Starting phenix.real_space_refine on Thu Jan 18 19:03:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0f_15779/01_2024/8b0f_15779_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0f_15779/01_2024/8b0f_15779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0f_15779/01_2024/8b0f_15779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0f_15779/01_2024/8b0f_15779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0f_15779/01_2024/8b0f_15779_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0f_15779/01_2024/8b0f_15779_trim.pdb" } resolution = 3.0 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= 0.004 sd= 0.126 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 Ca 2 9.91 5 S 211 5.16 5 C 19420 2.51 5 N 5319 2.21 5 O 5984 1.98 5 H 29718 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 824": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 331": "OD1" <-> "OD2" Residue "B TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 711": "OE1" <-> "OE2" Residue "E PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 60654 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 19692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1246, 19692 Classifications: {'peptide': 1246} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1187} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 11244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 735, 11244 Classifications: {'peptide': 735} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 697} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 10118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 10118 Classifications: {'peptide': 670} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 632} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 7842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 7842 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 23, 'TRANS': 477} Chain breaks: 2 Chain: "E" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 7866 Classifications: {'peptide': 513} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 497} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 2602 Classifications: {'peptide': 168} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 163} Chain: "G" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1193 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 22.22, per 1000 atoms: 0.37 Number of scatterers: 60654 At special positions: 0 Unit cell: (124.126, 169.795, 261.133, 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) Ca 2 19.99 S 211 16.00 O 5984 8.00 N 5319 7.00 C 19420 6.00 H 29718 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=80, symmetry=0 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 810 " distance=2.04 Simple disulfide: pdb=" SG CYS A 634 " - pdb=" SG CYS A 669 " distance=2.02 Simple disulfide: pdb=" SG CYS A 856 " - pdb=" SG CYS A 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A1101 " - pdb=" SG CYS A1159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 73 " distance=2.03 Simple disulfide: pdb=" SG CYS B 39 " - pdb=" SG CYS B 78 " distance=2.04 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 146 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 158 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 420 " distance=2.05 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 623 " distance=2.03 Simple disulfide: pdb=" SG CYS B 521 " - pdb=" SG CYS B 570 " distance=2.04 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 539 " distance=2.03 Simple disulfide: pdb=" SG CYS B 526 " - pdb=" SG CYS B 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 552 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 611 " distance=2.03 Simple disulfide: pdb=" SG CYS B 589 " - pdb=" SG CYS B 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 686 " distance=2.03 Simple disulfide: pdb=" SG CYS B 672 " - pdb=" SG CYS B 699 " distance=2.03 Simple disulfide: pdb=" SG CYS B 704 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 732 " - pdb=" SG CYS B 761 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 63 " distance=2.03 Simple disulfide: pdb=" SG CYS C 39 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 79 " distance=2.04 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 103 " - pdb=" SG CYS C 119 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 337 " - pdb=" SG CYS C 353 " distance=2.04 Simple disulfide: pdb=" SG CYS C 433 " - pdb=" SG CYS C 560 " distance=2.03 Simple disulfide: pdb=" SG CYS C 455 " - pdb=" SG CYS C 505 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 460 " - pdb=" SG CYS C 475 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 512 " - pdb=" SG CYS C 545 " distance=2.04 Simple disulfide: pdb=" SG CYS C 523 " - pdb=" SG CYS C 535 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 613 " distance=2.03 Simple disulfide: pdb=" SG CYS C 599 " - pdb=" SG CYS C 626 " distance=2.03 Simple disulfide: pdb=" SG CYS C 631 " - pdb=" SG CYS C 673 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 688 " distance=2.03 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 46 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 56 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 79 " distance=2.03 Simple disulfide: pdb=" SG CYS D 73 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 146 " distance=2.04 Simple disulfide: pdb=" SG CYS D 324 " - pdb=" SG CYS D 349 " distance=2.03 Simple disulfide: pdb=" SG CYS D 449 " - pdb=" SG CYS D 496 " distance=2.03 Simple disulfide: pdb=" SG CYS D 451 " - pdb=" SG CYS D 467 " distance=2.03 Simple disulfide: pdb=" SG CYS D 454 " - pdb=" SG CYS D 469 " distance=2.02 Simple disulfide: pdb=" SG CYS D 471 " - pdb=" SG CYS D 480 " distance=2.03 Simple disulfide: pdb=" SG CYS D 503 " - pdb=" SG CYS D 536 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 44 " distance=2.03 Simple disulfide: pdb=" SG CYS E 20 " - pdb=" SG CYS E 54 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 60 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 78 " distance=2.03 Simple disulfide: pdb=" SG CYS E 72 " - pdb=" SG CYS E 91 " distance=2.03 Simple disulfide: pdb=" SG CYS E 85 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 164 " - pdb=" SG CYS F 40 " distance=2.03 Simple disulfide: pdb=" SG CYS E 345 " - pdb=" SG CYS E 369 " distance=2.03 Simple disulfide: pdb=" SG CYS E 467 " - pdb=" SG CYS E 514 " distance=2.03 Simple disulfide: pdb=" SG CYS E 469 " - pdb=" SG CYS E 485 " distance=2.03 Simple disulfide: pdb=" SG CYS E 472 " - pdb=" SG CYS E 487 " distance=2.04 Simple disulfide: pdb=" SG CYS E 489 " - pdb=" SG CYS E 498 " distance=2.03 Simple disulfide: pdb=" SG CYS E 521 " - pdb=" SG CYS E 554 " distance=2.03 Simple disulfide: pdb=" SG CYS E 532 " - pdb=" SG CYS E 544 " distance=2.03 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 168 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 26 " distance=2.03 