helix chain 'D' and resid 426 through 429 No H-bonds generated for 'chain 'D' and resid 426 through 429' Processing helix chain 'D' and resid 485 through 492 removed outlier: 3.718A pdb=" N PHE D 492 " --> pdb=" O ALA D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 743 removed outlier: 3.530A pdb=" N TYR D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 767 Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 146 through 150 Processing helix chain 'E' and resid 403 through 409 Processing helix chain 'E' and resid 462 through 470 Processing helix chain 'E' and resid 475 through 477 No H-bonds generated for 'chain 'E' and resid 475 through 477' Processing helix chain 'E' and resid 530 through 534 removed outlier: 3.520A pdb=" N SER E 533 " --> pdb=" O CYS E 530 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY E 534 " --> pdb=" O ARG E 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 530 through 534' Processing helix chain 'E' and resid 536 through 545 Processing helix chain 'E' and resid 548 through 554 removed outlier: 4.180A pdb=" N ILE E 553 " --> pdb=" O TRP E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 604 Processing helix chain 'E' and resid 633 through 638 Processing helix chain 'E' and resid 654 through 660 Processing sheet with id= A, first strand: chain 'B' and resid 681 through 683 Processing sheet with id= B, first strand: chain 'C' and resid 1 through 6 Processing sheet with id= C, first strand: chain 'C' and resid 42 through 44 removed outlier: 3.752A pdb=" N VAL C 70 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 446 through 453 removed outlier: 3.530A pdb=" N LYS D 523 " --> pdb=" O GLN D 433 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL D 435 " --> pdb=" O PHE D 521 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N PHE D 521 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ARG D 437 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N LEU D 519 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ARG D 439 " --> pdb=" O ARG D 517 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ARG D 517 " --> pdb=" O ARG D 439 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 515 " --> pdb=" O ILE D 498 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 456 through 459 Processing sheet with id= F, first strand: chain 'D' and resid 504 through 506 removed outlier: 3.510A pdb=" N CYS D 506 " --> pdb=" O HIS D 511 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS D 511 " --> pdb=" O CYS D 506 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 575 through 577 removed outlier: 3.655A pdb=" N SER D 575 " --> pdb=" O LEU D 785 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 596 through 598 removed outlier: 5.880A pdb=" N HIS D 584 " --> pdb=" O PRO D 777 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 421 through 423 removed outlier: 4.209A pdb=" N LEU E 429 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 20 " --> pdb=" O PRO E 514 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU E 519 " --> pdb=" O THR E 524 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N THR E 524 " --> pdb=" O GLU E 519 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 33 through 39 removed outlier: 6.674A pdb=" N ALA E 48 " --> pdb=" O ASN E 34 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU E 36 " --> pdb=" O PHE E 46 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE E 46 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LEU E 38 " --> pdb=" O ARG E 44 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG E 44 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA E 69 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N SER E 58 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR E 67 " --> pdb=" O SER E 58 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 78 through 84 removed outlier: 6.694A pdb=" N ALA E 93 " --> pdb=" O ASN E 79 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE E 81 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE E 91 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LEU E 83 " --> pdb=" O THR E 89 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR E 89 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN E 103 " --> pdb=" O CYS E 109 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS E 109 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 162 through 164 removed outlier: 4.219A pdb=" N SER E 162 " --> pdb=" O LEU E 143 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE E 141 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 193 through 195 Processing sheet with id= N, first strand: chain 'E' and resid 213 through 218 removed outlier: 6.642A pdb=" N GLY E 228 " --> pdb=" O LYS E 214 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU E 216 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU E 226 " --> pdb=" O LEU E 216 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU E 218 " --> pdb=" O GLN E 224 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLN E 224 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA E 246 