Starting phenix.real_space_refine on Sat Mar 23 09:38:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uth_26770/03_2024/7uth_26770.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uth_26770/03_2024/7uth_26770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uth_26770/03_2024/7uth_26770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uth_26770/03_2024/7uth_26770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uth_26770/03_2024/7uth_26770.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uth_26770/03_2024/7uth_26770.pdb" } resolution = 3.9 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= -0.069 sd= 1.599 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: 5 Type Number sf(0) Gaussians S 70 5.16 5 C 11642 2.51 5 N 2930 2.21 5 O 3376 1.98 5 H 18572 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 18": "OE1" <-> "OE2" Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 558": "OD1" <-> "OD2" Residue "A GLU 597": "OE1" <-> "OE2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 852": "OD1" <-> "OD2" Residue "A PHE 857": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A GLU 1157": "OE1" <-> "OE2" Residue "A GLU 1286": "OE1" <-> "OE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "B TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 743": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1179": "OE1" <-> "OE2" Residue "B GLU 1204": "OE1" <-> "OE2" Residue "B GLU 1263": "OE1" <-> "OE2" Residue "B GLU 1329": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36590 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 18295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 18295 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 34, 'TRANS': 1086} Chain breaks: 14 Chain: "B" Number of atoms: 18295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 18295 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 34, 'TRANS': 1086} Chain breaks: 14 Time building chain proxies: 15.23, per 1000 atoms: 0.42 Number of scatterers: 36590 At special positions: 0 Unit cell: (317.824, 179.712, 121.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 O 3376 8.00 N 2930 7.00 C 11642 6.00 H 18572 1.00 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: 29.63 Conformation dependent library (CDL) restraints added in 3.6 seconds 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4352 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 0 sheets defined 76.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.78 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 removed outlier: 3.810A pdb=" N THR A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.812A pdb=" N ILE A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) Proline residue: A 100 - end of helix removed outlier: 3.585A pdb=" N ILE A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.501A pdb=" N THR A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 117 " --> pdb=" O TYR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.689A pdb=" N THR A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 179 Processing helix chain 'A' and resid 186 through 203 removed outlier: 3.780A pdb=" N ILE A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 228 removed outlier: 3.934A pdb=" N LYS A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 343 Processing helix chain 'A' and resid 352 through 370 removed outlier: 3.619A pdb=" N SER A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 376 Processing helix chain 'A' and resid 377 through 398 removed outlier: 3.773A pdb=" N LEU A 383 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Proline residue: A 387 - end of helix removed outlier: 3.930A pdb=" N LYS A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 391 " --> pdb=" O PRO A 387 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 419 removed outlier: 3.523A pdb=" N ALA A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 440 removed outlier: 4.048A pdb=" N ILE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 428 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 467 removed outlier: 3.535A pdb=" N GLU A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 473 removed outlier: 3.632A pdb=" N THR A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.535A pdb=" N PHE A 481 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 506 removed outlier: 3.545A pdb=" N ASN A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 removed outlier: 3.529A pdb=" N ALA A 510 " --> pdb=" O PRO A 507 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU A 511 " --> pdb=" O GLU A 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 507 through 511' Processing helix chain 'A' and resid 516 through 535 removed outlier: 3.877A pdb=" N ILE A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 529 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N MET A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 533 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 545 removed outlier: 4.170A pdb=" N PHE A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 545 " --> pdb=" O ARG A 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 545' Processing helix chain 'A' and resid 555 through 