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 13 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 39 " distance=2.03 Simple disulfide: pdb=" SG CYS G 45 " - pdb=" SG CYS G 63 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 69 " 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 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG E2001 " - " ASN E 407 " " NAG H 1 " - " ASN A 911 " " NAG I 1 " - " ASN B 324 " " NAG J 1 " - " ASN D 189 " Time building additional restraints: 39.27 Conformation dependent library (CDL) restraints added in 5.0 seconds 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7258 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 56 sheets defined 18.0% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.04 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 239 through 244 removed outlier: 4.439A pdb=" N LYS A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 622 through 628 Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 641 through 649 Processing helix chain 'A' and resid 993 through 995 No H-bonds generated for 'chain 'A' and resid 993 through 995' Processing helix chain 'A' and resid 996 through 1001 Processing helix chain 'A' and resid 1009 through 1027 Proline residue: A1017 - end of helix removed outlier: 3.722A pdb=" N TYR A1020 " --> pdb=" O VAL A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1032 removed outlier: 3.794A pdb=" N TRP A1031 " --> pdb=" O GLY A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1059 removed outlier: 3.671A pdb=" N TYR A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1091 removed outlier: 4.040A pdb=" N LYS A1091 " --> pdb=" O GLY A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1112 removed outlier: 3.920A pdb=" N ILE A1100 " --> pdb=" O ASN A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1156 Processing helix chain 'A' and resid 1157 through 1159 No H-bonds generated for 'chain 'A' and resid 1157 through 1159' Processing helix chain 'A' and resid 1161 through 1180 removed outlier: 4.472A pdb=" N LEU A1180 " --> pdb=" O LEU A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1198 Processing helix chain 'A' and resid 1202 through 1216 removed outlier: 3.673A pdb=" N ARG A1214 " --> pdb=" O SER A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1262 Processing helix chain 'A' and resid 1263 through 1275 Proline residue: A1269 - end of helix Processing helix chain 'A' and resid 1276 through 1281 Processing helix chain 'A' and resid 1286 through 1308 removed outlier: 4.219A pdb=" N THR A1290 " --> pdb=" O SER A1286 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.858A pdb=" N ILE B 357 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 358 " --> pdb=" O TYR B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 465 through 479 Processing helix chain 'B' and resid 491 through 494 Processing helix chain 'B' and resid 499 through 519 Processing helix chain 'B' and resid 520 through 523 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 288 through 300 removed outlier: 3.590A pdb=" N TYR C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 390 Processing helix chain 'C' and resid 399 through 410 Processing helix chain 'C' and resid 425 through 428 Processing helix chain 'C' and resid 433 through 452 removed outlier: 3.609A pdb=" N LEU C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 547 through 557 removed outlier: 4.192A pdb=" N GLU C 551 " --> pdb=" O ASP C 547 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS C 552 " --> pdb=" O GLU C 548 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ARG C 554 " --> pdb=" O LEU C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 561 removed outlier: 3.558A pdb=" N PHE C 561 " --> pdb=" O PRO C 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 558 through 561' Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.512A pdb=" N LEU D 85 " --> pdb=" O ARG D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.503A pdb=" N TYR D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 385 Processing helix chain 'D' and resid 391 through 405 removed outlier: 3.520A pdb=" N GLN D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 420 Processing helix chain 'D' and resid 427 through 447 removed outlier: 3.526A pdb=" N LYS D 444 " --> pdb=" O GLU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 451 Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'E' and resid 281 through 290 Processing helix chain 'E' and resid 296 through 307 Processing helix chain 'E' and resid 397 through 407 Processing helix chain 'E' and resid 409 through 423 removed outlier: 4.118A pdb=" N TYR E 422 " --> pdb=" O ARG E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 438 Processing helix chain 'E' and resid 446 through 464 removed outlier: 4.061A pdb=" N MET E 462 " --> pdb=" O ASP E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 470 removed outlier: 3.526A pdb=" N GLY E 470 " --> pdb=" O CYS E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 541 removed outlier: 4.183A pdb=" N GLY E 540 " --> pdb=" O PRO E 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 28 Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.749A pdb=" N GLN F 44 " --> pdb=" O CYS F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 152 Processing helix chain 'F' and resid 155 through 157 No H-bonds generated for 'chain 'F' and resid 155 through 157' Processing helix chain 'G' and resid 46 through 55 Processing helix chain 'G' and resid 71 through 75 removed outlier: 3.950A pdb=" N LEU G 75 " --> pdb=" O ASN G 72 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 86 removed outlier: 8.706A pdb=" N ASN A 38 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.410A pdb=" N PHE A 31 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER A 58 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N SER A 65 " --> pdb=" O SER A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 130 Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 135 removed outlier: 3.769A pdb=" N ASP A 172 " --> pdb=" O PHE A 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 233 removed outlier: 3.796A pdb=" N ARG A 253 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 249 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 237 through 238 removed outlier: 3.573A pdb=" N ILE A 325 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY A 344 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LEU A 323 " --> pdb=" O GLY A 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA9, first strand: chain 'A' and resid 362 through 363 removed outlier: 8.099A pdb=" N THR A 429 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ALA A 392 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP A 405 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N THR A 394 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASP A 403 