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER E 238 " --> pdb=" O CYS E 244 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N CYS E 244 " --> pdb=" O SER E 238 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 255 through 260 removed outlier: 7.064A pdb=" N GLY E 270 " --> pdb=" O TRP E 256 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU E 258 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR E 268 " --> pdb=" O LEU E 258 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL E 260 " --> pdb=" O HIS E 266 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N HIS E 266 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY E 271 " --> pdb=" O LYS E 275 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LYS E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS E 291 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N CYS E 278 " --> pdb=" O LEU E 289 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU E 289 " --> pdb=" O CYS E 278 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASP E 280 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG E 287 " --> pdb=" O ASP E 280 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 355 through 357 removed outlier: 3.571A pdb=" N GLN E 355 " --> pdb=" O LYS E 323 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN E 322 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS E 299 " --> pdb=" O ALA E 315 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 363 through 368 removed outlier: 6.790A pdb=" N LYS E 378 " --> pdb=" O ILE E 364 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS E 366 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU E 376 " --> pdb=" O CYS E 366 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE E 368 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N HIS E 374 " --> pdb=" O ILE E 368 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY E 399 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR E 386 " --> pdb=" O ASP E 397 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ASP E 397 " --> pdb=" O TYR E 386 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 442 through 444 Processing sheet with id= S, first strand: chain 'E' and resid 564 through 567 Processing sheet with id= T, first strand: chain 'E' and resid 568 through 570 1143 hydrogen bonds defined for protein. 3189 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.40 Time building geometry restraints manager: 9.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7900 1.34 - 1.46: 5211 1.46 - 1.58: 12248 1.58 - 1.70: 114 1.70 - 1.82: 208 Bond restraints: 25681 Sorted by residual: bond pdb=" C3' DN S 16 " pdb=" C4' DN S 16 " ideal model delta sigma weight residual 1.270 1.536 -0.266 2.00e-02 2.50e+03 1.77e+02 bond pdb=" C3' DN T 36 " pdb=" C4' DN T 36 " ideal model delta sigma weight residual 1.270 1.535 -0.265 2.00e-02 2.50e+03 1.76e+02 bond pdb=" C3' DN S 8 " pdb=" C4' DN S 8 " ideal model delta sigma weight residual 1.270 1.535 -0.265 2.00e-02 2.50e+03 1.75e+02 bond pdb=" C3' DN T 34 " pdb=" C4' DN T 34 " ideal model delta sigma weight residual 1.270 1.534 -0.264 2.00e-02 2.50e+03 1.74e+02 bond pdb=" C3' DN S 23 " pdb=" C4' DN S 23 " ideal model delta sigma weight residual 1.270 1.534 -0.264 2.00e-02 2.50e+03 1.74e+02 ... (remaining 25676 not shown) Histogram of bond angle deviations from ideal: 97.46 - 104.84: 557 104.84 - 112.21: 13352 112.21 - 119.58: 8687 119.58 - 126.95: 11959 126.95 - 134.32: 270 Bond angle restraints: 34825 Sorted by residual: angle pdb=" N HIS E 73 " pdb=" CA HIS E 73 " pdb=" C HIS E 73 " ideal model delta sigma weight residual 110.80 121.58 -10.78 2.13e+00 2.20e-01 2.56e+01 angle pdb=" N GLU E 602 " pdb=" CA GLU E 602 " pdb=" C GLU E 602 " ideal model delta sigma weight residual 111.40 105.91 5.49 1.22e+00 6.72e-01 2.02e+01 angle pdb=" C GLU A1067 " pdb=" N LYS A1068 " pdb=" CA LYS A1068 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 angle pdb=" C GLU E 189 " pdb=" N LYS E 190 " pdb=" CA LYS E 190 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 angle pdb=" CA LEU E 398 " pdb=" CB LEU E 398 " pdb=" CG LEU E 398 " ideal model delta sigma weight residual 116.30 130.47 -14.17 3.50e+00 8.16e-02 1.64e+01 ... (remaining 34820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 13363 18.08 - 36.16: 1737 36.16 - 54.25: 506 54.25 - 72.33: 111 72.33 - 90.41: 35 Dihedral angle restraints: 15752 sinusoidal: 6699 harmonic: 9053 Sorted by residual: dihedral pdb=" CA LEU A 641 " pdb=" C LEU A 641 " pdb=" N LEU A 642 " pdb=" CA LEU A 642 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLN A 973 " pdb=" C GLN A 973 " pdb=" N GLU A 974 " pdb=" CA GLU A 974 " ideal model delta harmonic sigma weight residual -180.00 -157.38 -22.62 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA GLY E 522 " pdb=" C GLY E 522 " pdb=" N ARG E 523 " pdb=" CA ARG E 523 " ideal model delta harmonic sigma weight residual 180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 15749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3503 0.072 - 0.144: 499 0.144 - 0.216: 30 0.216 - 0.287: 3 0.287 - 0.359: 58 Chirality restraints: 4093 Sorted by residual: chirality pdb=" C3' DN S 18 " pdb=" C2' DN S 18 " pdb=" C4' DN S 18 " pdb=" O3' DN S 18 " both_signs ideal model delta sigma weight residual False -2.33 -2.69 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" C3' DN S 2 " pdb=" C2' DN S 2 " pdb=" C4' DN S 2 " pdb=" O3' DN S 2 " both_signs ideal model delta sigma weight residual False -2.33 -2.68 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C3' DN S 25 " pdb=" C2' DN S 25 " pdb=" C4' DN S 25 " pdb=" O3' DN S 25 " both_signs ideal model delta sigma weight residual False -2.33 -2.68 0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 4090 not shown) Planarity restraints: 4243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 75 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C THR E 75 " -0.049 2.00e-02 2.50e+03 pdb=" O THR E 75 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP E 76 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 643 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.10e+00 pdb=" N PRO A 644 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 644 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 644 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 525 " -0.040 5.00e-02 4.00e+02 6.16e-02 6.08e+00 pdb=" N PRO B 526 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 526 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 526 " -0.034 5.00e-02 4.00e+02 ... (remaining 4240 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 1 2.02 - 2.74: 2278 2.74 - 3.46: 36472 3.46 - 4.18: 53651 4.18 - 4.90: 96572 Nonbonded interactions: 188974 Sorted by model distance: nonbonded pdb=" NZ LYS B 561 " pdb=" C GLY C 76 " model vdw 1.303 3.350 nonbonded pdb=" NZ LYS B 561 " pdb=" O GLY C 76 " model vdw 2.212 2.520 nonbonded pdb=" ND2 ASN D 85 " pdb=" O GLY D 87 " model vdw 2.236 2.520 nonbonded pdb=" CE LYS B 561 " pdb=" C GLY C 76 " model vdw 2.263 3.670 nonbonded pdb=" NE2 HIS B 550 " pdb=" OG SER D 772 " model vdw 2.264 2.520 ... (remaining 188969 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.020 Extract box with map and model: 8.250 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 68.600 Find NCS groups from input model: 0.790 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: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.018 0.266 25681 Z= 1.179 Angle : 1.022 14.171 34825 Z= 0.483 Chirality : 0.062 0.359 4093 Planarity : 0.005 0.071 4243 Dihedral : 18.224 90.408 9827 Min Nonbonded Distance : 1.303 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.80 % Rotamer: Outliers : 0.04 % Allowed : 1.46 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.74 (0.15), residues: 3018 helix: 0.34 (0.13), residues: 1612 sheet: -0.46 (0.32), residues: 252 loop : -1.63 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 375 HIS 0.009 0.001 HIS E 367 PHE 0.040 0.002 PHE E 567 TYR 0.025 0.002 TYR E 386 ARG 0.011 0.001 ARG B1392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 529 time to evaluate : 3.060 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: A 216 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8660 (tp-100) REVERT: A 413 MET cc_start: 0.7983 (tpt) cc_final: 0.7758 (tpp) REVERT: A 486 ASP cc_start: 0.7976 (m-30) cc_final: 0.7767 (m-30) REVERT: A 587 ILE cc_start: 0.9388 (tt) cc_final: 0.9143 (tt) REVERT: A 624 MET cc_start: 0.7979 (tpp) cc_final: 0.7649 (mmm) REVERT: A 725 LYS cc_start: 0.7633 (pptt) cc_final: 0.7003 (tppt) REVERT: A 909 LEU cc_start: 0.8609 (tp) cc_final: 0.8332 (tp) REVERT: A 1093 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7089 (tm-30) REVERT: A 1127 ASN cc_start: 0.7455 (m-40) cc_final: 0.7019 (m-40) REVERT: B 523 ASN cc_start: 0.7673 (t0) cc_final: 0.7223 (t0) REVERT: B 782 MET cc_start: 0.8048 (ttm) cc_final: 0.7616 (tpt) REVERT: B 1216 LYS cc_start: 0.9112 (tptt) cc_final: 0.8801 (tptm) REVERT: B 1270 MET cc_start: 0.8080 (mtt) cc_final: 0.7859 (mtm) REVERT: D 172 ASP cc_start: 0.8471 (p0) cc_final: 0.7989 (p0) REVERT: E 569 LEU cc_start: 0.8538 (mm) cc_final: 0.8334 (mt) REVERT: E 603 LYS cc_start: 0.7765 (mmtm) cc_final: 0.7311 (tmtt) REVERT: E 670 LEU cc_start: 0.9022 (mt) cc_final: 0.8816 (mp) outliers start: 1 outliers final: 0 residues processed: 530 average time/residue: 0.4030 time to fit residues: 335.3930 Evaluate side-chains 307 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.9990 chunk 231 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 239 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 178 optimal weight: 0.9980 chunk 277 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN A 621 ASN ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1063 GLN B1080 GLN B1308 GLN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN D 531 HIS ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 592 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25681 Z= 0.186 Angle : 0.679 11.859 34825 Z= 0.325 Chirality : 0.043 0.209 4093 Planarity : 0.005 0.074 4243 Dihedral : 10.215 59.555 3764 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.78 % Favored : 96.16 % Rotamer: Outliers : 2.17 % Allowed : 15.64 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3018 helix: 0.82 (0.13), residues: 1619 sheet: 0.03 (0.33), residues: 250 loop : -1.46 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 102 HIS 0.004 0.001 HIS E 251 PHE 0.014 0.001 PHE A 237 TYR 0.020 0.001 TYR A 359 ARG 0.005 0.000 ARG A 932 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 358 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8724 (tp-100) REVERT: A 413 MET cc_start: 0.7993 (tpt) cc_final: 0.7758 (tpp) REVERT: A 525 MET cc_start: 0.8659 (tpp) cc_final: 0.8385 (ttp) REVERT: A 581 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7996 (tt0) REVERT: A 624 MET cc_start: 0.7881 (tpp) cc_final: 0.7586 (mpp) REVERT: A 725 LYS cc_start: 0.7481 (pptt) cc_final: 0.6811 (mmmt) REVERT: A 1093 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7138 (tm-30) REVERT: B 304 LYS cc_start: 0.8776 (tptm) cc_final: 0.8301 (tppt) REVERT: B 380 PHE cc_start: 0.7851 (t80) cc_final: 0.7514 (t80) REVERT: B 523 ASN cc_start: 0.7501 (t0) cc_final: 0.7064 (t0) REVERT: B 782 MET cc_start: 0.8025 (ttm) cc_final: 0.7526 (tpt) REVERT: B 1063 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: B 1216 LYS cc_start: 0.8816 (tptt) cc_final: 0.8615 (tptp) REVERT: C 41 GLN cc_start: 0.8691 (mp10) cc_final: 0.8471 (mp10) REVERT: C 60 ASN cc_start: 0.8520 (t0) cc_final: 0.8268 (t0) REVERT: D 110 LYS cc_start: 0.8372 (tmtt) cc_final: 0.7843 (mtmt) REVERT: D 172 ASP cc_start: 0.8492 (p0) cc_final: 0.8017 (p0) REVERT: E 204 MET cc_start: 0.8628 (ppp) cc_final: 0.7336 (ppp) REVERT: E 603 LYS cc_start: 0.8011 (mmtm) cc_final: 0.7477 (tmtt) outliers start: 61 outliers final: 32 residues processed: 391 average time/residue: 0.3375 time to fit residues: 214.6124 Evaluate side-chains 323 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 290 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1293 ILE Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1063 GLN Chi-restraints excluded: chain B residue 1080 GLN Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1308 GLN Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 590 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 76 optimal weight: 0.0040 chunk 278 optimal weight: 1.9990 chunk 300 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN ** A 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 GLN A1076 ASN B 545 ASN B 744 GLN B1063 GLN C 25 ASN C 62 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25681 Z= 0.225 Angle : 0.641 10.647 34825 Z= 0.311 Chirality : 0.042 0.192 4093 Planarity : 0.004 0.080 4243 Dihedral : 10.046 58.990 3764 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 2.99 % Allowed : 18.84 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.16), residues: 3018 helix: 1.01 (0.13), residues: 1619 sheet: 0.02 (0.33), residues: 256 loop : -1.38 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 375 HIS 0.008 0.001 HIS B1339 PHE 0.017 0.001 PHE A 237 TYR 0.026 0.001 TYR A 359 ARG 0.003 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 303 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8663 (tp-100) REVERT: A 413 MET cc_start: 0.7959 (tpt) cc_final: 0.7757 (tpp) REVERT: A 525 MET cc_start: 0.8671 (tpp) cc_final: 0.8373 (ttp) REVERT: A 588 MET cc_start: 0.7470 (tmm) cc_final: 0.7193 (tmm) REVERT: A 624 MET cc_start: 0.7970 (tpp) cc_final: 0.7631 (mpp) REVERT: A 725 LYS cc_start: 0.7536 (pptt) cc_final: 0.6902 (mmmt) REVERT: A 1093 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7507 (tm-30) REVERT: B 380 PHE cc_start: 0.7887 (t80) cc_final: 0.7650 (t80) REVERT: B 523 ASN cc_start: 0.7491 (t0) cc_final: 0.7077 (t0) REVERT: B 782 MET cc_start: 0.8025 (ttm) cc_final: 0.7538 (tpt) REVERT: B 1099 LYS cc_start: 0.8702 (mtmm) cc_final: 0.8425 (tptp) REVERT: C 41 GLN cc_start: 0.8717 (mp10) cc_final: 0.8504 (mp10) REVERT: C 60 ASN cc_start: 0.8623 (t0) cc_final: 0.8313 (t0) REVERT: D 110 LYS cc_start: 0.8392 (tmtt) cc_final: 0.8096 (mtpt) REVERT: D 172 ASP cc_start: 0.8444 (p0) cc_final: 0.7949 (p0) REVERT: D 210 ASN cc_start: 0.7691 (t0) cc_final: 0.7471 (t0) REVERT: D 502 ASP cc_start: 0.7918 (m-30) cc_final: 0.7715 (m-30) REVERT: E 603 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7456 (tmtt) outliers start: 84 outliers final: 49 residues processed: 362 average time/residue: 0.3244 time to fit residues: 195.7892 Evaluate side-chains 321 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 272 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1076 ASN Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1293 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1063 GLN Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1208 VAL Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1239 MET Chi-restraints excluded: chain B residue 1314 ASP Chi-restraints excluded: chain B residue 1316 SER Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 71 MET Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 590 MET Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.9990 