573 Processing helix chain 'A' and resid 573 through 584 Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 591 through 602 removed outlier: 3.873A pdb=" N ILE A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 599 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 600 " --> pdb=" O ALA A 596 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN A 602 " --> pdb=" O PHE A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 617 removed outlier: 3.723A pdb=" N ILE A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS A 617 " --> pdb=" O LEU A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 622 removed outlier: 4.222A pdb=" N SER A 622 " --> pdb=" O ASP A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.962A pdb=" N ILE A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 removed outlier: 3.522A pdb=" N LYS A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 673 removed outlier: 3.848A pdb=" N ARG A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS A 670 " --> pdb=" O SER A 666 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN A 672 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A 673 " --> pdb=" O TYR A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 712 removed outlier: 3.784A pdb=" N TYR A 703 " --> pdb=" O PHE A 699 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 704 " --> pdb=" O ILE A 700 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET A 707 " --> pdb=" O TYR A 703 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASN A 709 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR A 710 " --> pdb=" O ILE A 706 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP A 711 " --> pdb=" O MET A 707 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 730 removed outlier: 3.565A pdb=" N TYR A 726 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 727 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 730 " --> pdb=" O TYR A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 754 removed outlier: 3.848A pdb=" N ARG A 746 " --> pdb=" O TRP A 742 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 747 " --> pdb=" O TYR A 743 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A 753 " --> pdb=" O CYS A 749 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 782 removed outlier: 3.908A pdb=" N TRP A 773 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN A 775 " --> pdb=" O ASP A 771 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 806 Processing helix chain 'A' and resid 809 through 812 removed outlier: 3.545A pdb=" N GLN A 812 " --> pdb=" O ILE A 809 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 809 through 812' Processing helix chain 'A' and resid 813 through 828 Processing helix chain 'A' and resid 830 through 851 removed outlier: 3.503A pdb=" N ARG A 836 " --> pdb=" O HIS A 832 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 851 " --> pdb=" O ILE A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 868 removed outlier: 3.602A pdb=" N ASP A 859 " --> pdb=" O ASP A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 915 removed outlier: 3.636A pdb=" N SER A 915 " --> pdb=" O ARG A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 931 removed outlier: 3.795A pdb=" N LEU A 920 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 926 " --> pdb=" O THR A 922 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A 931 " --> pdb=" O ARG A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 956 removed outlier: 3.899A pdb=" N ASP A 956 " --> pdb=" O THR A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 972 removed outlier: 3.726A pdb=" N GLN A 968 " --> pdb=" O PHE A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1026 removed outlier: 4.248A pdb=" N LYS A1014 " --> pdb=" O GLU A1010 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A1016 " --> pdb=" O GLU A1012 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A1018 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS A1024 " --> pdb=" O MET A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1033 removed outlier: 4.235A pdb=" N VAL A1032 " --> pdb=" O ILE A1028 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A1033 " --> pdb=" O ALA A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1039 removed outlier: 4.082A pdb=" N ASN A1038 " --> pdb=" O ASN A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1050 removed outlier: 3.561A pdb=" N ILE A1044 " --> pdb=" O THR A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1081 removed outlier: 3.718A pdb=" N LEU A1067 " --> pdb=" O PHE A1063 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU A1068 " --> pdb=" O GLU A1064 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A1080 " --> pdb=" O ALA A1076 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A1081 " --> pdb=" O LEU A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1099 removed outlier: 4.174A pdb=" N PHE A1090 " --> pdb=" O GLU A1086 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A1091 " --> pdb=" O LEU A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1123 removed outlier: 3.547A pdb=" N VAL A1109 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A1113 " --> pdb=" O VAL A1109 