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP A 396 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR A 401 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.438A pdb=" N ILE A 485 " --> pdb=" O ASP A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 508 through 516 removed outlier: 5.494A pdb=" N ILE A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER A 505 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N HIS A 498 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE A 545 " --> pdb=" O HIS A 498 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 572 through 575 removed outlier: 5.002A pdb=" N ARG A 782 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET A 596 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A 780 " --> pdb=" O MET A 596 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER A 598 " --> pdb=" O HIS A 778 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N HIS A 778 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 600 " --> pdb=" O GLU A 776 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU A 776 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU A 602 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU A 774 " --> pdb=" O LEU A 602 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA A 604 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER A 772 " --> pdb=" O ALA A 604 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 772 through 789 current: chain 'A' and resid 808 through 811 Processing sheet with id=AB4, first strand: chain 'A' and resid 823 through 827 Processing sheet with id=AB5, first strand: chain 'A' and resid 833 through 834 Processing sheet with id=AB6, first strand: chain 'A' and resid 934 through 944 Processing sheet with id=AB7, first strand: chain 'A' and resid 956 through 959 removed outlier: 5.797A pdb=" N TYR A1317 " --> pdb=" O ALA A1322 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ALA A1322 " --> pdb=" O TYR A1317 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1217 through 1219 removed outlier: 3.650A pdb=" N TYR A1225 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 47 Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 84 removed outlier: 6.387A pdb=" N LEU B 83 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 99 through 103 Processing sheet with id=AC3, first strand: chain 'B' and resid 144 through 145 Processing sheet with id=AC4, first strand: chain 'B' and resid 185 through 186 removed outlier: 6.829A pdb=" N ASN B 185 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 195 through 197 removed outlier: 4.179A pdb=" N GLY B 196 " --> pdb=" O ARG B 205 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 236 through 240 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 236 through 240 current: chain 'B' and resid 286 through 327 removed outlier: 6.812A pdb=" N LEU B 371 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN B 324 " --> pdb=" O GLY B 369 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLY B 369 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR B 326 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N THR B 367 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR B 421 " --> pdb=" O HIS B 398 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 400 " --> pdb=" O ARG B 419 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 413 through 445 current: chain 'C' and resid 151 through 154 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 151 through 154 current: chain 'C' and resid 225 through 263 removed outlier: 6.751A pdb=" N LEU C 309 " --> pdb=" O GLU C 258 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA C 260 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLY C 307 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE C 262 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN C 305 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 316 " --> pdb=" O GLU C 374 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 348 through 378 current: chain 'D' and resid 217 through 252 removed outlier: 6.921A pdb=" N LEU D 296 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N HIS D 249 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA D 294 " --> pdb=" O HIS D 249 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS D 251 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N THR D 292 " --> pdb=" O LYS D 251 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 347 through 360 current: chain 'E' and resid 132 through 136 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 132 through 136 current: chain 'E' and resid 240 through 273 removed outlier: 6.569A pdb=" N MET E 317 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N HIS E 270 " --> pdb=" O GLY E 315 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLY E 315 " --> pdb=" O HIS E 270 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LYS E 272 " --> pdb=" O THR E 313 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR E 313 " --> pdb=" O LYS E 272 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 370 through 394 current: chain 'G' and resid 34 through 38 Processing sheet with id=AC7, first strand: chain 'B' and resid 531 through 535 Processing sheet with id=AC8, first strand: chain 'B' and resid 547 through 548 Processing sheet with id=AC9, first strand: chain 'B' and resid 582 through 586 Processing sheet with id=AD1, first strand: chain 'B' and resid 644 through 645 Processing sheet with id=AD2, first strand: chain 'B' and resid 653 through 655 Processing sheet with id=AD3, first strand: chain 'B' and resid 676 through 680 Processing sheet with id=AD4, first strand: chain 'B' and resid 703 through 705 Processing sheet with id=AD5, first strand: chain 'B' and resid 727 through 729 Processing sheet with id=AD6, first strand: chain 'C' and resid 29 through 33 removed outlier: 6.638A pdb=" N GLN C 29 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N SER C 51 " --> pdb=" O ASP C 31 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR C 33 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG C 49 " --> pdb=" O TYR C 33 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 56 through 57 removed outlier: 7.060A pdb=" N GLY C 56 " --> pdb=" O CYS C 473 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N CYS C 475 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 465 " --> pdb=" O HIS C 476 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 89 through 90 Processing sheet with id=AD9, first strand: chain 'C' and resid 167 through 170 Processing sheet with id=AE1, first strand: chain 'C' and resid 481 through 482 Processing sheet with id=AE2, first strand: chain 'C' and resid 516 through 520 Processing sheet with id=AE3, first strand: chain 'C' and resid 580 through 582 Processing sheet with id=AE4, first strand: chain 'C' and resid 603 through 607 Processing sheet with id=AE5, first strand: chain 'C' and resid 641 