chunk 209 optimal weight: 0.0970 chunk 144 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 132 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 chunk 295 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 264 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 621 ASN ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A1076 ASN B1063 GLN ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 GLN ** E 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25681 Z= 0.157 Angle : 0.614 11.186 34825 Z= 0.292 Chirality : 0.040 0.190 4093 Planarity : 0.004 0.080 4243 Dihedral : 9.785 59.668 3764 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.02 % Allowed : 21.05 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.16), residues: 3018 helix: 1.14 (0.13), residues: 1622 sheet: -0.09 (0.32), residues: 254 loop : -1.37 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 102 HIS 0.007 0.001 HIS E 251 PHE 0.030 0.001 PHE B 380 TYR 0.027 0.001 TYR A 359 ARG 0.004 0.000 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 321 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8595 (tp-100) REVERT: A 525 MET cc_start: 0.8632 (tpp) cc_final: 0.8361 (ttp) REVERT: A 588 MET cc_start: 0.7376 (tmm) cc_final: 0.7171 (tmm) REVERT: A 624 MET cc_start: 0.7938 (tpp) cc_final: 0.7633 (mpp) REVERT: A 725 LYS cc_start: 0.7544 (pptt) cc_final: 0.6908 (mmmt) REVERT: A 1093 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7111 (tm-30) REVERT: B 523 ASN cc_start: 0.7533 (t0) cc_final: 0.7082 (t0) REVERT: B 782 MET cc_start: 0.8051 (ttm) cc_final: 0.7560 (tpt) REVERT: C 60 ASN cc_start: 0.8651 (t0) cc_final: 0.8305 (t0) REVERT: D 172 ASP cc_start: 0.8431 (p0) cc_final: 0.7933 (p0) REVERT: D 502 ASP cc_start: 0.7816 (m-30) cc_final: 0.7558 (m-30) REVERT: E 603 LYS cc_start: 0.8166 (mmtm) cc_final: 0.7514 (tmtt) outliers start: 85 outliers final: 49 residues processed: 383 average time/residue: 0.3178 time to fit residues: 202.7197 Evaluate side-chains 331 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 282 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1293 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1208 VAL Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1274 ASP Chi-restraints excluded: chain B residue 1314 ASP Chi-restraints excluded: chain B residue 1316 SER Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 25 ASN Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 590 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 220 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 252 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 151 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN B1063 GLN ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25681 Z= 0.257 Angle : 0.641 10.843 34825 Z= 0.311 Chirality : 0.042 0.185 4093 Planarity : 0.004 0.085 4243 Dihedral : 9.667 59.764 3764 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.74 % Favored : 95.23 % Rotamer: Outliers : 3.66 % Allowed : 22.36 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.11 (0.16), residues: 3018 helix: 1.11 (0.13), residues: 1628 sheet: -0.23 (0.32), residues: 261 loop : -1.37 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 375 HIS 0.007 0.001 HIS B1339 PHE 0.015 0.001 PHE A 237 TYR 0.033 0.001 TYR A 359 ARG 0.003 0.000 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 281 time to evaluate : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8627 (tp-100) REVERT: A 525 MET cc_start: 0.8643 (tpp) cc_final: 0.8417 (ttp) REVERT: A 588 MET cc_start: 0.7567 (tmm) cc_final: 0.7301 (tmm) REVERT: A 591 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8845 (mp) REVERT: A 725 LYS cc_start: 0.7598 (pptt) cc_final: 0.6929 (mmmt) REVERT: A 978 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7635 (p0) REVERT: A 1093 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7528 (tm-30) REVERT: B 304 LYS cc_start: 0.8893 (tptm) cc_final: 0.8381 (tppt) REVERT: B 523 ASN cc_start: 0.7545 (t0) cc_final: 0.7081 (t0) REVERT: B 782 MET cc_start: 0.8050 (ttm) cc_final: 0.7561 (tpt) REVERT: C 60 ASN cc_start: 0.8723 (t0) cc_final: 0.8404 (t0) REVERT: D 95 ILE cc_start: 0.9590 (mm) cc_final: 0.9300 (mt) REVERT: D 172 ASP cc_start: 0.8451 (p0) cc_final: 0.7889 (p0) outliers start: 103 outliers final: 70 residues processed: 355 average time/residue: 0.3166 time to fit residues: 187.2109 Evaluate side-chains 342 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 270 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1203 SER Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1208 VAL Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1274 ASP Chi-restraints excluded: chain B residue 1279 ILE Chi-restraints excluded: chain B residue 1294 CYS Chi-restraints excluded: chain B residue 1314 ASP Chi-restraints excluded: chain B residue 1316 SER Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 567 PHE Chi-restraints excluded: chain E residue 590 MET Chi-restraints excluded: chain E residue 654 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 296 optimal weight: 6.9990 chunk 245 optimal weight: 0.0060 chunk 137 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 155 optimal weight: 7.