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR A1114 " --> pdb=" O ARG A1110 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A1115 " --> pdb=" O ARG A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1136 Processing helix chain 'A' and resid 1152 through 1165 Processing helix chain 'A' and resid 1171 through 1178 Processing helix chain 'A' and resid 1178 through 1185 removed outlier: 4.028A pdb=" N TRP A1182 " --> pdb=" O ASN A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1232 removed outlier: 4.054A pdb=" N VAL A1221 " --> pdb=" O ASN A1217 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY A1232 " --> pdb=" O ILE A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1276 removed outlier: 4.271A pdb=" N LEU A1264 " --> pdb=" O LYS A1260 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A1276 " --> pdb=" O THR A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1298 through 1300 No H-bonds generated for 'chain 'A' and resid 1298 through 1300' Processing helix chain 'A' and resid 1302 through 1320 removed outlier: 3.703A pdb=" N PHE A1308 " --> pdb=" O GLN A1304 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A1312 " --> pdb=" O PHE A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1336 removed outlier: 3.728A pdb=" N LEU A1334 " --> pdb=" O SER A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1344 removed outlier: 3.848A pdb=" N LEU A1342 " --> pdb=" O GLY A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1354 No H-bonds generated for 'chain 'A' and resid 1352 through 1354' Processing helix chain 'A' and resid 1355 through 1370 removed outlier: 3.582A pdb=" N THR A1361 " --> pdb=" O SER A1357 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A1363 " --> pdb=" O ILE A1359 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A1368 " --> pdb=" O SER A1364 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR A1370 " --> pdb=" O VAL A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1381 through 1389 removed outlier: 3.623A pdb=" N LEU A1385 " --> pdb=" O PHE A1381 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASN A1389 " --> pdb=" O LEU A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1400 Processing helix chain 'A' and resid 1400 through 1414 removed outlier: 4.081A pdb=" N ASP A1407 " --> pdb=" O GLN A1403 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS A1408 " --> pdb=" O LEU A1404 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A1410 " --> pdb=" O LEU A1406 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A1412 " --> pdb=" O LYS A1408 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 24 removed outlier: 3.897A pdb=" N THR B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.581A pdb=" N LEU B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.597A pdb=" N THR B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 151 removed outlier: 3.795A pdb=" N VAL B 146 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 149 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B 150 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N HIS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 179 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.580A pdb=" N ILE B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASP B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 229 removed outlier: 3.621A pdb=" N LYS B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 344 Processing helix chain 'B' and resid 352 through 375 removed outlier: 3.772A pdb=" N ILE B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASP B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN B 375 " --> pdb=" O GLY B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 386 Processing helix chain 'B' and resid 386 through 399 removed outlier: 3.759A pdb=" N ILE B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 420 Processing helix chain 'B' and resid 426 through 440 removed outlier: 4.044A pdb=" N THR B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP B 440 " --> pdb=" O SER B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 467 Processing helix chain 'B' and resid 467 through 473 removed outlier: 3.849A pdb=" N THR B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.763A pdb=" N ASN B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 505 Processing helix chain 'B' and resid 508 through 513 removed outlier: 4.334A pdb=" N THR B 512 " --> pdb=" O GLU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 532 removed outlier: 3.755A pdb=" N ILE B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY B 524 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 525 " --> pdb=" O CYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 545 removed outlier: 3.547A pdb=" N GLY B 545 " --> pdb=" O GLU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 573 Processing helix chain 'B' and resid 573 through 585 Proline residue: B 579 - end of helix removed outlier: 3.504A pdb=" N GLY B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 602 removed outlier: 4.058A pdb=" N ILE B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 615 removed outlier: 3.680A pdb=" N LEU B 615 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 631 removed