through 642 removed outlier: 5.097A pdb=" N CYS C 673 " --> pdb=" O SER C 680 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER C 680 " --> pdb=" O CYS C 673 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AE7, first strand: chain 'D' and resid 28 through 32 Processing sheet with id=AE8, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AE9, first strand: chain 'D' and resid 123 through 126 removed outlier: 4.288A pdb=" N GLY D 124 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 148 through 151 Processing sheet with id=AF2, first strand: chain 'D' and resid 459 through 462 Processing sheet with id=AF3, first strand: chain 'D' and resid 506 through 509 Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 11 Processing sheet with id=AF5, first strand: chain 'E' and resid 26 through 30 Processing sheet with id=AF6, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AF7, first strand: chain 'E' and resid 149 through 151 Processing sheet with id=AF8, first strand: chain 'E' and resid 157 through 161 removed outlier: 3.698A pdb=" N GLU E 157 " --> pdb=" O GLY E 170 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 477 through 480 Processing sheet with id=AG1, first strand: chain 'E' and resid 525 through 529 Processing sheet with id=AG2, first strand: chain 'F' and resid 31 through 38 removed outlier: 3.513A pdb=" N ALA F 63 " --> pdb=" O GLN F 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 75 through 83 current: chain 'F' and resid 91 through 92 removed outlier: 6.792A pdb=" N VAL F 117 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR F 110 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N PHE F 115 " --> pdb=" O THR F 110 " (cutoff:3.500A) 1034 hydrogen bonds defined for protein. 2814 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: 22.34 Time building geometry restraints manager: 41.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.01: 29715 1.01 - 1.22: 4 1.22 - 1.43: 13790 1.43 - 1.65: 17575 1.65 - 1.86: 259 Bond restraints: 61343 Sorted by residual: bond pdb=" NE2 GLN B 747 " pdb="HE22 GLN B 747 " ideal model delta sigma weight residual 0.860 0.800 0.060 2.00e-02 2.50e+03 9.08e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.62e+00 bond pdb=" N GLN A 19 " pdb=" CA GLN A 19 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.19e+00 bond pdb=" N LEU G 1 " pdb=" CA LEU G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N ALA E 1 " pdb=" CA ALA E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 ... (remaining 61338 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.38: 2649 107.38 - 114.44: 72735 114.44 - 121.51: 22046 121.51 - 128.57: 12831 128.57 - 135.63: 242 Bond angle restraints: 110503 Sorted by residual: angle pdb="HE21 GLN B 747 " pdb=" NE2 GLN B 747 " pdb="HE22 GLN B 747 " ideal model delta sigma weight residual 120.00 103.14 16.86 3.00e+00 1.11e-01 3.16e+01 angle pdb=" CA CYS B 420 " pdb=" CB CYS B 420 " pdb=" SG CYS B 420 " ideal model delta sigma weight residual 114.40 126.39 -11.99 2.30e+00 1.89e-01 2.72e+01 angle pdb=" CD GLN B 747 " pdb=" NE2 GLN B 747 " pdb="HE22 GLN B 747 " ideal model delta sigma weight residual 120.00 135.63 -15.63 3.00e+00 1.11e-01 2.71e+01 angle pdb=" CD GLN B 747 " pdb=" NE2 GLN B 747 " pdb="HE21 GLN B 747 " ideal model delta sigma weight residual 120.00 105.24 14.76 3.00e+00 1.11e-01 2.42e+01 angle pdb=" N ILE A 987 " pdb=" CA ILE A 987 " pdb=" C ILE A 987 " ideal model delta sigma weight residual 106.21 110.89 -4.68 1.07e+00 8.73e-01 1.91e+01 ... (remaining 110498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.68: 26740 20.68 - 41.36: 1550 41.36 - 62.04: 403 62.04 - 82.72: 148 82.72 - 103.40: 17 Dihedral angle restraints: 28858 sinusoidal: 15431 harmonic: 13427 Sorted by residual: dihedral pdb=" CB CYS B 96 " pdb=" SG CYS B 96 " pdb=" SG CYS B 133 " pdb=" CB CYS B 133 " ideal model delta sinusoidal sigma weight residual -86.00 -144.68 58.68 1 1.00e+01 1.00e-02 4.61e+01 dihedral pdb=" CB CYS A 856 " pdb=" SG CYS A 856 " pdb=" SG CYS A 883 " pdb=" CB CYS A 883 " ideal model delta sinusoidal sigma weight residual 93.00 144.07 -51.07 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CA LEU A 379 " pdb=" C LEU A 379 " pdb=" N ASP A 380 " pdb=" CA ASP A 380 " ideal model delta harmonic sigma weight residual 180.00 -150.84 -29.16 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 28855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3394 0.046 - 0.091: 881 0.091 - 0.137: 313 0.137 - 0.182: 27 0.182 - 0.228: 4 Chirality restraints: 4619 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.39e+00 chirality pdb=" C5 BMA I 2 " pdb=" C4 BMA I 2 " pdb=" C6 BMA I 2 " pdb=" O5 BMA I 2 " both_signs ideal model delta sigma weight residual False -2.27 -2.50 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB THR B 691 " pdb=" CA THR B 691 " pdb=" OG1 THR B 691 " pdb=" CG2 THR B 691 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 4616 not shown) Planarity restraints: 9310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 747 " 0.064 2.00e-02 2.50e+03 9.53e-02 1.36e+02 pdb=" CD GLN B 747 " -0.027 2.00e-02 2.50e+03 pdb=" OE1 GLN B 747 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 GLN B 747 " -0.158 2.00e-02 2.50e+03 pdb="HE21 GLN B 747 " -0.030 2.00e-02 2.50e+03 pdb="HE22 GLN B 747 " 0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 500 " -0.054 2.00e-02 2.50e+03 6.77e-02 6.88e+01 pdb=" CD GLN E 500 " 0.046 2.00e-02 2.50e+03 pdb=" OE1 GLN E 500 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN E 500 " 0.107 2.00e-02 2.50e+03 pdb="HE21 GLN E 500 " 0.006 2.00e-02 2.50e+03 pdb="HE22 GLN E 500 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 372 " 0.372 9.50e-02 1.11e+02 1.31e-01 5.26e+01 pdb=" NE ARG C 372 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG C 372 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG C 372 " -0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG C 372 " -0.046 2.00e-02 2.50e+03 pdb="HH11 ARG C 372 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG C 372 " 0.058 2.00e-02 2.50e+03 pdb="HH21 ARG C 372 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 372 " 0.047 2.00e-02 2.50e+03 ... (remaining 9307 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 1584 2.07 - 2.70: 97166 2.70 - 3.34: 175199 3.34 - 3.97: 227242 3.97 - 4.60: 351040 Nonbonded interactions: 852231 Sorted by model distance: nonbonded pdb="HH12 ARG B 587 " pdb=" O GLU B 604 " model vdw 1.439 1.850 nonbonded pdb=" HG1 THR A 531 " pdb=" OD1 ASN A 533 " model vdw 1.446 1.850 nonbonded pdb=" HZ2 LYS C 517 " pdb=" OE2 GLU C 546 " model vdw 1.468 1.850 nonbonded pdb="HE21 GLN E 502 " pdb=" OE1 GLU E 504 " model vdw 1.491 1.850 nonbonded pdb=" O GLU A 621 " pdb="HH11 ARG A 622 " model vdw 1.493 1.850 ... (remaining 852226 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 'H' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.710 Extract box with map and model: 19.240 Check model and map are aligned: 0.740 Set scattering table: 0.430 Process input model: 157.290 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 198.