Starting phenix.real_space_refine on Tue Jul 23 09:45:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkt_37607/07_2024/8wkt_37607.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkt_37607/07_2024/8wkt_37607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkt_37607/07_2024/8wkt_37607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkt_37607/07_2024/8wkt_37607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkt_37607/07_2024/8wkt_37607.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wkt_37607/07_2024/8wkt_37607.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 14203 2.51 5 N 3548 2.21 5 O 4112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 101": "OD1" <-> "OD2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A PHE 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 547": "OD1" <-> "OD2" Residue "A TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 645": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 662": "OD1" <-> "OD2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 748": "OD1" <-> "OD2" Residue "A GLU 793": "OE1" <-> "OE2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 864": "OD1" <-> "OD2" Residue "A GLU 901": "OE1" <-> "OE2" Residue "A PHE 916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 923": "OE1" <-> "OE2" Residue "A ASP 945": "OD1" <-> "OD2" Residue "A GLU 982": "OE1" <-> "OE2" Residue "A GLU 998": "OE1" <-> "OE2" Residue "A TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "B ASP 119": "OD1" <-> "OD2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 238": "OD1" <-> "OD2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 306": "OD1" <-> "OD2" Residue "B ASP 310": "OD1" <-> "OD2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 369": "OE1" <-> "OE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B ASP 464": "OD1" <-> "OD2" Residue "B TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 509": "OD1" <-> "OD2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 526": "OD1" <-> "OD2" Residue "B GLU 534": "OE1" <-> "OE2" Residue "B ASP 554": "OD1" <-> "OD2" Residue "B GLU 560": "OE1" <-> "OE2" Residue "B ASP 581": "OD1" <-> "OD2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B GLU 624": "OE1" <-> "OE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B PHE 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "B GLU 731": "OE1" <-> "OE2" Residue "B TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 776": "OD1" <-> "OD2" Residue "B GLU 822": "OE1" <-> "OE2" Residue "B ASP 836": "OD1" <-> "OD2" Residue "B PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 940": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B ASP 993": "OD1" <-> "OD2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 249": "OD1" <-> "OD2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "D TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 55": "OD1" <-> "OD2" Residue "E TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 181": "OE1" <-> "OE2" Residue "E ASP 188": "OD1" <-> "OD2" Residue "E ASP 189": "OD1" <-> "OD2" Residue "E ASP 222": "OD1" <-> "OD2" Residue "E GLU 254": "OE1" <-> "OE2" Residue "E GLU 279": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 21944 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 8264 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 19, 'TRANS': 972} Chain: "B" Number of atoms: 8115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 8115 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 952} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 900 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "D" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2330 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain: "E" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2335 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Time building chain proxies: 14.46, per 1000 atoms: 0.66 Number of scatterers: 21944 At special positions: 0 Unit cell: (99.84, 128.96, 185.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 4112 8.00 N 3548 7.00 C 14203 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: 9.26 Conformation dependent library (CDL) restraints added in 3.9 seconds 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5034 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 8 sheets defined 63.3% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 removed outlier: 3.642A pdb=" N LEU A 20 " --> pdb=" O LYS A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 50 through 54 removed outlier: 3.914A pdb=" N SER A 54 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 removed outlier: 3.916A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 96 through 108 removed outlier: 3.756A pdb=" N PHE A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.650A pdb=" N ASP A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.915A pdb=" N VAL A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.539A pdb=" N ARG A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 296 removed outlier: 3.823A pdb=" N VAL A 289 " --> pdb=" O ARG A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 322 removed outlier: 3.791A pdb=" N ILE A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) Proline residue: A 318 - end of helix removed outlier: 4.109A pdb=" N ALA A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU A 322 " --> pdb=" O PRO A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 355 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 376 through 391 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 447 through 462 removed outlier: 3.563A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 494 Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.862A pdb=" N LEU A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 520 Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.675A pdb=" N GLU A 543 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP A 547 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 572 removed outlier: 3.698A pdb=" N TYR A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP A 553 " --> pdb=" O GLN A 549 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP A 554 " --> pdb=" O PHE A 550 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS A 557 " --> pdb=" O ASP A 553 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 558 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN A 563 " --> pdb=" O PHE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 583 removed outlier: 3.555A pdb=" N ILE A 582 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 583 " --> pdb=" O SER A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 583' Processing helix chain 'A' and resid 584 through 598 removed outlier: 3.545A pdb=" N TYR A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG A 593 " --> pdb=" O TYR A 589 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 628 removed outlier: 3.680A pdb=" N THR A 628 " --> pdb=" O GLU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 660 through 669 Processing helix chain 'A' and resid 670 through 671 No H-bonds generated for 'chain 'A' and resid 670 through 671' Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 680 through 699 Processing helix chain 'A' and resid 711 through 722 removed outlier: 3.554A pdb=" N LEU A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 Processing helix chain 'A' and resid 750 through 762 Processing helix chain 'A' and resid 768 through 786 Processing helix chain 'A' and resid 800 through 812 removed outlier: 3.611A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 825 Processing helix chain 'A' and resid 832 through 841 Processing helix chain 'A' and resid 846 through 855 removed outlier: 3.612A pdb=" N SER A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 870 removed outlier: 4.129A pdb=" N ARG A 870 " --> pdb=" O MET A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 903 Processing helix chain 'A' and resid 912 through 921 removed outlier: 4.197A pdb=" N TRP A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 921 " --> pdb=" O GLY A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 934 removed outlier: 3.954A pdb=" N MET A 930 " --> pdb=" O ASN A 927 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 957 through 962 removed outlier: 4.242A pdb=" N TYR A 962 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 972 Processing helix chain 'A' and resid 973 through 990 removed outlier: 3.941A pdb=" N LYS A 977 " --> pdb=" O ASN A 973 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS A 978 " --> pdb=" O LYS A 974 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU A 982 " --> pdb=" O HIS A 978 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 983 " --> pdb=" O HIS A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1003 removed outlier: 3.508A pdb=" N GLU A 998 " --> pdb=" O LYS A 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.588A pdb=" N GLY B 12 " --> pdb=" O SER B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 47 through 53 removed outlier: 4.141A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.592A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.560A pdb=" N ARG B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 97 through 109 removed outlier: 4.030A pdb=" N PHE B 107 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.915A pdb=" N ASP B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.594A pdb=" N TYR B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 210 Processing helix chain 'B' and resid 222 through 236 removed outlier: 3.693A pdb=" N TRP B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLN B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.878A pdb=" N ILE B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 271 through 275' Processing helix chain 'B' and resid 281 through 298 removed outlier: 3.899A pdb=" N VAL B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.644A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.732A pdb=" N VAL B 333 " --> pdb=" O ASP B 329 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 329 through 334' Processing helix chain 'B' and resid 355 through 366 removed outlier: 3.801A pdb=" N GLU B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 374 through 392 removed outlier: 4.193A pdb=" N GLU B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.743A pdb=" N ALA B 400 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 431 through 445 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 468 through 490 Processing helix chain 'B' and resid 495 through 500 removed outlier: 4.194A pdb=" N LEU B 498 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 519 Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.659A pdb=" N MET B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 540 through 543 removed outlier: 3.539A pdb=" N GLU B 543 " --> pdb=" O LYS B 540 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 540 through 543' Processing helix chain 'B' and resid 555 through 561 removed outlier: 3.557A pdb=" N LEU B 558 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 561 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 596 removed outlier: 3.650A pdb=" N LEU B 585 " --> pdb=" O ASP B 581 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 587 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 595 " --> pdb=" O ASN B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 627 removed outlier: 3.719A pdb=" N TYR B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 620 " --> pdb=" O MET B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 635 removed outlier: 4.127A pdb=" N GLU B 633 " --> pdb=" O ARG B 629 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B 635 " --> pdb=" O ILE B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 659 removed outlier: 3.876A pdb=" N ASN B 654 " --> pdb=" O TYR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 680 through 701 Processing helix chain 'B' and resid 705 through 723 removed outlier: 3.802A pdb=" N TYR B 709 " --> pdb=" O ASN B 705 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 726 No H-bonds generated for 'chain 'B' and resid 724 through 726' Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 750 through 762 Processing helix chain 'B' and resid 768 through 786 