Starting phenix.real_space_refine on Fri Feb 16 05:19:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwr_30234/02_2024/7bwr_30234_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwr_30234/02_2024/7bwr_30234.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwr_30234/02_2024/7bwr_30234_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwr_30234/02_2024/7bwr_30234_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwr_30234/02_2024/7bwr_30234_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwr_30234/02_2024/7bwr_30234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwr_30234/02_2024/7bwr_30234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwr_30234/02_2024/7bwr_30234_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwr_30234/02_2024/7bwr_30234_updated.pdb" } resolution = 3.5 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= 0.006 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1 atoms to isotropic. 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 1 9.91 5 P 1 5.49 5 S 54 5.16 5 C 9253 2.51 5 N 2539 2.21 5 O 2602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 27": "NH1" <-> "NH2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ASP 171": "OD1" <-> "OD2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ASP 266": "OD1" <-> "OD2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A ASP 735": "OD1" <-> "OD2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A ASP 765": "OD1" <-> "OD2" Residue "A ASP 772": "OD1" <-> "OD2" Residue "A ARG 777": "NH1" <-> "NH2" Residue "A ASP 795": "OD1" <-> "OD2" Residue "A ARG 822": "NH1" <-> "NH2" Residue "A ARG 890": "NH1" <-> "NH2" Residue "A ASP 893": "OD1" <-> "OD2" Residue "A ARG 901": "NH1" <-> "NH2" Residue "A GLU 954": "OE1" <-> "OE2" Residue "A ASP 965": "OD1" <-> "OD2" Residue "A ASP 971": "OD1" <-> "OD2" Residue "A PHE 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1010": "OD1" <-> "OD2" Residue "A ASP 1025": "OD1" <-> "OD2" Residue "A ARG 1029": "NH1" <-> "NH2" Residue "A ASP 1040": "OD1" <-> "OD2" Residue "A PHE 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 27": "NH1" <-> "NH2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 455": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 526": "NH1" <-> "NH2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B ARG 554": "NH1" <-> "NH2" Residue "B PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B PHE 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14450 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 7948 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 77, 'TRANS': 980} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 5400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 5400 Classifications: {'peptide': 850} Incomplete info: {'truncation_to_alanine': 306} Link IDs: {'PTRANS': 63, 'TRANS': 786} Chain breaks: 13 Unresolved chain link angles: 31 Unresolved non-hydrogen bonds: 1142 Unresolved non-hydrogen angles: 1486 Unresolved non-hydrogen dihedrals: 956 Unresolved non-hydrogen chiralities: 101 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 3, 'TYR:plan': 12, 'ASN:plan1': 7, 'TRP:plan': 7, 'ASP:plan': 29, 'PHE:plan': 18, 'GLU:plan': 22, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 656 Chain: "C" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 520 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 3, 'TRANS': 74} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 517 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 3, 'TRANS': 74} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {' CA': 1, 'F8L': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.09, per 1000 atoms: 0.56 Number of scatterers: 14450 At special positions: 0 Unit cell: (133.66, 121.36, 136.94, 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 1 19.99 S 54 16.00 P 1 15.00 O 2602 8.00 N 2539 7.00 C 9253 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.40 Conformation dependent library (CDL) restraints added in 2.9 seconds 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3796 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 11 sheets defined 32.6% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.538A pdb=" N THR A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 109 through 112 No H-bonds generated for 'chain 'A' and resid 109 through 112' Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 220 through 243 Processing helix chain 'A' and resid 266 through 269 No H-bonds generated for 'chain 'A' and resid 266 through 269' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 296 through 299 No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 319 through 326 removed outlier: 3.618A pdb=" N LEU A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 Proline residue: A 339 - end of helix No H-bonds generated for 'chain 'A' and resid 336 through 340' Processing helix chain 'A' and resid 342 through 345 No H-bonds generated for 'chain 'A' and resid 342 through 345' Processing helix chain 'A' and resid 348 through 351 No H-bonds generated for 'chain 'A' and resid 348 through 351' Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 