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 : 0.004 0.048 31625 Z= 0.234 Angle : 0.745 11.993 42802 Z= 0.427 Chirality : 0.047 0.228 4619 Planarity : 0.010 0.143 5587 Dihedral : 14.808 103.397 11813 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.40 % Allowed : 6.70 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.13), residues: 3880 helix: -2.37 (0.17), residues: 566 sheet: 0.41 (0.14), residues: 1221 loop : -1.32 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP D 494 HIS 0.013 0.002 HIS A 70 PHE 0.021 0.002 PHE C 196 TYR 0.048 0.005 TYR A 121 ARG 0.028 0.003 ARG B 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 378 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 330 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.8011 (tmm) cc_final: 0.7713 (tmm) REVERT: A 909 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7873 (t0) REVERT: A 1014 SER cc_start: 0.8767 (t) cc_final: 0.8321 (p) REVERT: A 1064 TYR cc_start: 0.7759 (m-80) cc_final: 0.7480 (m-80) REVERT: A 1097 GLN cc_start: 0.9082 (pm20) cc_final: 0.8878 (mp10) REVERT: B 559 TYR cc_start: 0.7293 (t80) cc_final: 0.6896 (t80) REVERT: B 586 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8861 (t) REVERT: C 222 ARG cc_start: 0.6771 (mtt90) cc_final: 0.5576 (tmt90) REVERT: C 244 LYS cc_start: 0.8411 (tttp) cc_final: 0.8072 (mttm) REVERT: C 254 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8250 (mm-30) REVERT: C 683 MET cc_start: 0.4501 (tpt) cc_final: 0.3923 (mmp) REVERT: D 27 LYS cc_start: 0.8789 (ptpt) cc_final: 0.8515 (pptt) REVERT: D 48 PHE cc_start: 0.8636 (t80) cc_final: 0.8349 (t80) REVERT: D 112 MET cc_start: 0.9043 (mtt) cc_final: 0.8728 (mtt) REVERT: D 365 MET cc_start: 0.8550 (ttm) cc_final: 0.8137 (ttp) REVERT: E 276 ASP cc_start: 0.6990 (p0) cc_final: 0.6625 (p0) REVERT: E 462 MET cc_start: 0.6079 (mmt) cc_final: 0.5478 (mmm) REVERT: F 156 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7412 (tm-30) outliers start: 48 outliers final: 7 residues processed: 365 average time/residue: 2.2787 time to fit residues: 1003.2009 Evaluate side-chains 192 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 182 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 1086 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain G residue 45 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 327 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 100 optimal weight: 0.0060 chunk 198 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 304 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 352 optimal weight: 0.0970 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 210 HIS C 255 ASN D 233 HIS D 457 ASN E 68 GLN F 113 GLN ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 31625 Z= 0.219 Angle : 0.617 11.826 42802 Z= 0.332 Chirality : 0.043 0.168 4619 Planarity : 0.004 0.072 5587 Dihedral : 7.236 64.715 4423 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 1.08 % Allowed : 11.06 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -0.48 (0.13), residues: 3880 helix: -0.46 (0.21), residues: 574 sheet: 0.38 (0.14), residues: 1234 loop : -0.66 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 506 HIS 0.007 0.001 HIS B 429 PHE 0.015 0.001 PHE D 186 TYR 0.013 0.001 TYR D 427 ARG 0.010 0.001 ARG F 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 201 time to evaluate : 3.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.8076 (tmm) cc_final: 0.7810 (tmm) REVERT: A 534 MET cc_start: 0.8400 (mtp) cc_final: 0.8196 (mtp) REVERT: A 1014 SER cc_start: 0.8783 (t) cc_final: 0.8331 (p) REVERT: B 559 TYR cc_start: 0.7373 (t80) cc_final: 0.6829 (t80) REVERT: B 624 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8398 (mt) REVERT: C 222 ARG cc_start: 0.6770 (mtt90) cc_final: 0.5610 (tmt90) REVERT: C 244 LYS cc_start: 0.8396 (tttp) cc_final: 0.8154 (mttm) REVERT: C 474 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8660 (tp) REVERT: D 27 LYS cc_start: 0.8813 (ptpt) cc_final: 0.8549 (pptt) REVERT: D 48 PHE cc_start: 0.8663 (t80) cc_final: 0.8451 (t80) REVERT: D 112 MET cc_start: 0.9084 (mtt) cc_final: 0.8777 (mtt) REVERT: D 365 MET cc_start: 0.8564 (ttm) cc_final: 0.8354 (ttp) REVERT: E 276 ASP cc_start: 0.7006 (p0) cc_final: 0.6652 (p0) REVERT: E 462 MET cc_start: 0.5971 (mmt) cc_final: 0.5471 (mmm) REVERT: F 156 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7389 (tm-30) REVERT: G 45 CYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8192 (m) outliers start: 37 outliers final: 10 residues processed: 226 average time/residue: 2.1700 time to fit residues: 600.1015 Evaluate side-chains 184 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 3.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1311 MET Chi-restraints excluded: chain B residue 531 ARG Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 73 CYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain G residue 45 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 195 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 293 optimal weight: 0.9980 chunk 239 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 352 optimal weight: 0.6980 chunk 381 optimal weight: 20.0000 chunk 314 optimal weight: 0.0770 chunk 350 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 283 optimal weight: 9.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 HIS C 210 HIS C 238 HIS C 255 ASN D 360 ASN E 68 GLN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 31625 Z= 0.232 Angle : 0.568 17.761 42802 Z= 0.302 Chirality : 0.043 0.318 4619 Planarity : 0.004 0.046 5587 Dihedral : 6.220 57.051 4409 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.32 % Allowed : 11.26 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -0.21 (0.13), residues: 3880 helix: 0.31 (0.22), residues: 574 sheet: 0.30 (0.14), residues: 1258 loop : -0.48 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 506 HIS 0.005 0.001 HIS B 429 PHE 0.011 0.001 PHE C 317 TYR 0.012 0.001 TYR D 302 ARG 0.012 0.001 ARG B 723 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 223 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 178 time to evaluate : 3.