outlier: 3.833A pdb=" N ILE B 628 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG B 629 " --> pdb=" O ASN B 625 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE B 631 " --> pdb=" O TYR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 649 removed outlier: 3.781A pdb=" N THR B 647 " --> pdb=" O ARG B 643 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS B 648 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 673 removed outlier: 3.661A pdb=" N GLU B 659 " --> pdb=" O SER B 655 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG B 660 " --> pdb=" O GLN B 656 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE B 661 " --> pdb=" O GLN B 657 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 662 " --> pdb=" O ILE B 658 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 663 " --> pdb=" O GLU B 659 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA B 664 " --> pdb=" O ARG B 660 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 665 " --> pdb=" O ILE B 661 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS B 670 " --> pdb=" O SER B 666 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 673 " --> pdb=" O TYR B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 680 removed outlier: 3.559A pdb=" N ILE B 680 " --> pdb=" O PRO B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 714 removed outlier: 3.847A pdb=" N MET B 707 " --> pdb=" O TYR B 703 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR B 710 " --> pdb=" O ILE B 706 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 729 removed outlier: 3.750A pdb=" N SER B 727 " --> pdb=" O GLU B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 754 removed outlier: 3.808A pdb=" N LYS B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 782 removed outlier: 3.974A pdb=" N TRP B 773 " --> pdb=" O PHE B 769 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN B 774 " --> pdb=" O GLU B 770 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN B 775 " --> pdb=" O ASP B 771 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 782 " --> pdb=" O SER B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 806 Processing helix chain 'B' and resid 807 through 828 removed outlier: 4.014A pdb=" N LYS B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 812 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Proline residue: B 815 - end of helix removed outlier: 3.732A pdb=" N ILE B 824 " --> pdb=" O THR B 820 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 827 " --> pdb=" O ASN B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 851 removed outlier: 3.578A pdb=" N ARG B 836 " --> pdb=" O HIS B 832 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 851 " --> pdb=" O ILE B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 868 Processing helix chain 'B' and resid 906 through 915 removed outlier: 3.620A pdb=" N SER B 915 " --> pdb=" O ARG B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 931 removed outlier: 4.409A pdb=" N GLN B 919 " --> pdb=" O SER B 915 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 920 " --> pdb=" O PHE B 916 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 931 " --> pdb=" O ARG B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 956 removed outlier: 4.014A pdb=" N ASP B 956 " --> pdb=" O THR B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 972 removed outlier: 3.620A pdb=" N GLN B 968 " --> pdb=" O PHE B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1027 removed outlier: 4.254A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS B1014 " --> pdb=" O GLU B1010 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N SER B1015 " --> pdb=" O GLU B1011 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS B1018 " --> pdb=" O LYS B1014 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B1019 " --> pdb=" O SER B1015 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS B1024 " --> pdb=" O MET B1020 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B1027 " --> pdb=" O ILE B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1033 removed outlier: 4.114A pdb=" N VAL B1032 " --> pdb=" O ILE B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1035 through 1039 removed outlier: 3.648A pdb=" N ASN B1038 " --> pdb=" O ASN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1051 removed outlier: 3.759A pdb=" N ILE B1044 " --> pdb=" O THR B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1057 through 1061 removed outlier: 3.644A pdb=" N SER B1060 " --> pdb=" O ALA B1057 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG B1061 " --> pdb=" O ASP B1058 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1057 through 1061' Processing helix chain 'B' and resid 1062 through 1081 removed outlier: 3.700A pdb=" N LEU B1067 " --> pdb=" O PHE B1063 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B1068 " --> pdb=" O GLU B1064 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE B1080 " --> pdb=" O ALA B1076 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS B1081 " --> pdb=" O LEU B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1100 removed outlier: 4.005A pdb=" N LYS B1089 " --> pdb=" O LYS B1085 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N