368 through 381 Processing helix chain 'A' and resid 392 through 411 removed outlier: 3.951A pdb=" N ALA A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 426 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 445 through 454 Processing helix chain 'A' and resid 462 through 470 removed outlier: 3.642A pdb=" N ALA A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 475 through 479 removed outlier: 3.680A pdb=" N VAL A 479 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 498 removed outlier: 3.837A pdb=" N ILE A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 537 through 545 Processing helix chain 'A' and resid 556 through 570 removed outlier: 3.696A pdb=" N LEU A 560 " --> pdb=" O PRO A 556 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 569 " --> pdb=" O PHE A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 586 No H-bonds generated for 'chain 'A' and resid 584 through 586' Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'A' and resid 608 through 625 removed outlier: 3.720A pdb=" N PHE A 614 " --> pdb=" O ASN A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 675 removed outlier: 3.916A pdb=" N LEU A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 675 " --> pdb=" O TRP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 686 No H-bonds generated for 'chain 'A' and resid 683 through 686' Processing helix chain 'A' and resid 690 through 712 Processing helix chain 'A' and resid 719 through 725 removed outlier: 3.681A pdb=" N ASN A 723 " --> pdb=" O ASN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 736 No H-bonds generated for 'chain 'A' and resid 734 through 736' Processing helix chain 'A' and resid 851 through 854 No H-bonds generated for 'chain 'A' and resid 851 through 854' Processing helix chain 'A' and resid 958 through 961 No H-bonds generated for 'chain 'A' and resid 958 through 961' Processing helix chain 'A' and resid 1002 through 1008 Processing helix chain 'A' and resid 1021 through 1023 No H-bonds generated for 'chain 'A' and resid 1021 through 1023' Processing helix chain 'B' and resid 28 through 42 removed outlier: 3.954A pdb=" N LEU B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.952A pdb=" N ILE B 230 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 341 through 354 removed outlier: 3.695A pdb=" N ARG B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 380 Processing helix chain 'B' and resid 392 through 410 Processing helix chain 'B' and resid 415 through 429 Processing helix chain 'B' and resid 436 through 443 Processing helix chain 'B' and resid 445 through 454 Processing helix chain 'B' and resid 461 through 472 removed outlier: 4.239A pdb=" N ALA B 466 " --> pdb=" O TRP B 462 " (cutoff:3.500A) Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 474 through 480 Processing helix chain 'B' and resid 485 through 488 No H-bonds generated for 'chain 'B' and resid 485 through 488' Processing helix chain 'B' and resid 530 through 546 Proline residue: B 538 - end of helix removed outlier: 3.656A pdb=" N PHE B 541 " --> pdb=" O PHE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 588 through 599 Processing helix chain 'B' and resid 609 through 625 Processing helix chain 'B' and resid 658 through 675 removed outlier: 3.734A pdb=" N ILE B 664 " --> pdb=" O ALA B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 686 No H-bonds generated for 'chain 'B' and resid 683 through 686' Processing helix chain 'B' and resid 691 through 702 removed outlier: 3.789A pdb=" N ALA B 694 " --> pdb=" O ILE B 691 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 696 " --> pdb=" O VAL B 693 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 701 " --> pdb=" O MET B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 796 No H-bonds generated for 'chain 'B' and resid 794 through 796' Processing helix chain 'B' and resid 920 through 922 No H-bonds generated for 'chain 'B' and resid 920 through 922' Processing helix chain 'B' and resid 958 through 961 No H-bonds generated for 'chain 'B' and resid 958 through 961' Processing helix chain 'B' and resid 1020 through 1027 removed outlier: 4.043A pdb=" N LEU B1027 " --> pdb=" O ILE B1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 43 through 54 removed outlier: 3.610A pdb=" N ILE C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 66 removed outlier: 4.180A pdb=" N ALA C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.617A pdb=" N ILE C 77 " --> pdb=" O VAL C 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'D' and resid 43 through 54 removed outlier: 3.610A pdb=" N ILE D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.925A pdb=" N ALA D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 77 removed outlier: 3.617A pdb=" N ILE D 77 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 216 through 218 removed outlier: 3.816A pdb=" N HIS A 217 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 49 " --> pdb=" O SER A1070 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 51 " --> pdb=" O THR A1068 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N