Processing helix chain 'B' and resid 800 through 812 removed outlier: 4.199A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 805 " --> pdb=" O SER B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 Processing helix chain 'B' and resid 831 through 841 Processing helix chain 'B' and resid 842 through 845 Processing helix chain 'B' and resid 846 through 855 removed outlier: 3.991A pdb=" N SER B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 878 through 897 Processing helix chain 'B' and resid 912 through 922 Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.706A pdb=" N LYS B 953 " --> pdb=" O ASP B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 955 through 962 removed outlier: 3.905A pdb=" N TYR B 962 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 973 Processing helix chain 'B' and resid 973 through 990 removed outlier: 4.513A pdb=" N HIS B 978 " --> pdb=" O LYS B 974 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N HIS B 979 " --> pdb=" O HIS B 975 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1004 removed outlier: 3.718A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 101 Processing helix chain 'D' and resid 14 through 22 removed outlier: 3.778A pdb=" N VAL D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 39 removed outlier: 4.022A pdb=" N CYS D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.760A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 95 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 97 through 108 removed outlier: 4.112A pdb=" N ILE D 103 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU D 104 " --> pdb=" O PHE D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.635A pdb=" N ASP D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.517A pdb=" N VAL D 158 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D 161 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 222 through 234 Processing helix chain 'D' and resid 254 through 264 Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.657A pdb=" N ARG D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 22 removed outlier: 4.298A pdb=" N PHE E 19 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET E 21 " --> pdb=" O GLU E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 40 Processing helix chain 'E' and resid 47 through 54 removed outlier: 3.954A pdb=" N SER E 51 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER E 54 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 71 removed outlier: 3.801A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.752A pdb=" N TYR E 84 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 95 removed outlier: 3.519A pdb=" N VAL E 94 " --> pdb=" O ILE E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 109 Processing helix chain 'E' and resid 115 through 124 removed outlier: 3.589A pdb=" N ASP E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 146 Processing helix chain 'E' and resid 155 through 160 removed outlier: 4.479A pdb=" N ALA E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 155 through 160' Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 192 through 197 Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 222 through 234 removed outlier: 3.938A pdb=" N LYS E 234 " --> pdb=" O ASN E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 240 removed outlier: 3.576A pdb=" N PHE E 240 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 263 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 296 removed outlier: 4.008A pdb=" N ARG E 285 " --> pdb=" O ASP E 281 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER E 296 " --> pdb=" O LEU E 292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 152 removed outlier: 6.100A pdb=" N SER A 150 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LYS A 169 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 152 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A 42 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ILE A 130 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE A 44 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 213 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE A 246 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N PHE A 215 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N PHE A 245 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 575 removed outlier: 3.959A pdb=" N THR C 22 " --> pdb=" O HIS C 17 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N PHE C 23 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 removed outlier: 6.169A pdb=" N SER B 150 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS B 169 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 152 " --> pdb=" O LYS B 169 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU B 42 " --> pdb=" O HIS B 128 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE B 130 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE B 44 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 338 through 340 Processing sheet with id=AA6, first strand: chain 'C' and resid 65 through 67 removed outlier: 4.048A pdb=" N LYS C 41 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N PHE C 29 " --> pdb=" O LYS C 41 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 150 through 152 removed outlier: 6.483A pdb=" N SER D 150 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS D 169 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE D 152 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 129 " --> pdb=" O TYR D 166 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU D 42 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE D 130 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE D 44 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE D 216 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY D 217 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE D 245 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 150 through 152 removed outlier: 6.412A pdb=" N SER E 150 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS E 169 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE E 152 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS E 128 " --> pdb=" O LEU E 42 " (cutoff:3.500A) 1028 hydrogen bonds defined for protein. 