PHE B1090 " --> pdb=" O GLU B1086 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS B1100 " --> pdb=" O PHE B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1123 removed outlier: 3.521A pdb=" N VAL B1109 " --> pdb=" O THR B1105 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG B1110 " --> pdb=" O LYS B1106 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B1114 " --> pdb=" O ARG B1110 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR B1115 " --> pdb=" O ARG B1111 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B1118 " --> pdb=" O THR B1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1137 Processing helix chain 'B' and resid 1146 through 1152 removed outlier: 3.863A pdb=" N PHE B1150 " --> pdb=" O THR B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1165 removed outlier: 3.617A pdb=" N LYS B1156 " --> pdb=" O THR B1152 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B1157 " --> pdb=" O ASN B1153 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B1158 " --> pdb=" O GLN B1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 1168 through 1177 removed outlier: 4.531A pdb=" N GLY B1173 " --> pdb=" O GLU B1169 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N PHE B1174 " --> pdb=" O PHE B1170 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B1175 " --> pdb=" O TYR B1171 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B1176 " --> pdb=" O ARG B1172 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY B1177 " --> pdb=" O GLY B1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1190 removed outlier: 3.764A pdb=" N TRP B1182 " --> pdb=" O ASN B1178 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B1190 " --> pdb=" O ARG B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1191 through 1193 No H-bonds generated for 'chain 'B' and resid 1191 through 1193' Processing helix chain 'B' and resid 1194 through 1207 removed outlier: 3.655A pdb=" N PHE B1199 " --> pdb=" O SER B1195 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR B1201 " --> pdb=" O SER B1197 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1232 removed outlier: 4.149A pdb=" N VAL B1221 " --> pdb=" O ASN B1217 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY B1232 " --> pdb=" O ILE B1228 " (cutoff:3.500A) Processing helix chain 'B' and resid 1261 through 1279 removed outlier: 3.523A pdb=" N ILE B1269 " --> pdb=" O SER B1265 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B1270 " --> pdb=" O LEU B1266 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B1276 " --> pdb=" O THR B1272 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU B1277 " --> pdb=" O SER B1273 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B1278 " --> pdb=" O HIS B1274 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN B1279 " --> pdb=" O LEU B1275 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1296 removed outlier: 3.705A pdb=" N PHE B1288 " --> pdb=" O LYS B1284 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B1289 " --> pdb=" O ASN B1285 " (cutoff:3.500A) Processing helix chain 'B' and resid 1297 through 1300 Processing helix chain 'B' and resid 1302 through 1320 removed outlier: 3.517A pdb=" N GLU B1314 " --> pdb=" O VAL B1310 " (cutoff:3.500A) Processing helix chain 'B' and resid 1330 through 1339 removed outlier: 3.663A pdb=" N LEU B1334 " --> pdb=" O SER B1330 " (cutoff:3.500A) Processing helix chain 'B' and resid 1340 through 1343 Processing helix chain 'B' and resid 1355 through 1374 removed outlier: 3.919A pdb=" N ILE B1359 " --> pdb=" O LEU B1355 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY B1374 " --> pdb=" O TYR B1370 " (cutoff:3.500A) Processing helix chain 'B' and resid 1379 through 1391 removed outlier: 3.993A pdb=" N LYS B1383 " --> pdb=" O GLU B1379 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B1387 " --> pdb=" O LYS B1383 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE B1391 " --> pdb=" O ILE B1387 " (cutoff:3.500A) Processing helix chain 'B' and resid 1396 through 1415 removed outlier: 3.744A pdb=" N LYS B1400 " --> pdb=" O ASP B1396 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B1412 " --> pdb=" O LYS B1408 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASN B1415 " --> pdb=" O ILE B1411 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2736 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: 13.41 Time building geometry restraints manager: 30.