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.8128 (tmm) cc_final: 0.7814 (tmm) REVERT: A 1014 SER cc_start: 0.8804 (t) cc_final: 0.8339 (p) REVERT: B 559 TYR cc_start: 0.7438 (t80) cc_final: 0.6850 (t80) REVERT: B 586 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8846 (t) REVERT: B 624 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8453 (mt) REVERT: B 723 ARG cc_start: 0.8335 (ttm110) cc_final: 0.8033 (ttp-110) REVERT: C 210 HIS cc_start: 0.7250 (OUTLIER) cc_final: 0.7040 (t-90) REVERT: C 222 ARG cc_start: 0.6861 (mtt90) cc_final: 0.5661 (tmt90) REVERT: C 244 LYS cc_start: 0.8448 (tttp) cc_final: 0.8162 (mttm) REVERT: C 474 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8707 (tp) REVERT: C 589 PHE cc_start: 0.8013 (m-80) cc_final: 0.7704 (m-80) REVERT: D 27 LYS cc_start: 0.8788 (ptpt) cc_final: 0.8515 (pptt) REVERT: D 48 PHE cc_start: 0.8639 (t80) cc_final: 0.8420 (t80) REVERT: D 112 MET cc_start: 0.9083 (mtt) cc_final: 0.8796 (mtt) REVERT: D 281 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7855 (t0) REVERT: D 365 MET cc_start: 0.8576 (ttm) cc_final: 0.8369 (ttp) REVERT: E 276 ASP cc_start: 0.7052 (p0) cc_final: 0.6690 (p0) REVERT: E 462 MET cc_start: 0.6212 (mmt) cc_final: 0.5667 (mmm) REVERT: F 156 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7406 (tm-30) outliers start: 45 outliers final: 14 residues processed: 208 average time/residue: 2.1497 time to fit residues: 551.7162 Evaluate side-chains 184 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 165 time to evaluate : 3.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 939 TYR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain C residue 73 CYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 688 CYS Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 45 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 348 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 237 optimal weight: 0.8980 chunk 354 optimal weight: 3.9990 chunk 375 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 335 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 418 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 31625 Z= 0.346 Angle : 0.589 18.254 42802 Z= 0.314 Chirality : 0.044 0.347 4619 Planarity : 0.004 0.066 5587 Dihedral : 5.876 57.116 4409 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.20 % Favored : 95.77 % Rotamer: Outliers : 1.14 % Allowed : 11.90 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -0.22 (0.13), residues: 3880 helix: 0.51 (0.22), residues: 568 sheet: 0.13 (0.14), residues: 1258 loop : -0.43 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 574 HIS 0.018 0.001 HIS C 210 PHE 0.018 0.001 PHE D 186 TYR 0.014 0.001 TYR D 302 ARG 0.007 0.001 ARG A 962 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 174 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8624 (mp0) REVERT: A 287 MET cc_start: 0.8180 (tmm) cc_final: 0.7857 (tmm) REVERT: A 853 MET cc_start: 0.7800 (mtt) cc_final: 0.7496 (mtp) REVERT: A 1014 SER cc_start: 0.8822 (t) cc_final: 0.8362 (p) REVERT: B 212 SER cc_start: 0.9108 (t) cc_final: 0.8904 (p) REVERT: B 559 TYR cc_start: 0.7490 (t80) cc_final: 0.6867 (t80) REVERT: B 624 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8539 (mt) REVERT: C 222 ARG cc_start: 0.6953 (mtt90) cc_final: 0.5695 (tmt90) REVERT: D 27 LYS cc_start: 0.8850 (ptpt) cc_final: 0.8559 (pptt) REVERT: D 112 MET cc_start: 0.9112 (mtt) cc_final: 0.8853 (mtt) REVERT: D 281 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7917 (t0) REVERT: D 446 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8949 (t) REVERT: E 276 ASP cc_start: 0.7185 (p0) cc_final: 0.6849 (p0) REVERT: E 462 MET cc_start: 0.6294 (mmt) cc_final: 0.5725 (mmm) REVERT: F 156 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7444 (tm-30) REVERT: G 71 PHE cc_start: 0.8503 (p90) cc_final: 0.7885 (p90) REVERT: G 73 GLU cc_start: 0.8226 (tp30) cc_final: 0.7995 (pm20) outliers start: 39 outliers final: 19 residues processed: 202 average time/residue: 2.1491 time to fit residues: 532.4243 Evaluate side-chains 187 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 4.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 939 TYR Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1311 MET Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain C residue 73 CYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 625 HIS Chi-restraints excluded: chain C residue 688 CYS Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 45 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 312 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 279 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 320 optimal weight: 10.0000 chunk 259 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 336 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS C 210 HIS C 255 ASN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 31625 Z= 0.242 Angle : 0.557 18.657 42802 Z= 0.293 Chirality : 0.043 0.314 4619 Planarity : 0.003 0.043 5587 Dihedral : 5.558 56.635 4409 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.23 % Allowed : 11.96 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -0.07 (0.13), residues: 3880 helix: 0.77 (0.22), residues: 568 sheet: 0.24 (0.14), residues: 1231 loop : -0.39 (0.14), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 29 HIS 0.024 0.001 HIS C 210 PHE 0.013 0.001 PHE A1174 TYR 0.017 0.001 TYR A 831 ARG 0.005 0.000 ARG B 685 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 221 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 3.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.8231 (tmm) cc_final: 0.7907 (tmm) REVERT: A 962 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7873 (ttp80) REVERT: A 1014 SER cc_start: 0.8826 (t) cc_final: 0.8368 (p) REVERT: B 559 TYR cc_start: 0.7506 (t80) cc_final: 0.7036 (t80) REVERT: B 616 MET cc_start: 0.9220 (mmm) cc_final: 0.9008 (mmm) REVERT: D 7 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7338 (tmm) REVERT: D 27 LYS cc_start: 0.8848 (ptpt) cc_final: 0.8564 (pptt) REVERT: D 112 MET cc_start: 0.9123 (mtt) cc_final: 0.8875 (mtt) REVERT: D 281 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7897 (t0) REVERT: E 276 ASP cc_start: 0.7165 (p0) cc_final: 0.6829 (p0) REVERT: E 462 MET cc_start: 0.6184 (mmt) cc_final: 0.5610 (mmm) REVERT: F 156 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7460 (tm-30) outliers start: 42 outliers final: 20 residues processed: 214 average time/residue: 2.1554 time to fit residues: 563.4188 Evaluate side-chains 185 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 962 ARG Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1311 MET Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain C residue 73 CYS Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 688 CYS Chi-restraints excluded: chain D residue 7 MET Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 45 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 126 optimal weight: 0.6980 chunk 337 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 375 optimal weight: 2.9990 chunk 311 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 197 optimal weight: 0.0470 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS C 210 HIS C 255 ASN C 488 GLN C 583 GLN D 100 ASN ** F 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 31625 Z= 0.221 Angle : 0.543 15.840 42802 Z= 0.285 Chirality : 0.042 0.332 4619 Planarity : 0.003 0.043 5587 Dihedral : 5.346 56.717 4409 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.37 % Allowed : 12.34 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.01 (0.13), residues: 3880 helix: 0.88 (0.22), residues: 568 sheet: 0.26 (0.14), residues: 1226 loop : -0.35 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 574 HIS 0.012 0.001 HIS C 210 PHE 0.023 0.001 PHE D 186 TYR 0.014 0.001 TYR E 252 ARG 0.005 0.000 ARG C 533 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 214 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 167 time to evaluate : 3.