2949 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.11 Time building geometry restraints manager: 10.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6936 1.34 - 1.46: 5202 1.46 - 1.58: 10186 1.58 - 1.70: 0 1.70 - 1.83: 135 Bond restraints: 22459 Sorted by residual: bond pdb=" N GLN B 323 " pdb=" CA GLN B 323 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.23e-02 6.61e+03 1.59e+01 bond pdb=" N ILE B 862 " pdb=" CA ILE B 862 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.06e-02 8.90e+03 1.41e+01 bond pdb=" N TYR B 324 " pdb=" CA TYR B 324 " ideal model delta sigma weight residual 1.456 1.504 -0.047 1.27e-02 6.20e+03 1.39e+01 bond pdb=" N VAL B 603 " pdb=" CA VAL B 603 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.07e-02 8.73e+03 1.17e+01 bond pdb=" N ILE B 934 " pdb=" CA ILE B 934 " ideal model delta sigma weight residual 1.455 1.495 -0.039 1.18e-02 7.18e+03 1.12e+01 ... (remaining 22454 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.42: 373 106.42 - 113.38: 11769 113.38 - 120.35: 9079 120.35 - 127.32: 8902 127.32 - 134.29: 169 Bond angle restraints: 30292 Sorted by residual: angle pdb=" N VAL D 50 " pdb=" CA VAL D 50 " pdb=" C VAL D 50 " ideal model delta sigma weight residual 113.43 107.04 6.39 1.09e+00 8.42e-01 3.43e+01 angle pdb=" N ILE A 582 " pdb=" CA ILE A 582 " pdb=" C ILE A 582 " ideal model delta sigma weight residual 113.53 108.58 4.95 9.80e-01 1.04e+00 2.55e+01 angle pdb=" C ASN B 861 " pdb=" CA ASN B 861 " pdb=" CB ASN B 861 " ideal model delta sigma weight residual 116.54 110.88 5.66 1.15e+00 7.56e-01 2.42e+01 angle pdb=" N ASP A 590 " pdb=" CA ASP A 590 " pdb=" C ASP A 590 " ideal model delta sigma weight residual 112.93 107.06 5.87 1.33e+00 5.65e-01 1.95e+01 angle pdb=" CB LYS A 540 " pdb=" CG LYS A 540 " pdb=" CD LYS A 540 " ideal model delta sigma weight residual 111.30 121.03 -9.73 2.30e+00 1.89e-01 1.79e+01 ... (remaining 30287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 11165 17.87 - 35.73: 1677 35.73 - 53.60: 434 53.60 - 71.46: 76 71.46 - 89.33: 25 Dihedral angle restraints: 13377 sinusoidal: 5538 harmonic: 7839 Sorted by residual: dihedral pdb=" CA PHE A 107 " pdb=" C PHE A 107 " pdb=" N PHE A 108 " pdb=" CA PHE A 108 " ideal model delta harmonic sigma weight residual -180.00 -158.94 -21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ILE A 871 " pdb=" C ILE A 871 " pdb=" N GLY A 872 " pdb=" CA GLY A 872 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA PRO E 74 " pdb=" C PRO E 74 " pdb=" N LYS E 75 " pdb=" CA LYS E 75 " ideal model delta harmonic sigma weight residual 180.00 161.95 18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 13374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2301 0.043 - 0.085: 755 0.085 - 0.128: 150 0.128 - 0.171: 20 0.171 - 0.213: 6 Chirality restraints: 3232 Sorted by residual: chirality pdb=" CG LEU E 266 " pdb=" CB LEU E 266 " pdb=" CD1 LEU E 266 " pdb=" CD2 LEU E 266 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA LEU A 841 " pdb=" N LEU A 841 " pdb=" C LEU A 841 " pdb=" CB LEU A 841 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE A 695 " pdb=" CA ILE A 695 " pdb=" CG1 ILE A 695 " pdb=" CG2 ILE A 695 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.32e-01 ... (remaining 3229 not shown) Planarity restraints: 3864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 73 " -0.077 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO A 74 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 52 " 0.236 9.50e-02 1.11e+02 1.06e-01 6.86e+00 pdb=" NE ARG C 52 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 52 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 52 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 52 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 933 " 0.011 2.00e-02 2.50e+03 1.62e-02 4.59e+00 pdb=" CG PHE B 933 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 933 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 933 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE B 933 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 933 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 933 " 0.002 2.00e-02 2.50e+03 ... (remaining 3861 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1778 2.74 - 3.28: 22665 3.28 - 3.82: 36880 3.82 - 4.36: 42342 4.36 - 4.90: 72983 Nonbonded interactions: 176648 Sorted by model distance: nonbonded pdb=" OH TYR A 687 " pdb=" OE2 GLU A 715 " model vdw 2.197 2.440 nonbonded pdb=" OE2 GLU B 730 " pdb=" OG SER B 770 " model vdw 2.214 2.440 nonbonded pdb=" OG1 THR B 257 " pdb=" OH TYR E 71 " model vdw 2.216 2.440 nonbonded pdb=" OH TYR B 414 " pdb=" OD1 ASN B 654 " model vdw 2.219 2.440 nonbonded pdb=" OD2 ASP D 249 " pdb=" OG SER D 251 " model vdw 2.222 2.440 ... (remaining 176643 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 'A' and (resid 14 through 565 or (resid 580 and (name N or name CA or nam \ e C or name O or name CB )) or resid 581 through 897 or resid 911 through 1005)) \ selection = (chain 'B' and resid 14 through 1005) } ncs_group { reference = (chain 'D' and resid 13 through 296) selection = (chain 'E' and resid 13 through 296) } 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: 11.