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18538 1.03 - 1.23: 259 1.23 - 1.43: 7090 1.43 - 1.63: 10881 1.63 - 1.82: 106 Bond restraints: 36874 Sorted by residual: bond pdb=" CB ILE B1228 " pdb=" CG2 ILE B1228 " ideal model delta sigma weight residual 1.521 1.596 -0.075 3.30e-02 9.18e+02 5.19e+00 bond pdb=" CB GLN B 78 " pdb=" CG GLN B 78 " ideal model delta sigma weight residual 1.520 1.586 -0.066 3.00e-02 1.11e+03 4.81e+00 bond pdb=" CB ILE A1411 " pdb=" CG2 ILE A1411 " ideal model delta sigma weight residual 1.521 1.591 -0.070 3.30e-02 9.18e+02 4.51e+00 bond pdb=" C CYS B 616 " pdb=" N HIS B 617 " ideal model delta sigma weight residual 1.329 1.390 -0.062 3.03e-02 1.09e+03 4.14e+00 bond pdb=" CA LYS A 854 " pdb=" CB LYS A 854 " ideal model delta sigma weight residual 1.529 1.562 -0.033 1.62e-02 3.81e+03 4.03e+00 ... (remaining 36869 not shown) Histogram of bond angle deviations from ideal: 73.71 - 85.81: 3 85.81 - 97.90: 0 97.90 - 110.00: 33195 110.00 - 122.10: 28680 122.10 - 134.20: 5110 Bond angle restraints: 66988 Sorted by residual: angle pdb=" C PHE A 851 " pdb=" CA PHE A 851 " pdb=" HA PHE A 851 " ideal model delta sigma weight residual 109.00 73.71 35.29 3.00e+00 1.11e-01 1.38e+02 angle pdb=" N PHE A 851 " pdb=" CA PHE A 851 " pdb=" HA PHE A 851 " ideal model delta sigma weight residual 110.00 76.66 33.34 3.00e+00 1.11e-01 1.23e+02 angle pdb=" CB PHE A 851 " pdb=" CA PHE A 851 " pdb=" HA PHE A 851 " ideal model delta sigma weight residual 109.00 76.42 32.58 3.00e+00 1.11e-01 1.18e+02 angle pdb=" CA LYS A 854 " pdb=" CB LYS A 854 " pdb=" CG LYS A 854 " ideal model delta sigma weight residual 114.10 124.24 -10.14 2.00e+00 2.50e-01 2.57e+01 angle pdb=" CA GLU A1277 " pdb=" CB GLU A1277 " pdb=" CG GLU A1277 " ideal model delta sigma weight residual 114.10 123.47 -9.37 2.00e+00 2.50e-01 2.19e+01 ... (remaining 66983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 14542 17.84 - 35.68: 1923 35.68 - 53.52: 548 53.52 - 71.35: 112 71.35 - 89.19: 25 Dihedral angle restraints: 17150 sinusoidal: 9474 harmonic: 7676 Sorted by residual: dihedral pdb=" CA GLU A1193 " pdb=" C GLU A1193 " pdb=" N GLN A1194 " pdb=" CA GLN A1194 " ideal model delta harmonic sigma weight residual -180.00 -153.03 -26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA LEU B 83 " pdb=" C LEU B 83 " pdb=" N ASN B 84 " pdb=" CA ASN B 84 " ideal model delta harmonic sigma weight residual 180.00 153.88 26.12 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA GLU A1277 " pdb=" C GLU A1277 " pdb=" N ASP A1278 " pdb=" CA ASP A1278 " ideal model delta harmonic sigma weight residual 180.00 -153.94 -26.06 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 17147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2774 0.085 - 0.171: 173 0.171 - 0.256: 9 0.256 - 0.341: 1 0.341 - 0.427: 1 Chirality restraints: 2958 Sorted by residual: chirality pdb=" CA PHE A 851 " pdb=" N PHE A 851 " pdb=" C PHE A 851 " pdb=" CB PHE A 851 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" CG LEU A1119 " pdb=" CB LEU A1119 " pdb=" CD1 LEU A1119 " pdb=" CD2 LEU A1119 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB ILE A1384 " pdb=" CA ILE A1384 " pdb=" CG1 ILE A1384 " pdb=" CG2 ILE A1384 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 2955 not shown) Planarity restraints: 5218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1340 " 0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO A1341 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A1341 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A1341 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B1340 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO B1341 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B1341 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B1341 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 329 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO A 330 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " 0.035 5.00e-02 4.00e+02 ... (remaining 5215 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 5577 2.27 - 2.85: 81124 2.85 - 3.43: 93207 3.43 - 4.02: 116876 4.02 - 4.60: 179188 Nonbonded interactions: 475972 Sorted by model distance: nonbonded pdb=" H PHE A 851 " pdb=" HA PHE A 851 " model vdw 1.686 1.816 nonbonded pdb=" OE1 GLU B1263 " pdb=" H GLU B1263 " model vdw 1.715 1.850 nonbonded pdb=" O MET B 218 " pdb=" HG1 THR B 222 " model vdw 1.735 1.850 nonbonded pdb=" OE1 GLU B1277 " pdb=" HZ2 LYS B1320 " model vdw 1.739 1.850 nonbonded pdb=" HG SER B 722 " pdb=" OD2 ASP B 725 " model vdw 1.752 1.850 ... (remaining 475967 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.540 Extract box with map and model: 7.850 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 109.410 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 18302 Z= 0.385 Angle : 0.977 10.136 24688 Z= 0.497 Chirality : 0.045 0.427 2958 Planarity : 0.005 0.088 3068 Dihedral : 18.375 89.192 6874 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.50 % Rotamer: Outliers : 0.72 % Allowed : 29.41 % Favored : 69.87 % Cbeta Deviations : 0.05 % 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: -0.70 (0.17), residues: 2182 helix: 0.15 (0.13), residues: 1391 sheet: None (None), residues: 0 loop : -1.47 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1182 HIS 0.004 0.001 HIS A1369 PHE 0.037 0.002 PHE B1158 TYR 0.020 0.002 TYR B 377 ARG 0.014 0.001 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 518 time to evaluate : 3.