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.8268 (tmm) cc_final: 0.7940 (tmm) REVERT: A 1014 SER cc_start: 0.8817 (t) cc_final: 0.8342 (p) REVERT: B 559 TYR cc_start: 0.7524 (t80) cc_final: 0.7057 (t80) REVERT: B 586 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8912 (t) REVERT: B 616 MET cc_start: 0.9243 (mmm) cc_final: 0.9020 (mmm) REVERT: C 198 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.6602 (m-10) REVERT: C 450 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8039 (t0) REVERT: D 27 LYS cc_start: 0.8873 (ptpt) cc_final: 0.8560 (pptt) REVERT: D 112 MET cc_start: 0.9131 (mtt) cc_final: 0.8884 (mtt) REVERT: D 281 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7873 (t0) REVERT: E 284 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8102 (ttt) REVERT: E 462 MET cc_start: 0.6166 (mmt) cc_final: 0.5599 (mmm) REVERT: F 156 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7470 (tm-30) REVERT: G 71 PHE cc_start: 0.8595 (p90) cc_final: 0.7903 (p90) outliers start: 47 outliers final: 24 residues processed: 207 average time/residue: 2.1857 time to fit residues: 558.3305 Evaluate side-chains 187 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 3.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1311 MET Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain C residue 73 CYS Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain C residue 688 CYS Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 45 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 361 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 213 optimal weight: 0.6980 chunk 274 optimal weight: 0.6980 chunk 212 optimal weight: 0.6980 chunk 316 optimal weight: 9.9990 chunk 209 optimal weight: 0.9980 chunk 373 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 227 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS C 210 HIS C 255 ASN C 645 GLN ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 31625 Z= 0.223 Angle : 0.538 14.225 42802 Z= 0.282 Chirality : 0.042 0.355 4619 Planarity : 0.003 0.043 5587 Dihedral : 5.244 56.717 4409 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.29 % Allowed : 12.72 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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 (0.13), residues: 3880 helix: 0.99 (0.23), residues: 568 sheet: 0.27 (0.14), residues: 1228 loop : -0.32 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 574 HIS 0.009 0.001 HIS B 418 PHE 0.016 0.001 PHE A1174 TYR 0.013 0.001 TYR C 235 ARG 0.005 0.000 ARG D 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 160 time to evaluate : 3.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.8404 (tmm) cc_final: 0.8078 (tmm) REVERT: A 1014 SER cc_start: 0.8814 (t) cc_final: 0.8361 (p) REVERT: B 616 MET cc_start: 0.9276 (mmm) cc_final: 0.9030 (mmm) REVERT: C 254 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8026 (tp30) REVERT: C 450 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8067 (t0) REVERT: D 27 LYS cc_start: 0.8868 (ptpt) cc_final: 0.8470 (pptt) REVERT: D 281 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7868 (t0) REVERT: E 284 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8092 (ttt) REVERT: E 462 MET cc_start: 0.6021 (mmt) cc_final: 0.5485 (mmm) REVERT: F 156 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7498 (tm-30) outliers start: 44 outliers final: 24 residues processed: 197 average time/residue: 2.1602 time to fit residues: 520.6132 Evaluate side-chains 188 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 3.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1311 MET Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain C residue 73 CYS Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 45 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 231 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 223 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 237 optimal weight: 0.7980 chunk 254 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 293 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS C 210 HIS C 255 ASN ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 31625 Z= 0.227 Angle : 0.534 13.957 42802 Z= 0.281 Chirality : 0.042 0.351 4619 Planarity : 0.003 0.044 5587 Dihedral : 5.178 56.786 4409 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.35 % Allowed : 12.61 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 0.07 (0.13), residues: 3880 helix: 1.02 (0.22), residues: 575 sheet: 0.26 (0.14), residues: 1237 loop : -0.29 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 574 HIS 0.010 0.001 HIS B 418 PHE 0.022 0.001 PHE D 186 TYR 0.016 0.001 TYR E 252 ARG 0.005 0.000 ARG F 122 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 166 time to evaluate : 4.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.8414 (tmm) cc_final: 0.8085 (tmm) REVERT: A 1002 HIS cc_start: 0.8174 (t70) cc_final: 0.7947 (t70) REVERT: A 1014 SER cc_start: 0.8825 (t) cc_final: 0.8375 (p) REVERT: B 616 MET cc_start: 0.9302 (mmm) cc_final: 0.9041 (mmm) REVERT: C 38 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: C 254 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8136 (mm-30) REVERT: C 450 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8035 (t0) REVERT: D 27 LYS cc_start: 0.8846 (ptpt) cc_final: 0.8438 (pptt) REVERT: D 112 MET cc_start: 0.9148 (mtt) cc_final: 0.8910 (mtt) REVERT: D 281 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7868 (t0) REVERT: E 284 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8107 (ttt) REVERT: E 462 MET cc_start: 0.5984 (mmt) cc_final: 0.5446 (mmm) REVERT: F 156 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7528 (tm-30) outliers start: 46 outliers final: 26 residues processed: 204 average time/residue: 2.1461 time to fit residues: 537.8191 Evaluate side-chains 189 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 159 time to evaluate : 3.