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 62.610 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 22459 Z= 0.246 Angle : 0.632 12.094 30292 Z= 0.371 Chirality : 0.043 0.213 3232 Planarity : 0.004 0.113 3864 Dihedral : 18.080 89.330 8343 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.62 % Allowed : 26.37 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 2630 helix: 0.57 (0.14), residues: 1455 sheet: -1.79 (0.47), residues: 100 loop : -1.22 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 143 HIS 0.007 0.001 HIS B 118 PHE 0.036 0.001 PHE B 933 TYR 0.020 0.001 TYR B 625 ARG 0.008 0.000 ARG E 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 363 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6704 (m-10) cc_final: 0.6380 (m-10) REVERT: A 208 ILE cc_start: 0.8870 (mt) cc_final: 0.8538 (mt) REVERT: B 10 ARG cc_start: 0.8320 (mmp-170) cc_final: 0.7726 (ttt180) REVERT: B 14 LYS cc_start: 0.7942 (tttt) cc_final: 0.7464 (mmtp) REVERT: B 396 MET cc_start: 0.8315 (mmm) cc_final: 0.7828 (mmm) REVERT: B 662 ASP cc_start: 0.8530 (p0) cc_final: 0.7957 (t0) REVERT: C 12 HIS cc_start: 0.7766 (p-80) cc_final: 0.7517 (p-80) REVERT: C 74 LEU cc_start: 0.8042 (mp) cc_final: 0.7436 (tp) REVERT: C 120 ASP cc_start: 0.7908 (m-30) cc_final: 0.7073 (t0) REVERT: D 28 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8946 (tp30) REVERT: D 32 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8772 (mm-30) REVERT: D 122 LEU cc_start: 0.8988 (mt) cc_final: 0.8624 (mp) REVERT: E 27 VAL cc_start: 0.8686 (t) cc_final: 0.8396 (t) REVERT: E 268 ILE cc_start: 0.9131 (mm) cc_final: 0.8683 (tp) outliers start: 15 outliers final: 4 residues processed: 373 average time/residue: 0.3699 time to fit residues: 208.0152 Evaluate side-chains 179 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain E residue 134 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 222 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 134 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 206 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN C 80 ASN D 118 HIS ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22459 Z= 0.187 Angle : 0.554 10.771 30292 Z= 0.286 Chirality : 0.041 0.207 3232 Planarity : 0.004 0.072 3864 Dihedral : 4.259 52.553 2914 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.64 % Allowed : 26.74 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.17), residues: 2630 helix: 0.77 (0.14), residues: 1486 sheet: -1.74 (0.47), residues: 108 loop : -1.07 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 60 HIS 0.006 0.001 HIS A 658 PHE 0.016 0.001 PHE B 301 TYR 0.012 0.001 TYR B 134 ARG 0.009 0.001 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 180 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 MET cc_start: 0.8063 (tpp) cc_final: 0.7816 (mmm) REVERT: A 936 MET cc_start: 0.6133 (mmm) cc_final: 0.5749 (tpt) REVERT: B 10 ARG cc_start: 0.8366 (mmp-170) cc_final: 0.7776 (ttt180) REVERT: B 14 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7512 (mmtp) REVERT: B 391 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.7902 (t0) REVERT: B 531 MET cc_start: 0.9052 (mmm) cc_final: 0.8807 (mmm) REVERT: B 662 ASP cc_start: 0.8520 (p0) cc_final: 0.7888 (t0) REVERT: B 938 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7403 (p0) REVERT: C 74 LEU cc_start: 0.8033 (mp) cc_final: 0.7482 (tp) REVERT: C 88 HIS cc_start: 0.7226 (t70) cc_final: 0.6568 (t70) REVERT: C 120 ASP cc_start: 0.7998 (m-30) cc_final: 0.7228 (t0) REVERT: D 134 TYR cc_start: 0.7175 (OUTLIER) cc_final: 0.6233 (m-10) REVERT: E 145 ARG cc_start: 0.8164 (mtp-110) cc_final: 0.7875 (mtp-110) REVERT: E 171 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.8435 (m-70) REVERT: E 268 ILE cc_start: 0.8965 (mm) cc_final: 0.8699 (tp) REVERT: E 290 MET cc_start: 0.9538 (mmm) cc_final: 0.9174 (mtm) REVERT: E 294 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8538 (mm) outliers start: 64 outliers final: 24 residues processed: 235 average time/residue: 0.3414 time to fit residues: 127.1716 Evaluate side-chains 176 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 938 ASP Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 171 HIS Chi-restraints excluded: chain E residue 294 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 132 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 239 optimal weight: 0.9980 chunk 258 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 191 optimal weight: 0.3980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN B 834 GLN ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22459 Z= 0.163 Angle : 0.517 8.964 30292 Z= 0.264 Chirality : 0.039 0.151 3232 Planarity : 0.003 0.059 3864 Dihedral : 4.006 40.768 2910 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.10 % Allowed : 26.50 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2630 helix: 0.99 (0.14), residues: 1477 sheet: -1.81 (0.46), residues: 108 loop : -1.07 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 231 HIS 0.011 0.001 HIS E 171 PHE 0.011 0.001 PHE C 79 TYR 0.012 0.001 TYR B 134 ARG 0.004 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 152 time to evaluate : 2.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9055 (mm) REVERT: A 936 MET cc_start: 0.6238 (mmm) cc_final: 0.5857 (tpt) REVERT: B 10 ARG cc_start: 0.8368 (mmp-170) cc_final: 0.7745 (ttt180) REVERT: B 14 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7493 (mmtp) REVERT: B 391 ASN cc_start: 0.8359 (OUTLIER) cc_final: 0.7970 (t0) REVERT: B 454 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8906 (tp) REVERT: B 519 MET cc_start: 0.8510 (tpp) cc_final: 0.8212 (mmt) REVERT: B 647 MET cc_start: 0.8187 (mmm) cc_final: 0.7752 (mmm) REVERT: B 662 ASP cc_start: 0.8516 (p0) cc_final: 0.7870 (t0) REVERT: C 72 ARG cc_start: 0.7148 (mmm160) cc_final: 0.6816 (mmm160) REVERT: C 74 LEU cc_start: 0.8100 (mp) cc_final: 0.7552 (tp) REVERT: C 88 HIS cc_start: 0.7230 (t70) cc_final: 0.6414 (t70) REVERT: C 115 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7624 (tm-30) REVERT: D 134 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6208 (m-10) REVERT: E 124 MET cc_start: 0.8769 (mmm) cc_final: 0.8410 (mmm) REVERT: E 145 ARG cc_start: 0.8052 (mtp-110) cc_final: 0.7837 (mtp-110) REVERT: E 297 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7731 (pm20) outliers start: 75 outliers final: 32 residues processed: 218 average time/residue: 0.3157 time to fit residues: 109.9550 Evaluate side-chains 171 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 236 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 160 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 125 optimal weight: 0.4980 chunk 227 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN E 67 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22459 Z= 0.144 Angle : 0.503 14.248 30292 Z= 0.254 Chirality : 0.040 0.326 3232 Planarity : 0.003 0.058 