THR A 53 " --> pdb=" O SER A1066 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER A1066 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 54 through 57 removed outlier: 4.524A pdb=" N ALA A 54 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 78 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 115 through 117 removed outlier: 3.763A pdb=" N VAL A 125 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ALA A 133 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL A 127 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N VAL A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1035 through 1037 Processing sheet with id= E, first strand: chain 'A' and resid 837 through 840 removed outlier: 3.834A pdb=" N SER A 837 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 882 " --> pdb=" O GLU A 935 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 859 through 864 removed outlier: 3.551A pdb=" N ILE A 862 " --> pdb=" O LEU A 916 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1028 through 1033 removed outlier: 4.558A pdb=" N LEU A1048 " --> pdb=" O MET A1033 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 148 through 151 Processing sheet with id= I, first strand: chain 'B' and resid 115 through 117 Processing sheet with id= J, first strand: chain 'B' and resid 825 through 827 Processing sheet with id= K, first strand: chain 'B' and resid 837 through 840 removed outlier: 3.932A pdb=" N SER B 837 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 839 " --> pdb=" O ALA B 934 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 934 " --> pdb=" O LEU B 839 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1221 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: 5.09 Time building geometry restraints manager: 5.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2350 1.30 - 1.43: 3604 1.43 - 1.56: 8652 1.56 - 1.69: 27 1.69 - 1.81: 95 Bond restraints: 14728 Sorted by residual: bond pdb=" C61 F8L A2002 " pdb=" O56 F8L A2002 " ideal model delta sigma weight residual 1.272 1.540 -0.268 2.00e-02 2.50e+03 1.80e+02 bond pdb=" C59 F8L A2002 " pdb=" C61 F8L A2002 " ideal model delta sigma weight residual 1.568 1.369 0.199 2.00e-02 2.50e+03 9.87e+01 bond pdb=" C57 F8L A2002 " pdb=" C59 F8L A2002 " ideal model delta sigma weight residual 1.517 1.629 -0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" C ILE A 523 " pdb=" O ILE A 523 " ideal model delta sigma weight residual 1.237 1.175 0.063 1.23e-02 6.61e+03 2.59e+01 bond pdb=" C ILE A 579 " pdb=" N HIS A 580 " ideal model delta sigma weight residual 1.331 1.401 -0.070 1.42e-02 4.96e+03 2.42e+01 ... (remaining 14723 not shown) Histogram of bond angle deviations from ideal: 92.09 - 103.47: 300 103.47 - 114.85: 9061 114.85 - 126.23: 10544 126.23 - 137.61: 313 137.61 - 148.99: 1 Bond angle restraints: 20219 Sorted by residual: angle pdb=" N PHE B 569 " pdb=" CA PHE B 569 " pdb=" C PHE B 569 " ideal model delta sigma weight residual 112.13 148.99 -36.86 1.37e+00 5.33e-01 7.24e+02 angle pdb=" C11 F8L A2002 " pdb=" C12 F8L A2002 " pdb=" C13 F8L A2002 " ideal model delta sigma weight residual 68.17 120.05 -51.88 3.00e+00 1.11e-01 2.99e+02 angle pdb=" C6 F8L A2002 " pdb=" C7 F8L A2002 " pdb=" C8 F8L A2002 " ideal model delta sigma weight residual 68.20 120.00 -51.80 3.00e+00 1.11e-01 2.98e+02 angle pdb=" C26 F8L A2002 " pdb=" C27 F8L A2002 " pdb=" C28 F8L A2002 " ideal model delta sigma weight residual 74.52 120.05 -45.53 3.00e+00 1.11e-01 2.30e+02 angle pdb=" C36 F8L A2002 " pdb=" C37 F8L A2002 " pdb=" C38 F8L A2002 " ideal model delta sigma weight residual 74.50 120.00 -45.50 3.00e+00 1.11e-01 2.30e+02 ... (remaining 20214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.66: 7880 18.66 - 37.32: 637 37.32 - 55.98: 100 55.98 - 74.63: 19 74.63 - 93.29: 13 Dihedral angle restraints: 8649 sinusoidal: 2773 harmonic: 5876 Sorted by residual: dihedral pdb=" N PHE B 570 " pdb=" C PHE B 570 " pdb=" CA PHE B 570 " pdb=" CB PHE B 570 " ideal model delta harmonic sigma weight residual 122.80 99.76 23.04 0 2.50e+00 1.60e-01 8.49e+01 dihedral pdb=" C VAL A 527 " pdb=" N VAL A 527 " pdb=" CA VAL A 527 " pdb=" CB VAL A 527 " ideal model delta harmonic sigma weight residual -122.00 -141.26 19.26 0 2.50e+00 1.60e-01 5.94e+01 dihedral pdb=" CA GLN B 60 " pdb=" C GLN B 60 " pdb=" N GLN B 61 " pdb=" CA GLN B 61 " ideal model delta harmonic sigma weight residual 180.00 150.66 29.34 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 8646 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.254: 2482 0.254 - 0.508: 10 0.508 - 0.762: 4 0.762 - 1.017: 0 1.017 - 1.271: 1 Chirality restraints: 2497 Sorted by residual: chirality pdb=" CA PHE B 569 " pdb=" N PHE B 569 " pdb=" C PHE B 569 " pdb=" CB PHE B 569 " both_signs ideal model delta sigma weight residual False 2.51 1.24 1.27 2.00e-01 2.50e+01 4.04e+01 chirality pdb=" CA PRO A 575 " pdb=" N PRO A 575 " pdb=" C PRO A 575 " pdb=" CB PRO A 575 " both_signs ideal model delta sigma weight residual False 2.72 2.15 0.57 2.00e-01 2.50e+01 7.99e+00 chirality pdb=" CB ILE B 44 " pdb=" CA ILE B 44 " pdb=" CG1 