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25681 Z= 0.173 Angle : 0.609 10.345 34825 Z= 0.291 Chirality : 0.040 0.185 4093 Planarity : 0.004 0.087 4243 Dihedral : 9.480 59.826 3764 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.48 % Allowed : 23.85 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.16), residues: 3018 helix: 1.24 (0.13), residues: 1626 sheet: -0.25 (0.32), residues: 261 loop : -1.34 (0.18), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 651 HIS 0.006 0.001 HIS B1339 PHE 0.013 0.001 PHE A 237 TYR 0.024 0.001 TYR A 359 ARG 0.004 0.000 ARG B1097 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 302 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8616 (tp-100) REVERT: A 218 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8879 (mp) REVERT: A 525 MET cc_start: 0.8584 (tpp) cc_final: 0.8369 (ttp) REVERT: A 588 MET cc_start: 0.7522 (tmm) cc_final: 0.7279 (tmm) REVERT: A 591 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8770 (mp) REVERT: A 725 LYS cc_start: 0.7570 (pptt) cc_final: 0.6988 (mmmt) REVERT: A 978 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7519 (p0) REVERT: A 1093 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7469 (tm-30) REVERT: B 523 ASN cc_start: 0.7523 (t0) cc_final: 0.7104 (t0) REVERT: B 782 MET cc_start: 0.8017 (ttm) cc_final: 0.7538 (tpt) REVERT: C 60 ASN cc_start: 0.8690 (t0) cc_final: 0.8376 (t0) REVERT: D 172 ASP cc_start: 0.8411 (p0) cc_final: 0.7846 (p0) outliers start: 98 outliers final: 65 residues processed: 377 average time/residue: 0.3083 time to fit residues: 195.4059 Evaluate side-chains 349 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 281 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 382 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1139 MET Chi-restraints excluded: chain B residue 1208 VAL Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1274 ASP Chi-restraints excluded: chain B residue 1279 ILE Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 774 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 590 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 167 optimal weight: 7.9990 chunk 249 optimal weight: 0.0970 chunk 165 optimal weight: 0.0870 chunk 294 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 179 optimal weight: 0.1980 chunk 136 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 ASN ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1032 ASN ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 HIS E 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25681 Z= 0.155 Angle : 0.604 11.667 34825 Z= 0.287 Chirality : 0.040 0.184 4093 Planarity : 0.004 0.089 4243 Dihedral : 9.256 59.950 3764 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.55 % Allowed : 24.07 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.36 (0.16), residues: 3018 helix: 1.33 (0.13), residues: 1622 sheet: -0.20 (0.32), residues: 262 loop : -1.26 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 651 HIS 0.005 0.001 HIS B1339 PHE 0.017 0.001 PHE A1287 TYR 0.023 0.001 TYR A 215 ARG 0.007 0.000 ARG A1285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 304 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8591 (tp-100) REVERT: A 588 MET cc_start: 0.7511 (tmm) cc_final: 0.7229 (tmm) REVERT: A 591 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8732 (mp) REVERT: A 725 LYS cc_start: 0.7573 (pptt) cc_final: 0.6995 (mmmt) REVERT: A 1029 MET cc_start: 0.8659 (tpp) cc_final: 0.8431 (mmp) REVERT: A 1093 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 1273 VAL cc_start: 0.6479 (OUTLIER) cc_final: 0.6243 (p) REVERT: B 523 ASN cc_start: 0.7365 (t0) cc_final: 0.7033 (t0) REVERT: B 782 MET cc_start: 0.8054 (ttm) cc_final: 0.7548 (tpt) REVERT: B 1020 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8591 (tt) REVERT: C 60 ASN cc_start: 0.8706 (t0) cc_final: 0.8400 (t0) REVERT: D 172 ASP cc_start: 0.8478 (p0) cc_final: 0.7950 (p0) REVERT: E 81 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8900 (mt) REVERT: E 283 ASN cc_start: 0.6138 (OUTLIER) cc_final: 0.5904 (p0) outliers start: 100 outliers final: 68 residues processed: 381 average time/residue: 0.3261 time to fit residues: 206.4177 Evaluate side-chains 349 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 276 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1139 MET Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1239 MET Chi-restraints excluded: chain B residue 1274 ASP Chi-restraints excluded: chain B residue 1294 CYS Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 774 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 567 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 176 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 187 optimal weight: 0.0970 chunk 200 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 231 optimal weight: 2.9990 chunk 268 optimal weight: 7.