3864 Dihedral : 3.936 41.989 2910 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.56 % Allowed : 26.78 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2630 helix: 1.07 (0.14), residues: 1484 sheet: -1.72 (0.48), residues: 97 loop : -1.09 (0.19), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 143 HIS 0.003 0.001 HIS A 658 PHE 0.012 0.001 PHE C 59 TYR 0.013 0.001 TYR D 280 ARG 0.003 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 151 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 874 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.6927 (tp) REVERT: A 936 MET cc_start: 0.6190 (mmm) cc_final: 0.5739 (tpt) REVERT: B 10 ARG cc_start: 0.8444 (mmp-170) cc_final: 0.7794 (ttt180) REVERT: B 14 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7493 (mmtp) REVERT: B 391 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8042 (t0) REVERT: B 454 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8914 (tp) REVERT: B 662 ASP cc_start: 0.8494 (p0) cc_final: 0.7835 (t0) REVERT: B 977 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8469 (tptm) REVERT: C 30 ASP cc_start: 0.7474 (m-30) cc_final: 0.7258 (m-30) REVERT: C 72 ARG cc_start: 0.7177 (mmm160) cc_final: 0.6870 (mmm160) REVERT: C 74 LEU cc_start: 0.8072 (mp) cc_final: 0.7511 (tp) REVERT: C 88 HIS cc_start: 0.7274 (t70) cc_final: 0.6393 (t70) REVERT: C 115 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7491 (tm-30) REVERT: D 21 MET cc_start: 0.7708 (ppp) cc_final: 0.7385 (ppp) REVERT: D 134 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6225 (m-10) REVERT: E 124 MET cc_start: 0.8901 (mmm) cc_final: 0.8417 (mmm) REVERT: E 297 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7676 (pm20) outliers start: 62 outliers final: 31 residues processed: 206 average time/residue: 0.3081 time to fit residues: 102.4330 Evaluate side-chains 171 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain B residue 977 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 211 optimal weight: 0.9980 chunk 144 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 129 optimal weight: 0.7980 chunk 228 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 790 ASN ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS E 115 ASN E 118 HIS ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22459 Z= 0.155 Angle : 0.493 10.820 30292 Z= 0.252 Chirality : 0.039 0.181 3232 Planarity : 0.003 0.057 3864 Dihedral : 3.922 42.599 2910 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.39 % Allowed : 26.95 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2630 helix: 1.16 (0.14), residues: 1486 sheet: -1.86 (0.50), residues: 92 loop : -0.95 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 143 HIS 0.003 0.001 HIS A 658 PHE 0.033 0.001 PHE D 149 TYR 0.013 0.001 TYR A 223 ARG 0.004 0.000 ARG D 165 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 144 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7905 (mmt) cc_final: 0.7532 (mmt) REVERT: A 874 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.6844 (tp) REVERT: A 936 MET cc_start: 0.6267 (mmm) cc_final: 0.5798 (tpt) REVERT: B 10 ARG cc_start: 0.8420 (mmp-170) cc_final: 0.7774 (ttt180) REVERT: B 14 LYS cc_start: 0.7966 (ttpt) cc_final: 0.7500 (mmtp) REVERT: B 124 MET cc_start: 0.8789 (mmm) cc_final: 0.8530 (mmm) REVERT: B 391 ASN cc_start: 0.8526 (OUTLIER) cc_final: 0.8089 (t0) REVERT: B 454 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8953 (tp) REVERT: B 662 ASP cc_start: 0.8497 (p0) cc_final: 0.7801 (t0) REVERT: C 74 LEU cc_start: 0.8237 (mp) cc_final: 0.7656 (tp) REVERT: C 98 ILE cc_start: 0.8901 (mp) cc_final: 0.8228 (tp) REVERT: C 115 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7329 (tm-30) REVERT: C 120 ASP cc_start: 0.8003 (m-30) cc_final: 0.7181 (t0) REVERT: D 134 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6170 (m-10) REVERT: E 85 LEU cc_start: 0.8990 (mt) cc_final: 0.8002 (mm) REVERT: E 297 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7619 (pm20) outliers start: 58 outliers final: 31 residues processed: 193 average time/residue: 0.3139 time to fit residues: 98.4560 Evaluate side-chains 163 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 874 ILE Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain D residue 134 TYR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 85 optimal weight: 10.0000 chunk 228 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 254 optimal weight: 0.0770 chunk 211 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 351 ASN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS E 118 HIS E 133 ASN ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22459 Z= 0.148 Angle : 0.509 9.273 30292 Z= 0.255 Chirality : 0.039 0.212 3232 Planarity : 0.003 0.056 3864 Dihedral : 3.885 42.936 2910 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.35 % Allowed : 27.40 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2630 helix: 1.27 (0.14), residues: 1486 sheet: -1.82 (0.45), residues: 109 loop : -0.92 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP B 143 HIS 0.003 0.001 HIS A 658 PHE 0.015 0.001 PHE D 149 TYR 0.016 0.001 TYR A 223 ARG 0.011 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 137 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7886 (mmt) cc_final: 0.7514 (mmt) REVERT: A 902 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.6827 (pttt) REVERT: A 936 MET cc_start: 0.6189 (mmm) cc_final: 0.5730 (tpt) REVERT: B 10 ARG cc_start: 0.8423 (mmp-170) cc_final: 0.8005 (ttt-90) REVERT: B 124 MET cc_start: 0.8804 (mmm) cc_final: 0.8512 (mmm) REVERT: B 391 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8140 (t0) REVERT: B 454 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8964 (tp) REVERT: B 662 ASP cc_start: 0.8509 (p0) cc_final: 0.7796 (t0) REVERT: B 704 MET cc_start: 0.6460 (tpt) cc_final: 0.6236 (tpp) REVERT: C 74 LEU cc_start: 0.8303 (mp) cc_final: 0.7714 (tp) REVERT: C 88 HIS cc_start: 0.6373 (t-170) cc_final: 0.5693 (t70) REVERT: C 98 ILE cc_start: 0.8915 (mp) cc_final: 0.8259 (tp) REVERT: D 21 MET cc_start: 0.7669 (ppp) cc_final: 0.7369 (ppp) REVERT: E 85 LEU cc_start: 