ILE B 44 " pdb=" CG2 ILE B 44 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.56 2.00e-01 2.50e+01 7.79e+00 ... (remaining 2494 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 695 " 0.021 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C ALA B 695 " -0.075 2.00e-02 2.50e+03 pdb=" O ALA B 695 " 0.028 2.00e-02 2.50e+03 pdb=" N GLY B 696 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 476 " -0.019 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C LEU A 476 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU A 476 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA A 477 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 28 " -0.060 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO D 29 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO D 29 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO D 29 " -0.050 5.00e-02 4.00e+02 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 5 2.13 - 2.82: 4605 2.82 - 3.52: 19330 3.52 - 4.21: 31684 4.21 - 4.90: 53507 Nonbonded interactions: 109131 Sorted by model distance: nonbonded pdb=" OG SER A 524 " pdb=" O HIS A 580 " model vdw 1.442 2.440 nonbonded pdb=" OD2 ASP A 936 " pdb="CA CA A2001 " model vdw 1.632 2.510 nonbonded pdb=" OG1 THR A 518 " pdb=" O60 F8L A2002 " model vdw 1.679 2.440 nonbonded pdb=" O PHE B 570 " pdb=" OG1 THR B 574 " model vdw 1.984 2.440 nonbonded pdb=" CB SER A 524 " pdb=" O HIS A 580 " model vdw 2.108 3.440 ... (remaining 109126 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 'C' and (resid 3 through 60 or (resid 61 through 63 and (name N or name C \ A or name C or name O or name CB )) or resid 64 through 80)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 4.550 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 40.770 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 0.008 0.268 14728 Z= 0.532 Angle : 1.705 51.876 20219 Z= 0.839 Chirality : 0.075 1.271 2497 Planarity : 0.010 0.091 2595 Dihedral : 14.637 93.292 4853 Min Nonbonded Distance : 1.442 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.17 % Favored : 85.64 % Rotamer: Outliers : 1.55 % Allowed : 15.93 % Favored : 82.52 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.14), residues: 2026 helix: -3.43 (0.13), residues: 713 sheet: -2.12 (0.42), residues: 133 loop : -3.88 (0.14), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1041 HIS 0.012 0.002 HIS A 548 PHE 0.038 0.003 PHE B 214 TYR 0.042 0.003 TYR B 180 ARG 0.007 0.001 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 311 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.6690 (mpp) cc_final: 0.6092 (mmm) REVERT: A 490 GLU cc_start: 0.8077 (tt0) cc_final: 0.7792 (tt0) REVERT: A 526 ARG cc_start: 0.7047 (mmt-90) cc_final: 0.6832 (mtp180) REVERT: A 534 MET cc_start: 0.8708 (ppp) cc_final: 0.7925 (ptt) REVERT: A 592 MET cc_start: 0.8506 (tpt) cc_final: 0.8121 (tpp) REVERT: A 736 ASP cc_start: 0.8852 (p0) cc_final: 0.8202 (p0) REVERT: A 1041 TRP cc_start: 0.7944 (m-90) cc_final: 0.7417 (m-90) REVERT: B 90 ASP cc_start: 0.8140 (p0) cc_final: 0.7786 (p0) REVERT: B 146 GLN cc_start: 0.8505 (pt0) cc_final: 0.8210 (mt0) REVERT: B 349 LEU cc_start: 0.9002 (tp) cc_final: 0.8666 (tp) REVERT: B 370 MET cc_start: 0.8553 (tmm) cc_final: 0.7901 (tpp) REVERT: B 459 VAL cc_start: 0.8269 (m) cc_final: 0.8051 (m) REVERT: B 565 PHE cc_start: 0.7589 (t80) cc_final: 0.7294 (t80) REVERT: C 5 GLN cc_start: 0.6149 (mm110) cc_final: 0.5934 (tp-100) REVERT: C 78 GLN cc_start: 0.7762 (pt0) cc_final: 0.7525 (pp30) outliers start: 20 outliers final: 10 residues processed: 327 average time/residue: 0.2679 time to fit residues: 127.8212 Evaluate side-chains 226 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 216 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain C residue 70 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 159 optimal weight: 0.0970 chunk 61 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 185 optimal weight: 0.9980 overall best weight: 1.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 74 GLN A 153 ASN A 252 HIS A 298 HIS A 580 HIS ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 GLN B 57 ASN B 66 ASN B 129 ASN B 881 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14728 Z= 0.200 Angle : 1.031 22.884 20219 Z= 0.435 Chirality : 0.045 0.252 2497 Planarity : 0.006 0.069 2595 Dihedral : 7.832 92.472 2228 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.02 % Favored : 89.78 % Rotamer: Outliers : 4.97 % Allowed : 21.83 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.16), residues: 2026 helix: -1.83 (0.17), residues: 718 sheet: -1.80 (0.40), residues: 152 loop : -3.33 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 913 HIS 0.004 0.001 HIS A 217 PHE 0.019 0.001 PHE B 565 TYR 0.012 0.001 TYR A 288 ARG 0.005 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 242 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.6666 (mpp) cc_final: 0.6070 (mmm) REVERT: A 526 ARG cc_start: 0.7778 (mmt-90) cc_final: 0.6380 (mtp180) REVERT: A 534 MET cc_start: 0.8530 (ppp) cc_final: 0.7702 (ptt) REVERT: A 572 MET cc_start: 0.5527 (mmm) cc_final: 0.5233 (mmt) REVERT: A 736 ASP cc_start: 0.8787 (p0) cc_final: 0.8268 (p0) REVERT: A 859 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7924 (pp) REVERT: A 1041 TRP cc_start: 0.7863 (m-90) cc_final: 0.7408 (m-90) REVERT: B 57 ASN cc_start: 0.6970 (m-40) cc_final: 0.6665 (m-40) REVERT: B 90 ASP cc_start: 0.8143 (p0) cc_final: 0.7880 (p0) REVERT: B 146 GLN cc_start: 0.8552 (pt0) cc_final: 0.8317 (mt0) REVERT: B 349 LEU cc_start: 0.8993 (tp) cc_final: 0.8654 (tp) REVERT: B 370 MET cc_start: 0.8570 (tmm) cc_final: 0.7995 (tpp) REVERT: B 381 TRP cc_start: 0.7850 (OUTLIER) cc_final: 0.7228 (m-10) REVERT: C 5 GLN cc_start: 0.6002 (mm110) cc_final: 0.5751 (tp-100) outliers start: 64 outliers final: 38 residues processed: 290 average time/residue: 0.2246 time to fit residues: 101.0448 Evaluate side-chains 254 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 214 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 49 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 154 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 200 optimal weight: 2.9990 chunk 165 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 ASN B 66 ASN C 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14728 Z= 0.198 Angle : 0.995 22.486 20219 Z= 0.411 Chirality : 0.044 0.189 2497 Planarity : 0.005 0.063 2595 Dihedral : 7.324 83.721 2225 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.56 % Favored : 89.29 % Rotamer: Outliers : 6.29 % Allowed : 24.16 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.17), residues: 2026 helix: -0.95 (0.18), residues: 743 sheet: -1.51 (0.41), residues: 155 loop : -3.09 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 671 HIS 0.003 0.001 HIS A 217 PHE 0.010 0.001 PHE A 585 TYR 0.022 0.001 TYR A 402 ARG 0.003 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 235 time to evaluate : 1.614 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7182 (pt0) cc_final: 0.6974 (pt0) REVERT: A 451 ILE cc_start: 0.9530 (OUTLIER) cc_final: 0.9262 (tt) REVERT: A 490 GLU cc_start: 0.8368 (tt0) cc_final: 0.8160 (tt0) REVERT: A 534 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7878 (ptt) REVERT: A 572 MET cc_start: 0.5731 (mmm) cc_final: 0.5389 (mmt) REVERT: A 736 ASP cc_start: 0.8768 (p0) cc_final: 0.8282 (p0) REVERT: A 935 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7118 (mt-10) REVERT: A 1041 TRP cc_start: 0.7866 (m-90) cc_final: 0.7643 (m-90) REVERT: B 57 ASN cc_start: 0.6917 (m-40) cc_final: 0.6673 (m-40) REVERT: B 90 ASP cc_start: 0.8119 (p0) cc_final: 0.7903 (p0) REVERT: B 146 GLN cc_start: 0.8470 (pt0) cc_final: 0.8260 (mt0) REVERT: B 251 MET cc_start: 0.6345 (mtm) cc_final: 0.6080 (mtm) REVERT: B 349 LEU cc_start: 0.8978 (tp) cc_final: 0.8637 (tp) REVERT: B 359 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7130 (pp) REVERT: B 370 MET cc_start: 0.8536 (tmm) cc_final: 0.7969 (tpp) REVERT: B 381 TRP cc_start: 0.7902 (OUTLIER) cc_final: 0.7394 (m-10) outliers start: 81 outliers final: 52 residues processed: 294 average time/residue: 0.2180 time to fit residues: 100.1621 Evaluate side-chains 273 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 217 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 186 optimal weight: 0.0050 chunk 197 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 176 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 548 HIS C 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14728 Z= 0.280 Angle : 1.006 22.655 20219 Z= 0.416 Chirality : 0.044 0.188 2497 Planarity : 0.005 0.061 2595 Dihedral : 7.145 83.078 2224 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.06 % Favored : 88.80 % Rotamer: Outliers : 7.23 % Allowed : 25.10 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.18), residues: 2026 helix: -0.57 (0.19), residues: 759 sheet: -1.31 (0.42), residues: 149 loop : -2.98 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 671 HIS 0.010 0.001 HIS B 548 PHE 0.014 0.001 PHE A 585 TYR 0.018 0.001 TYR A 288 ARG 0.006 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 214 time to evaluate : 1.559 Fit side-chains revert: symmetry clash REVERT: A 451 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9123 (tt) REVERT: A 490 GLU cc_start: 0.8445 (tt0) cc_final: 0.8187 (tt0) REVERT: A 534 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7946 (ptt) REVERT: A 736 ASP cc_start: 0.8849 (p0) cc_final: 0.8311 (p0) REVERT: A 859 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8109 (pp) REVERT: A 1014 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8388 (p0) REVERT: A 1041 TRP cc_start: 0.7935 (m-90) cc_final: 0.7612 (m-90) REVERT: B 57 ASN cc_start: 0.7104 (m-40) cc_final: 0.6859 (m-40) REVERT: B 90 ASP cc_start: 0.8082 (p0) cc_final: 0.7806 (p0) REVERT: B 146 GLN cc_start: 0.8501 (pt0) cc_final: 0.8286 (mt0) REVERT: B 359 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7139 (pp) REVERT: B 370 MET cc_start: 0.8498 (tmm) cc_final: 0.7932 (tpp) REVERT: B 381 TRP cc_start: 0.7967 (OUTLIER) cc_final: 0.7499 (m-10) REVERT: B 435 LEU cc_start: 0.8630 (mt) cc_final: 0.8347 (tp) REVERT: B 543 MET cc_start: 