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 606 MET cc_start: 0.6971 (mmm) cc_final: 0.6585 (mmm) REVERT: B 82 MET cc_start: 0.9121 (tpp) cc_final: 0.8915 (tpp) REVERT: B 126 PHE cc_start: 0.7879 (t80) cc_final: 0.7669 (t80) REVERT: B 346 GLU cc_start: 0.7882 (tp30) cc_final: 0.7645 (tp30) outliers start: 15 outliers final: 10 residues processed: 524 average time/residue: 0.5346 time to fit residues: 456.0555 Evaluate side-chains 516 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 506 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 1020 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.0870 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A 812 GLN B 397 GLN B 921 ASN B1038 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18302 Z= 0.238 Angle : 0.572 6.815 24688 Z= 0.308 Chirality : 0.036 0.377 2958 Planarity : 0.004 0.069 3068 Dihedral : 5.868 57.625 2363 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.41 % Favored : 94.41 % Rotamer: Outliers : 4.17 % Allowed : 27.83 % Favored : 67.99 % Cbeta Deviations : 0.05 % 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: 0.01 (0.18), residues: 2182 helix: 0.75 (0.13), residues: 1444 sheet: None (None), residues: 0 loop : -1.43 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 470 HIS 0.004 0.001 HIS A1369 PHE 0.014 0.001 PHE B 926 TYR 0.011 0.001 TYR A 138 ARG 0.003 0.000 ARG B 650 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 523 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8982 (mt) REVERT: A 375 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8456 (tm-30) REVERT: A 424 GLN cc_start: 0.8287 (pt0) cc_final: 0.7951 (pt0) REVERT: A 431 LEU cc_start: 0.7966 (mm) cc_final: 0.7687 (mm) REVERT: A 460 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8449 (tm-30) REVERT: A 464 GLU cc_start: 0.8701 (tp30) cc_final: 0.8319 (tp30) REVERT: A 508 GLU cc_start: 0.7453 (tt0) cc_final: 0.6702 (tm-30) REVERT: A 562 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8713 (mt-10) REVERT: A 590 ASP cc_start: 0.4980 (OUTLIER) cc_final: 0.4353 (m-30) REVERT: A 677 PRO cc_start: 0.7688 (Cg_endo) cc_final: 0.7068 (Cg_exo) REVERT: A 736 HIS cc_start: 0.6464 (t-90) cc_final: 0.6105 (t-90) REVERT: A 810 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: A 1157 GLU cc_start: 0.7927 (mm-30) cc_final: 0.6636 (tp30) REVERT: A 1264 LEU cc_start: 0.9112 (tp) cc_final: 0.8809 (tp) REVERT: B 78 GLN cc_start: 0.9347 (mm110) cc_final: 0.8552 (tm-30) REVERT: B 346 GLU cc_start: 0.7929 (tp30) cc_final: 0.7714 (tp30) REVERT: B 422 ASN cc_start: 0.8530 (m-40) cc_final: 0.8187 (m110) REVERT: B 464 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8297 (tm-30) REVERT: B 1027 ASN cc_start: 0.8573 (t0) cc_final: 0.8324 (t0) outliers start: 87 outliers final: 68 residues processed: 562 average time/residue: 0.5904 time to fit residues: 538.6097 Evaluate side-chains 586 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 515 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 945 ASN Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1038 ASN Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1136 ASP Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1287 ILE Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1411 ILE Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 606 MET Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 839 THR Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1226 ASP Chi-restraints excluded: chain B residue 1228 ILE Chi-restraints excluded: chain B residue 1298 CYS Chi-restraints excluded: chain B residue 1360 LEU Chi-restraints excluded: chain B residue 1363 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 203 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 202 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 334 GLN A 422 ASN A1415 ASN B 683 ASN B 932 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18302 Z= 0.230 Angle : 0.552 7.754 24688 Z= 0.296 Chirality : 0.035 0.362 2958 Planarity : 0.004 0.061 3068 Dihedral : 5.488 50.592 2354 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.00 % Favored : 93.81 % Rotamer: Outliers : 4.89 % Allowed : 28.36 % Favored : 66.75 % Cbeta Deviations : 0.05 % 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: 0.14 (0.18), residues: 2182 helix: 0.91 (0.14), residues: 1432 sheet: None (None), residues: 0 loop : -1.48 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 470 HIS 0.009 0.001 HIS B1369 PHE 0.014 0.001 PHE A 126 TYR 0.008 0.001 TYR A 191 ARG 0.004 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 530 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8007 (tm-30) REVERT: A 117 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.9012 (mt) REVERT: A 375 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8514 (tm-30) REVERT: A 431 LEU cc_start: 0.7876 (mm) cc_final: 0.7470 (mm) REVERT: A 460 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8196 (tm-30) REVERT: A 464 GLU cc_start: 0.8711 (tp30) cc_final: 0.8343 (tp30) REVERT: A 508 GLU cc_start: 0.7477 (tt0) cc_final: 0.6714 (tm-30) REVERT: A 562 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8711 (mt-10) REVERT: A 590 ASP cc_start: 0.5031 (OUTLIER) cc_final: 0.4451 (m-30) REVERT: A 677 PRO cc_start: 0.7297 (Cg_endo) cc_final: 0.6734 (Cg_exo) REVERT: A 736 HIS cc_start: 0.6416 (t-90) cc_final: 0.5929 (t-90) REVERT: A 810 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7439 (m-80) REVERT: A 1157 GLU cc_start: 0.7846 (mm-30) cc_final: 0.6480 (tp30) REVERT: A 1178 ASN cc_start: 0.8820 (t0) cc_final: 0.8480 (t0) REVERT: A 1264 LEU cc_start: 0.9001 (tp) cc_final: 