0.9011 (mt) cc_final: 0.8728 (mm) REVERT: E 297 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7531 (pm20) outliers start: 57 outliers final: 34 residues processed: 188 average time/residue: 0.2991 time to fit residues: 92.6046 Evaluate side-chains 164 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 902 LYS Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 977 LYS Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 245 optimal weight: 0.8980 chunk 28 optimal weight: 0.0030 chunk 144 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 214 optimal weight: 0.6980 chunk 142 optimal weight: 0.7980 chunk 253 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 351 ASN B 503 HIS B 698 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 GLN E 118 HIS ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22459 Z= 0.159 Angle : 0.509 9.421 30292 Z= 0.257 Chirality : 0.040 0.256 3232 Planarity : 0.003 0.055 3864 Dihedral : 3.867 43.302 2910 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.64 % Allowed : 27.32 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2630 helix: 1.32 (0.14), residues: 1486 sheet: -1.71 (0.45), residues: 109 loop : -0.87 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP B 143 HIS 0.006 0.001 HIS B 503 PHE 0.022 0.001 PHE D 19 TYR 0.014 0.001 TYR A 223 ARG 0.008 0.000 ARG E 145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 127 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7908 (mmt) cc_final: 0.7504 (mmt) REVERT: A 421 MET cc_start: 0.8789 (tpp) cc_final: 0.8586 (mmm) REVERT: A 634 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7949 (mt) REVERT: A 902 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.6875 (pttt) REVERT: A 936 MET cc_start: 0.6221 (mmm) cc_final: 0.5735 (tpt) REVERT: B 10 ARG cc_start: 0.8462 (mmp-170) cc_final: 0.8012 (ttt180) REVERT: B 124 MET cc_start: 0.8870 (mmm) cc_final: 0.8657 (mmm) REVERT: B 391 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8177 (t0) REVERT: B 454 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.9004 (tp) REVERT: B 662 ASP cc_start: 0.8534 (p0) cc_final: 0.7776 (t0) REVERT: B 704 MET cc_start: 0.6492 (tpt) cc_final: 0.6270 (tpp) REVERT: C 74 LEU cc_start: 0.8372 (mp) cc_final: 0.7754 (tp) REVERT: C 120 ASP cc_start: 0.7716 (m-30) cc_final: 0.7491 (p0) REVERT: E 21 MET cc_start: 0.8644 (ppp) cc_final: 0.8407 (ppp) REVERT: E 85 LEU cc_start: 0.9033 (mt) cc_final: 0.8767 (mm) REVERT: E 204 MET cc_start: 0.9174 (tmm) cc_final: 0.8750 (tmm) REVERT: E 297 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7460 (pm20) outliers start: 64 outliers final: 41 residues processed: 185 average time/residue: 0.2942 time to fit residues: 90.5286 Evaluate side-chains 168 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 122 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 500 PHE Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 902 LYS Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 688 LEU Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 911 ASP Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 156 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 23 optimal weight: 0.0570 chunk 199 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 ASN B 503 HIS ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS ** E 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22459 Z= 0.164 Angle : 0.533 10.614 30292 Z= 0.265 Chirality : 0.040 0.238 3232 Planarity : 0.003 0.053 3864 Dihedral : 3.851 43.280 2910 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.60 % Allowed : 27.65 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2630 helix: 1.42 (0.14), residues: 1479 sheet: -1.58 (0.47), residues: 99 loop : -0.80 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 143 HIS 0.003 0.001 HIS C 17 PHE 0.021 0.001 PHE D 19 TYR 0.020 0.001 TYR E 148 ARG 0.014 0.000 ARG E 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 129 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.7965 (mmt) cc_final: 0.7561 (mmt) REVERT: A 421 MET cc_start: 0.8773 (tpp) cc_final: 0.8561 (mmm) REVERT: A 634 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7978 (mt) REVERT: A 902 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.6856 (pttt) REVERT: A 936 MET cc_start: 0.6190 (mmm) cc_final: 0.5424 (tpt) REVERT: B 10 ARG cc_start: 0.8434 (mmp-170) cc_final: 0.7999 (ttt180) REVERT: B 391 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8212 (t0) REVERT: B 662 ASP cc_start: 0.8555 (p0) cc_final: 0.7846 (t0) REVERT: B 976 MET cc_start: 0.8031 (pmm) cc_final: 0.7587 (pmm) REVERT: C 74 LEU cc_start: 0.8359 (mp) cc_final: 0.7758 (tp) REVERT: C 98 ILE cc_start: 0.9000 (mp) cc_final: 0.8376 (tp) REVERT: C 120 ASP cc_start: 0.7876 (m-30) cc_final: 0.7312 (t0) REVERT: D 21 MET cc_start: 0.7439 (ppp) cc_final: 0.7102 (ppp) REVERT: D 220 LEU cc_start: 0.7685 (tp) cc_final: 0.7408 (pp) REVERT: D 290 MET cc_start: 0.9352 (OUTLIER) cc_final: 0.9089 (ttt) REVERT: E 85 LEU cc_start: 0.9069 (mt) cc_final: 0.8801 (mm) REVERT: E 124 MET cc_start: 0.8640 (mmm) cc_final: 0.8262 (mmm) REVERT: E 297 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7476 (pm20) outliers start: 63 outliers final: 39 residues processed: 183 average time/residue: 0.3012 time to fit residues: 91.7527 Evaluate side-chains 162 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 118 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 902 LYS Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 242 optimal weight: 2.9990 chunk 221 optimal weight: 0.4980 chunk 236 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 223 optimal weight: 0.7980 chunk 235 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 351 ASN B 503 HIS B 563 ASN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22459 Z= 0.179 Angle : 0.557 13.270 30292 Z= 0.277 Chirality : 0.040 0.230 3232 Planarity : 0.003 0.052 3864 Dihedral : 3.902 42.839 2910 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.19 % Allowed : 28.06 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.17), residues: 2630 helix: 1.44 (0.14), residues: 1477 sheet: -1.78 (0.43), residues: 