0.7171 (tmm) cc_final: 0.6734 (tmm) REVERT: B 703 MET cc_start: 0.7815 (ppp) cc_final: 0.7496 (ppp) outliers start: 93 outliers final: 68 residues processed: 283 average time/residue: 0.2175 time to fit residues: 97.6375 Evaluate side-chains 276 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 202 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 168 optimal weight: 50.0000 chunk 136 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 7.9990 chunk 176 optimal weight: 50.0000 chunk 49 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 981 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14728 Z= 0.361 Angle : 1.034 22.841 20219 Z= 0.431 Chirality : 0.045 0.190 2497 Planarity : 0.005 0.060 2595 Dihedral : 7.251 85.269 2224 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.14 % Favored : 87.71 % Rotamer: Outliers : 8.31 % Allowed : 25.25 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.18), residues: 2026 helix: -0.35 (0.19), residues: 756 sheet: -1.38 (0.42), residues: 150 loop : -2.88 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 671 HIS 0.002 0.001 HIS B 580 PHE 0.012 0.001 PHE A 769 TYR 0.026 0.002 TYR A 288 ARG 0.008 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 199 time to evaluate : 1.553 Fit side-chains revert: symmetry clash REVERT: A 192 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8849 (t) REVERT: A 285 ASP cc_start: 0.9052 (p0) cc_final: 0.8572 (p0) REVERT: A 534 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7939 (ptt) REVERT: A 572 MET cc_start: 0.6635 (mmt) cc_final: 0.6274 (mmt) REVERT: A 736 ASP cc_start: 0.8889 (p0) cc_final: 0.8255 (p0) REVERT: A 859 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8166 (pp) REVERT: A 1014 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8357 (p0) REVERT: A 1041 TRP cc_start: 0.7993 (m-90) cc_final: 0.7635 (m-90) REVERT: B 57 ASN cc_start: 0.7229 (m-40) cc_final: 0.6974 (m-40) REVERT: B 359 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7306 (pp) REVERT: B 381 TRP cc_start: 0.7995 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: B 543 MET cc_start: 0.7499 (tmm) cc_final: 0.6773 (tmm) outliers start: 107 outliers final: 71 residues processed: 280 average time/residue: 0.2033 time to fit residues: 90.6623 Evaluate side-chains 266 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 189 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 598 VAL Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 57 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 0.7980 chunk 177 optimal weight: 30.0000 chunk 38 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 163 optimal weight: 50.0000 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 103 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14728 Z= 0.172 Angle : 0.991 22.298 20219 Z= 0.402 Chirality : 0.043 0.231 2497 Planarity : 0.004 0.060 2595 Dihedral : 6.951 79.777 2224 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.97 % Favored : 89.88 % Rotamer: Outliers : 6.60 % Allowed : 27.04 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.19), residues: 2026 helix: -0.07 (0.20), residues: 758 sheet: -1.20 (0.42), residues: 160 loop : -2.76 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 671 HIS 0.004 0.001 HIS A 217 PHE 0.013 0.001 PHE B 161 TYR 0.011 0.001 TYR A 288 ARG 0.005 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 210 time to evaluate : 2.487 Fit side-chains revert: symmetry clash REVERT: A 192 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8780 (t) REVERT: A 534 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.7824 (ptt) REVERT: A 736 ASP cc_start: 0.8785 (p0) cc_final: 0.8323 (p0) REVERT: A 1014 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8008 (p0) REVERT: A 1041 TRP cc_start: 0.7831 (m-90) cc_final: 0.7630 (m-90) REVERT: B 57 ASN cc_start: 0.7129 (m-40) cc_final: 0.6884 (m-40) REVERT: B 359 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7404 (pp) REVERT: B 381 TRP cc_start: 0.7913 (OUTLIER) cc_final: 0.7440 (m-10) REVERT: B 435 LEU cc_start: 0.8718 (tp) cc_final: 0.8288 (tp) REVERT: B 543 MET cc_start: 0.7461 (tmm) cc_final: 0.6744 (tmm) outliers start: 85 outliers final: 65 residues processed: 277 average time/residue: 0.2022 time to fit residues: 91.3751 Evaluate side-chains 267 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 197 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 610 ASN Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 112 optimal weight: 0.0670 chunk 144 optimal weight: 0.0010 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 50.0000 chunk 110 optimal weight: 7.9990 chunk 196 optimal weight: 50.0000 chunk 123 optimal weight: 0.0470 chunk 119 optimal weight: 0.0040 chunk 90 optimal weight: 10.0000 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 HIS ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14728 Z= 0.153 Angle : 0.986 22.164 20219 Z= 0.395 Chirality : 0.042 0.164 2497 Planarity : 0.004 0.060 2595 Dihedral : 6.654 71.644 2224 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.92 % Favored : 89.93 % Rotamer: Outliers : 6.06 % Allowed : 28.21 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.19), residues: 2026 helix: 0.06 (0.20), residues: 756 sheet: -0.95 (0.42), residues: 158 loop : -2.65 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 671 HIS 0.003 0.001 HIS A 217 PHE 0.011 0.001 PHE B 161 TYR 0.009 0.001 TYR A 319 ARG 0.004 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 222 time to evaluate : 2.420 Fit side-chains REVERT: A 192 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8773 (t) REVERT: A 534 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7811 (ptt) REVERT: A 736 ASP cc_start: 0.8665 (p0) cc_final: 0.8316 (p0) REVERT: A 935 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6965 (mt-10) REVERT: A 1014 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7952 (p0) REVERT: B 227 LEU cc_start: 0.9199 (mt) cc_final: 0.8705 (tp) REVERT: B 359 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7400 (pp) REVERT: B 381 TRP cc_start: 0.7924 (OUTLIER) cc_final: 0.7456 (m-10) REVERT: B 435 LEU cc_start: 0.8671 (tp) cc_final: 0.8223 (tp) REVERT: B 573 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.6102 (t80) REVERT: C 5 GLN cc_start: 0.6679 (mm-40) cc_final: 0.6475 (tp-100) REVERT: C 33 PHE cc_start: 0.7493 (m-10) cc_final: 0.7263 (m-10) outliers start: 78 outliers final: 62 residues processed: 280 average time/residue: 0.2074 time to fit residues: 94.1457 Evaluate side-chains 265 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 197 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 347 CYS Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 789 GLN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14728 Z= 0.265 Angle : 1.014 22.389 20219 Z= 0.411 Chirality : 0.044 0.267 2497 Planarity : 0.004 0.057 2595 Dihedral : 6.697 76.298 2223 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.66 % Favored : 89.19 % Rotamer: Outliers : 5.91 % Allowed : 28.52 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.19), residues: 2026 helix: 0.15 (0.20), residues: 747 sheet: -0.94 (0.42), residues: 158 loop : -2.62 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 671 HIS 0.003 0.001 HIS A 580 PHE 0.009 0.001 PHE A 697 TYR 0.046 0.002 TYR A 918 ARG 0.006 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 199 time to evaluate : 1.650 Fit side-chains revert: symmetry clash REVERT: A 192 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8795 (t) REVERT: A 316 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.7257 (p90) REVERT: A 534 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7875 (ptt) REVERT: A 572 MET cc_start: 0.6310 (mmt) cc_final: 0.5426 (mmt) REVERT: A 736 ASP cc_start: 0.8778 (p0) cc_final: 0.8356 (p0) REVERT: A 859 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.8020 (pt) REVERT: A 935 GLU cc_start: 0.7331 (mt-10) cc_final: 0.7066 (mt-10) REVERT: A 1014 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8061 (p0) REVERT: B 227 LEU cc_start: 0.9226 (mt) cc_final: 0.8863 (tp) REVERT: B 359 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7369 (pp) REVERT: B 381 TRP cc_start: 0.7943 (OUTLIER) cc_final: 0.7503 (m-10) REVERT: B 435 LEU cc_start: 0.8737 (tp) cc_final: 0.8289 (tp) REVERT: B 543 MET cc_start: 0.7057 (tmm) cc_final: 0.6785 (tmm) REVERT: B 573 PHE cc_start: 0.6626 (OUTLIER) cc_final: 0.6124 (t80) REVERT: C 5 GLN cc_start: 0.6787 (mm-40) cc_final: 0.6584 (tp-100) outliers start: 76 outliers final: 61 residues processed: 255 average time/residue: 0.2121 time to fit residues: 87.0828 Evaluate side-chains 262 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 193 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 161 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 563 ILE Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.2980 chunk 171 optimal weight: 50.0000 chunk 183 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 165 optimal weight: 0.0870 chunk 173 optimal weight: 50.0000 chunk 182 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14728 Z= 0.174 Angle : 0.995 22.215 20219 Z= 0.397 Chirality : 0.043 0.261 2497 Planarity : 0.004 0.059 2595 Dihedral : 6.553 72.369 2223 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.72 % Favored : 90.13 % Rotamer: Outliers : 5.91 % Allowed : 28.28 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.19), residues: 2026 helix: 0.24 (0.20), residues: 743 sheet: -0.82 (0.42), residues: 170 loop : -2.57 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 671 HIS 0.002 0.000 HIS A 217 PHE 0.009 0.001 PHE B 614 TYR 0.036 0.001 TYR A 918 ARG 0.003 0.000 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 205 time to evaluate : 1.585 Fit side-chains REVERT: A 114 MET cc_start: 0.8594 (ttp) cc_final: 0.8288 (ttp) REVERT: A 192 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8771 (t) REVERT: A 534 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7763 (ptt) REVERT: A 572 MET cc_start: 0.6417 (mmt) cc_final: 0.5599 (mmt) REVERT: A 736 ASP cc_start: 0.8679 (p0) cc_final: 0.8352 (p0) REVERT: A 935 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6969 (mt-10) REVERT: A 1014 