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 1125 GLN Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1311 MET Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 73 CYS Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 45 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 340 optimal weight: 0.7980 chunk 358 optimal weight: 10.0000 chunk 326 optimal weight: 1.9990 chunk 348 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 151 optimal weight: 0.8980 chunk 273 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 314 optimal weight: 10.0000 chunk 329 optimal weight: 0.9980 chunk 347 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS C 210 HIS C 255 ASN ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 31625 Z= 0.243 Angle : 0.539 13.842 42802 Z= 0.282 Chirality : 0.042 0.332 4619 Planarity : 0.003 0.046 5587 Dihedral : 5.131 56.720 4409 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.08 % Allowed : 13.04 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 0.06 (0.13), residues: 3880 helix: 1.04 (0.22), residues: 569 sheet: 0.24 (0.14), residues: 1240 loop : -0.29 (0.14), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 574 HIS 0.008 0.001 HIS C 210 PHE 0.019 0.001 PHE A1174 TYR 0.013 0.001 TYR D 302 ARG 0.008 0.000 ARG B 419 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 3.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.8416 (tmm) cc_final: 0.8065 (tmm) REVERT: A 1014 SER cc_start: 0.8828 (t) cc_final: 0.8383 (p) REVERT: B 534 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.8944 (tt) REVERT: B 559 TYR cc_start: 0.7580 (t80) cc_final: 0.7369 (t80) REVERT: C 38 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: C 450 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8037 (t0) REVERT: D 27 LYS cc_start: 0.8845 (ptpt) cc_final: 0.8434 (pptt) REVERT: D 112 MET cc_start: 0.9159 (mtt) cc_final: 0.8921 (mtt) REVERT: D 281 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7868 (t0) REVERT: E 284 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8123 (ttt) REVERT: E 414 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8922 (ttt180) REVERT: E 462 MET cc_start: 0.5996 (mmt) cc_final: 0.5460 (mmm) REVERT: F 156 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7546 (tm-30) outliers start: 37 outliers final: 27 residues processed: 189 average time/residue: 2.2580 time to fit residues: 521.2099 Evaluate side-chains 188 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 1169 ILE Chi-restraints excluded: chain A residue 1311 MET Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 73 CYS Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 414 ARG Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 45 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 228 optimal weight: 2.9990 chunk 368 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 chunk 174 optimal weight: 0.7980 chunk 256 optimal weight: 4.9990 chunk 386 optimal weight: 10.0000 chunk 355 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 237 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS C 210 HIS C 255 ASN C 495 GLN ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 31625 Z= 0.349 Angle : 0.566 13.745 42802 Z= 0.299 Chirality : 0.043 0.328 4619 Planarity : 0.004 0.045 5587 Dihedral : 5.202 56.714 4409 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.17 % Allowed : 13.02 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -0.02 (0.13), residues: 3880 helix: 0.96 (0.22), residues: 569 sheet: 0.21 (0.14), residues: 1229 loop : -0.35 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 574 HIS 0.035 0.001 HIS C 210 PHE 0.022 0.001 PHE D 186 TYR 0.014 0.001 TYR D 302 ARG 0.005 0.000 ARG D 512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 346 is missing expected H atoms. Skipping. Residue THR 714 is missing expected H atoms. Skipping. Residue VAL 738 is missing expected H atoms. Skipping. Residue SER 750 is missing expected H atoms. Skipping. Residue ALA 397 is missing expected H atoms. Skipping. Residue ALA 405 is missing expected H atoms. Skipping. Residue ALA 407 is missing expected H atoms. Skipping. Residue THR 264 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 157 time to evaluate : 3.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.8424 (tmm) cc_final: 0.8091 (tmm) REVERT: A 1012 LEU cc_start: 0.8351 (mt) cc_final: 0.7883 (mt) REVERT: A 1014 SER cc_start: 0.8837 (t) cc_final: 0.8398 (p) REVERT: B 421 THR cc_start: 0.7212 (OUTLIER) cc_final: 0.6713 (p) REVERT: B 534 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.8963 (tt) REVERT: C 38 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8017 (mt-10) REVERT: C 211 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.7997 (p) REVERT: C 244 LYS cc_start: 0.8456 (tttp) cc_final: 0.8152 (mttm) REVERT: C 450 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8057 (t0) REVERT: D 27 LYS cc_start: 0.8853 (ptpt) cc_final: 0.8436 (pptt) REVERT: D 112 MET cc_start: 0.9153 (mtt) cc_final: 0.8912 (mtt) REVERT: D 281 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7880 (t0) REVERT: E 284 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8111 (ttt) REVERT: E 462 MET cc_start: 0.6027 (mmt) cc_final: 0.5486 (mmm) REVERT: F 156 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7584 (tm-30) outliers start: 40 outliers final: 27 residues processed: 191 average time/residue: 2.2177 time to fit residues: 516.4232 Evaluate side-chains 187 residues out of total 3430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 153 time to evaluate : 3.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 1125 GLN Chi-restraints excluded: chain A residue 1311 MET Chi-restraints excluded: chain B residue 26 HIS Chi-restraints excluded: chain B residue 117 CYS Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 613 PHE Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 73 CYS Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 450 ASP Chi-restraints excluded: chain D residue 146 CYS Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 284 MET Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 42 PHE Chi-restraints excluded: chain G residue 45 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 0.6980 chunk 327 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 308 optimal weight: 0.1980 chunk 129 optimal weight: 0.5980 chunk 316 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN C 255 ASN ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.121507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.078754 restraints weight = 152434.750| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.46 r_work: 0.3017 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 31625 Z= 0.338 Angle : 0.570 13.693 42802 Z= 0.299 Chirality : 0.043 0.321 4619 Planarity : 0.004 0.047 5587 Dihedral : 5.223 56.320 4407 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.02 % Allowed : 13.22 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -0.08 (0.13), residues: 3880 helix: 1.00 (0.22), residues: 563 sheet: 0.12 (0.14), residues: 1225 loop : -0.38 (0.14), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 574 HIS 0.012 0.001 HIS C 210 PHE 0.022 0.001 PHE A1174 TYR 0.013 0.001 TYR D 302 ARG 0.006 0.000 ARG D 512 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13809.77 seconds wall clock time: 239 minutes 35.88 seconds (14375.88 seconds total)