111 loop : -0.77 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 143 HIS 0.004 0.001 HIS D 171 PHE 0.018 0.001 PHE D 19 TYR 0.039 0.001 TYR A 223 ARG 0.004 0.000 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 128 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8046 (mmt) cc_final: 0.7651 (mmt) REVERT: A 634 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8210 (mt) REVERT: A 902 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6462 (pttt) REVERT: A 913 MET cc_start: 0.8506 (mtp) cc_final: 0.8147 (ttt) REVERT: B 10 ARG cc_start: 0.8436 (mmp-170) cc_final: 0.8006 (ttt180) REVERT: B 391 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8234 (t0) REVERT: B 662 ASP cc_start: 0.8565 (p0) cc_final: 0.8215 (p0) REVERT: B 704 MET cc_start: 0.6524 (tpt) cc_final: 0.6315 (tpt) REVERT: B 976 MET cc_start: 0.8083 (pmm) cc_final: 0.7631 (pmm) REVERT: C 74 LEU cc_start: 0.8423 (mp) cc_final: 0.7849 (tp) REVERT: C 98 ILE cc_start: 0.9005 (mp) cc_final: 0.8490 (tp) REVERT: C 120 ASP cc_start: 0.7869 (m-30) cc_final: 0.7236 (t0) REVERT: D 21 MET cc_start: 0.7412 (ppp) cc_final: 0.7073 (ppp) REVERT: D 220 LEU cc_start: 0.7777 (tp) cc_final: 0.7479 (pp) REVERT: D 290 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.9108 (ttt) REVERT: E 21 MET cc_start: 0.8596 (ppp) cc_final: 0.8323 (ppp) REVERT: E 124 MET cc_start: 0.8680 (mmm) cc_final: 0.8333 (mmm) outliers start: 53 outliers final: 42 residues processed: 172 average time/residue: 0.3256 time to fit residues: 92.7635 Evaluate side-chains 163 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 117 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 877 PHE Chi-restraints excluded: chain A residue 902 LYS Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 702 ASN Chi-restraints excluded: chain B residue 844 LEU Chi-restraints excluded: chain B residue 914 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 249 optimal weight: 2.9990 chunk 152 optimal weight: 0.0000 chunk 118 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 262 optimal weight: 1.9990 chunk 241 optimal weight: 0.0270 chunk 208 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 161 optimal weight: 0.0770 chunk 127 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 351 ASN B 503 HIS ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 22459 Z= 0.140 Angle : 0.564 13.182 30292 Z= 0.277 Chirality : 0.040 0.244 3232 Planarity : 0.003 0.070 3864 Dihedral : 3.847 43.780 2910 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.65 % Allowed : 28.48 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2630 helix: 1.44 (0.14), residues: 1482 sheet: -1.67 (0.43), residues: 111 loop : -0.76 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 143 HIS 0.003 0.001 HIS D 171 PHE 0.017 0.001 PHE D 19 TYR 0.029 0.001 TYR A 223 ARG 0.008 0.000 ARG E 145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8576 (m-40) REVERT: A 634 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8111 (mt) REVERT: A 902 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6275 (pttt) REVERT: B 10 ARG cc_start: 0.8388 (mmp-170) cc_final: 0.8006 (ttt180) REVERT: B 291 ASP cc_start: 0.8554 (m-30) cc_final: 0.8240 (m-30) REVERT: B 391 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8211 (t0) REVERT: B 662 ASP cc_start: 0.8530 (p0) cc_final: 0.8171 (p0) REVERT: B 976 MET cc_start: 0.8014 (pmm) cc_final: 0.7560 (pmm) REVERT: C 74 LEU cc_start: 0.8374 (mp) cc_final: 0.7825 (tp) REVERT: C 88 HIS cc_start: 0.6510 (t-170) cc_final: 0.6179 (t70) REVERT: C 98 ILE cc_start: 0.9019 (mp) cc_final: 0.8448 (tp) REVERT: C 120 ASP cc_start: 0.7832 (m-30) cc_final: 0.7207 (t0) REVERT: D 21 MET cc_start: 0.7369 (ppp) cc_final: 0.7035 (ppp) REVERT: D 220 LEU cc_start: 0.7614 (tp) cc_final: 0.7341 (pp) REVERT: D 290 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9147 (ttt) REVERT: E 21 MET cc_start: 0.8578 (ppp) cc_final: 0.8316 (ppp) REVERT: E 85 LEU cc_start: 0.9051 (mt) cc_final: 0.8773 (mm) REVERT: E 124 MET cc_start: 0.8653 (mmm) cc_final: 0.8299 (mmm) outliers start: 40 outliers final: 30 residues processed: 167 average time/residue: 0.3088 time to fit residues: 85.8052 Evaluate side-chains 164 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 129 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 744 PHE Chi-restraints excluded: chain A residue 902 LYS Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 938 ASP Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 936 MET Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 290 MET Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 134 TYR Chi-restraints excluded: chain E residue 190 TYR Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 297 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 263 random chunks: chunk 222 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 214 optimal weight: 0.0770 chunk 26 optimal weight: 0.0370 chunk 38 optimal weight: 0.0040 chunk 183 optimal weight: 2.9990 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 351 ASN B 503 HIS ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 ASN C 21 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.054060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.042205 restraints weight = 124020.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.043693 restraints weight = 69997.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.044717 restraints weight = 47676.408| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 22459 Z= 0.137 Angle : 0.560 16.953 30292 Z= 0.274 Chirality : 0.039 0.239 3232 Planarity : 0.003 0.065 3864 Dihedral : 3.791 43.804 2910 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.61 % Allowed : 28.44 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2630 helix: 1.48 (0.14), residues: 1477 sheet: -1.59 (0.43), residues: 111 loop : -0.76 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 143 HIS 0.003 0.000 HIS C 17 PHE 0.017 0.001 PHE D 19 TYR 0.037 0.001 TYR A 223 ARG 0.006 0.000 ARG E 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3928.86 seconds wall clock time: 72 minutes 28.86 seconds (4348.86 seconds total)