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7971 (p0) REVERT: B 227 LEU cc_start: 0.9156 (mt) cc_final: 0.8648 (tp) REVERT: B 359 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7417 (pp) REVERT: B 381 TRP cc_start: 0.7895 (OUTLIER) cc_final: 0.7507 (m-10) REVERT: B 435 LEU cc_start: 0.8680 (tp) cc_final: 0.8210 (tp) REVERT: B 543 MET cc_start: 0.6917 (tmm) cc_final: 0.6621 (tmm) REVERT: B 573 PHE cc_start: 0.6561 (OUTLIER) cc_final: 0.6184 (t80) REVERT: C 5 GLN cc_start: 0.6746 (mm-40) cc_final: 0.6502 (tp-100) REVERT: C 44 MET cc_start: 0.8401 (tpp) cc_final: 0.8082 (tpp) outliers start: 76 outliers final: 56 residues processed: 264 average time/residue: 0.1939 time to fit residues: 82.6606 Evaluate side-chains 259 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 197 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 187 optimal weight: 0.3980 chunk 161 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14728 Z= 0.262 Angle : 1.015 22.343 20219 Z= 0.411 Chirality : 0.044 0.245 2497 Planarity : 0.004 0.055 2595 Dihedral : 6.619 76.042 2223 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.66 % Favored : 89.19 % Rotamer: Outliers : 5.44 % Allowed : 28.59 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.19), residues: 2026 helix: 0.20 (0.20), residues: 749 sheet: -0.82 (0.42), residues: 165 loop : -2.53 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 671 HIS 0.002 0.001 HIS A 580 PHE 0.010 0.001 PHE A 316 TYR 0.043 0.002 TYR A 918 ARG 0.007 0.000 ARG A 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 196 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: A 114 MET cc_start: 0.8672 (ttp) cc_final: 0.8409 (ttp) REVERT: A 192 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8775 (t) REVERT: A 316 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7258 (p90) REVERT: A 490 GLU cc_start: 0.8385 (tt0) cc_final: 0.8182 (tt0) REVERT: A 534 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7862 (ptt) REVERT: A 572 MET cc_start: 0.6490 (mmt) cc_final: 0.5680 (mmt) REVERT: A 736 ASP cc_start: 0.8745 (p0) cc_final: 0.8356 (p0) REVERT: A 935 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7059 (mt-10) REVERT: A 1014 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.8001 (p0) REVERT: B 78 GLU cc_start: 0.6682 (tp30) cc_final: 0.6479 (tp30) REVERT: B 146 GLN cc_start: 0.8266 (mt0) cc_final: 0.8018 (mt0) REVERT: B 227 LEU cc_start: 0.9183 (mt) cc_final: 0.8832 (tp) REVERT: B 359 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7396 (pp) REVERT: B 381 TRP cc_start: 0.7915 (OUTLIER) cc_final: 0.7499 (m-10) REVERT: B 435 LEU cc_start: 0.8739 (tp) cc_final: 0.8267 (tp) REVERT: B 543 MET cc_start: 0.6984 (tmm) cc_final: 0.6662 (tmm) REVERT: B 573 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6332 (t80) outliers start: 70 outliers final: 59 residues processed: 253 average time/residue: 0.2074 time to fit residues: 85.6962 Evaluate side-chains 262 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 196 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 534 MET Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 774 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 828 THR Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 875 ASN Chi-restraints excluded: chain A residue 882 THR Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 897 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 985 LEU Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1014 ASP Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 381 TRP Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 558 TRP Chi-restraints excluded: chain B residue 573 PHE Chi-restraints excluded: chain B residue 812 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain D residue 47 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 8.9990 chunk 49 optimal weight: 0.0870 chunk 149 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 162 optimal weight: 40.0000 chunk 67 optimal weight: 0.8980 chunk 166 optimal weight: 40.0000 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.151625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.116748 restraints weight = 26823.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114045 restraints weight = 21708.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.114991 restraints weight = 22384.287| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14728 Z= 0.204 Angle : 1.006 22.258 20219 Z= 0.403 Chirality : 0.044 0.228 2497 Planarity : 0.004 0.055 2595 Dihedral : 6.548 74.420 2223 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.07 % Favored : 89.78 % Rotamer: Outliers : 5.59 % Allowed : 28.75 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.19), residues: 2026 helix: 0.29 (0.20), residues: 743 sheet: -0.77 (0.42), residues: 165 loop : -2.46 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 671 HIS 0.002 0.001 HIS A 217 PHE 0.009 0.001 PHE B 614 TYR 0.035 0.001 TYR A 918 ARG 0.007 0.000 ARG A 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3130.71 seconds wall clock time: 57 minutes 19.14 seconds (3439.14 seconds total)