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1070 ASN ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25681 Z= 0.176 Angle : 0.615 14.713 34825 Z= 0.292 Chirality : 0.040 0.184 4093 Planarity : 0.004 0.092 4243 Dihedral : 9.123 59.935 3764 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.38 % Allowed : 24.28 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.40 (0.16), residues: 3018 helix: 1.38 (0.13), residues: 1623 sheet: -0.21 (0.32), residues: 262 loop : -1.26 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 651 HIS 0.005 0.001 HIS B1339 PHE 0.016 0.001 PHE B1078 TYR 0.022 0.001 TYR A 215 ARG 0.008 0.000 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 281 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 588 MET cc_start: 0.7561 (tmm) cc_final: 0.7297 (tmm) REVERT: A 591 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8690 (mp) REVERT: A 725 LYS cc_start: 0.7558 (pptt) cc_final: 0.6970 (mmmt) REVERT: A 1093 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7511 (tm-30) REVERT: A 1273 VAL cc_start: 0.6493 (OUTLIER) cc_final: 0.6266 (p) REVERT: B 523 ASN cc_start: 0.7497 (t0) cc_final: 0.7131 (t0) REVERT: B 782 MET cc_start: 0.8086 (ttm) cc_final: 0.7545 (tpt) REVERT: C 60 ASN cc_start: 0.8735 (t0) cc_final: 0.8430 (t0) REVERT: D 172 ASP cc_start: 0.8472 (p0) cc_final: 0.7917 (p0) REVERT: E 81 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8883 (mt) REVERT: E 283 ASN cc_start: 0.6257 (OUTLIER) cc_final: 0.6008 (p0) outliers start: 95 outliers final: 73 residues processed: 353 average time/residue: 0.3185 time to fit residues: 188.8549 Evaluate side-chains 349 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 272 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 734 SER Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1070 ASN Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1203 SER Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 824 ILE Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1139 MET Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1239 MET Chi-restraints excluded: chain B residue 1274 ASP Chi-restraints excluded: chain B residue 1279 ILE Chi-restraints excluded: chain B residue 1294 CYS Chi-restraints excluded: chain B residue 1316 SER Chi-restraints excluded: chain B residue 1328 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 774 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 652 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 2.9990 chunk 257 optimal weight: 0.1980 chunk 274 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 HIS ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25681 Z= 0.226 Angle : 0.651 13.553 34825 Z= 0.308 Chirality : 0.041 0.179 4093 Planarity : 0.004 0.095 4243 Dihedral : 9.053 59.362 3764 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 3.38 % Allowed : 24.46 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.16), residues: 3018 helix: 1.32 (0.13), residues: 1632 sheet: -0.19 (0.33), residues: 254 loop : -1.30 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 651 HIS 0.007 0.001 HIS A1071 PHE 0.018 0.001 PHE B 800 TYR 0.022 0.001 TYR A 359 ARG 0.009 0.000 ARG A 767 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 276 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.8911 (pmm) cc_final: 0.8621 (pmm) REVERT: A 218 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8759 (mp) REVERT: A 588 MET cc_start: 0.7576 (tmm) cc_final: 0.7334 (tmm) REVERT: A 591 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8751 (mp) REVERT: A 725 LYS cc_start: 0.7645 (pptt) cc_final: 0.7054 (mmmt) REVERT: A 978 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7594 (p0) REVERT: A 1093 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7490 (tm-30) REVERT: A 1273 VAL cc_start: 0.6543 (OUTLIER) cc_final: 0.6314 (p) REVERT: B 246 LEU cc_start: 0.8718 (mm) cc_final: 0.8506 (mt) REVERT: B 523 ASN cc_start: 0.7551 (t0) cc_final: 0.7180 (t0) REVERT: B 782 MET cc_start: 0.8066 (ttm) cc_final: 0.7561 (tpt) REVERT: C 60 ASN cc_start: 0.8747 (t0) cc_final: 0.8451 (t0) REVERT: D 172 ASP cc_start: 0.8500 (p0) cc_final: 0.7973 (p0) REVERT: E 81 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8870 (mt) REVERT: E 283 ASN cc_start: 0.6410 (OUTLIER) cc_final: 0.6169 (p0) outliers start: 95 outliers final: 74 residues processed: 345 average time/residue: 0.3134 time to fit residues: 180.8412 Evaluate side-chains 347 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 267 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 863 ASP Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1151 THR Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1203 SER Chi-restraints excluded: chain A residue 1273 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 556 HIS Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 559 ILE Chi-restraints excluded: chain B residue 697 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1094 LEU Chi-restraints excluded: chain B residue 1139 MET Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1239 MET Chi-restraints excluded: chain B residue 1274 ASP Chi-restraints excluded: chain B residue 1279 ILE Chi-restraints excluded: chain B residue 1294 CYS Chi-restraints excluded: chain B residue 1316 SER Chi-restraints excluded: chain B residue 1328 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 774 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 652 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 202 optimal weight: 3.9990 chunk 304 optimal weight: 0.9980 chunk 280 optimal weight: 3.9990 chunk 242 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 187 optimal weight: 0.2980 chunk 148 optimal weight: 0.3980 chunk 192 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25681 Z= 0.157 Angle : 0.632 13.040 34825 Z= 0.296 Chirality : 0.040 0.182 4093 Planarity : 0.004 0.094 4243 Dihedral : 8.923 59.176 3764 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.77 % Allowed : 25.38 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.16), residues: 3018 helix: 1.45 (0.13), residues: 1619 sheet: -0.13 (0.33), residues: 254 loop : -1.26 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 651 HIS 0.006 0.001 HIS B 556 PHE 0.017 0.001 PHE B 800 TYR 0.024 0.001 TYR A 215 ARG 0.007 0.000 ARG A 767 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6036 Ramachandran restraints generated. 3018 Oldfield, 0 Emsley, 3018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 288 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8611 (mp) REVERT: A 588 MET cc_start: 0.7488 (tmm) cc_final: 0.7258 (tmm) REVERT: A 591 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8626 (mp) REVERT: A 725 LYS cc_start: 0.7610 (pptt) cc_final: 0.6974 (mmmt) REVERT: A 1029 MET cc_start: 0.8660 (tpp) cc_final: 0.8418 (mmp) REVERT: A 1093 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7477 (tm-30) REVERT: B 523 ASN cc_start: 0.7497 (t0) cc_final: 0.7227 (t0) REVERT: B 782 MET cc_start: 0.8097 (ttm) cc_final: 0.7544 (tpt) REVERT: B 1374 MET cc_start: 0.8541 (ttp) cc_final: 0.8312 (tmm) REVERT: C 60 ASN cc_start: 0.8730 (t0) cc_final: 0.8455 (t0) REVERT: D 172 ASP cc_start: 0.8483 (p0) cc_final: 0.7950 (p0) REVERT: E 81 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8844 (mt) REVERT: E 283 ASN cc_start: 0.6200 (OUTLIER) cc_final: 0.5932 (p0) outliers start: 78 outliers final: 64 residues processed: 347 average time/residue: 0.3142 time to fit residues: 182.3033 Evaluate side-chains 339 residues out of total 2813 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 271 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain A residue 609 PHE Chi-restraints excluded: chain A residue 747 MET Chi-restraints excluded: chain A residue 766 ASN Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 978 ASN Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1025 CYS Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1183 VAL Chi-restraints excluded: chain A residue 1279 MET Chi-restraints excluded: chain A residue 1294 LEU Chi-restraints excluded: chain B residue 206 ASN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 1021 THR Chi-restraints excluded: chain B residue 1190 LEU Chi-restraints excluded: chain B residue 1217 ASP Chi-restraints excluded: chain B residue 1239 MET Chi-restraints excluded: chain B residue 1274 ASP Chi-restraints excluded: chain B residue 1279 ILE Chi-restraints excluded: chain B residue 1316 SER Chi-restraints excluded: chain B residue 1328 LEU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 205 GLN Chi-restraints excluded: chain D residue 215 CYS Chi-restraints excluded: chain D residue 575 SER Chi-restraints excluded: chain D residue 774 THR Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 102 TRP Chi-restraints excluded: chain E residue 118 ASP Chi-restraints excluded: chain E residue 173 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 283 ASN Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 668 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 0.0980 chunk 243 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 249 optimal weight: 0.0060 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 213 optimal weight: 1.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.131380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101306 restraints weight = 49795.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104308 restraints weight = 25406.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.106274 restraints weight = 16452.265| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 25681 Z= 0.152 Angle : 0.635 12.959 34825 Z= 0.296 Chirality : 0.040 0.184 4093 Planarity : 0.004 0.094 4243 Dihedral : 8.756 59.924 3764 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.60 % Allowed : 25.70 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.16), residues: 3018 helix: 1.50 (0.13), residues: 1623 sheet: -0.11 (0.32), residues: 263 loop : -1.19 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 651 HIS 0.005 0.001 HIS B1339 PHE 0.014 0.001 PHE B 800 TYR 0.023 0.001 TYR A 215 ARG 0.008 0.000 ARG A 767 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4924.17 seconds wall clock time: 90 minutes 57.95 seconds (5457.95 seconds total)