0.8780 (tp) REVERT: B 78 GLN cc_start: 0.9338 (mm110) cc_final: 0.8547 (tm-30) REVERT: B 346 GLU cc_start: 0.7938 (tp30) cc_final: 0.7715 (tp30) REVERT: B 464 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8263 (tm-30) REVERT: B 921 ASN cc_start: 0.9243 (OUTLIER) cc_final: 0.8536 (t0) REVERT: B 941 GLU cc_start: 0.6831 (tm-30) cc_final: 0.6211 (tm-30) REVERT: B 1323 ILE cc_start: 0.8218 (mt) cc_final: 0.7851 (mm) outliers start: 102 outliers final: 81 residues processed: 579 average time/residue: 0.5528 time to fit residues: 514.9703 Evaluate side-chains 603 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 518 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 851 PHE Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 945 ASN Chi-restraints excluded: chain A residue 947 VAL Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1038 ASN Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1136 ASP Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1204 GLU Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 841 LEU Chi-restraints excluded: chain B residue 860 ILE Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1152 THR Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1226 ASP Chi-restraints excluded: chain B residue 1228 ILE Chi-restraints excluded: chain B residue 1298 CYS Chi-restraints excluded: chain B residue 1311 VAL Chi-restraints excluded: chain B residue 1363 ILE Chi-restraints excluded: chain B residue 1370 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 chunk 136 optimal weight: 0.6980 chunk 204 optimal weight: 0.0770 chunk 216 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A1274 HIS A1415 ASN B 932 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18302 Z= 0.166 Angle : 0.509 7.096 24688 Z= 0.269 Chirality : 0.034 0.362 2958 Planarity : 0.003 0.054 3068 Dihedral : 5.276 50.464 2354 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.27 % Favored : 94.59 % Rotamer: Outliers : 4.46 % Allowed : 28.69 % Favored : 66.84 % Cbeta Deviations : 0.05 % 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 (0.18), residues: 2182 helix: 1.14 (0.14), residues: 1428 sheet: None (None), residues: 0 loop : -1.42 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1182 HIS 0.004 0.001 HIS B1369 PHE 0.017 0.001 PHE A 126 TYR 0.007 0.001 TYR A 138 ARG 0.005 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 534 time to evaluate : 2.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 117 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.9009 (mt) REVERT: A 126 PHE cc_start: 0.8185 (t80) cc_final: 0.7984 (t80) REVERT: A 460 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8180 (tm-30) REVERT: A 464 GLU cc_start: 0.8730 (tp30) cc_final: 0.8359 (tp30) REVERT: A 562 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8701 (mt-10) REVERT: A 590 ASP cc_start: 0.5003 (OUTLIER) cc_final: 0.4452 (m-30) REVERT: A 606 MET cc_start: 0.7421 (mmm) cc_final: 0.7144 (mmm) REVERT: A 677 PRO cc_start: 0.7269 (Cg_endo) cc_final: 0.6796 (Cg_exo) REVERT: A 736 HIS cc_start: 0.6484 (t-90) cc_final: 0.5991 (t-90) REVERT: A 810 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7255 (m-80) REVERT: A 1157 GLU cc_start: 0.7822 (mm-30) cc_final: 0.6461 (tp30) REVERT: A 1182 TRP cc_start: 0.8941 (m100) cc_final: 0.8580 (m100) REVERT: A 1342 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8670 (mm) REVERT: B 78 GLN cc_start: 0.9336 (mm110) cc_final: 0.8512 (tm-30) REVERT: B 346 GLU cc_start: 0.7969 (tp30) cc_final: 0.7754 (tp30) REVERT: B 464 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8271 (tm-30) REVERT: B 831 ASP cc_start: 0.8045 (m-30) cc_final: 0.7795 (m-30) REVERT: B 921 ASN cc_start: 0.9218 (OUTLIER) cc_final: 0.8445 (t0) REVERT: B 986 ASN cc_start: 0.5836 (OUTLIER) cc_final: 0.4686 (t0) REVERT: B 1319 ASN cc_start: 0.8855 (m-40) cc_final: 0.8642 (m-40) REVERT: B 1323 ILE cc_start: 0.8207 (mt) cc_final: 0.7848 (mm) outliers start: 93 outliers final: 75 residues processed: 579 average time/residue: 0.5788 time to fit residues: 543.2139 Evaluate side-chains 603 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 522 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 945 ASN Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1038 ASN Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1136 ASP Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1204 GLU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1226 ASP Chi-restraints excluded: chain B residue 1228 ILE Chi-restraints excluded: chain B residue 1298 CYS Chi-restraints excluded: chain B residue 1363 ILE Chi-restraints excluded: chain B residue 1370 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 161 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 184 optimal weight: 0.0570 chunk 149 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 194 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 603 ASN B1180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 18302 Z= 0.185 Angle : 0.511 7.172 24688 Z= 0.271 Chirality : 0.034 0.366 2958 Planarity : 0.003 0.052 3068 Dihedral : 5.144 50.392 2352 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.14 % Favored : 93.72 % Rotamer: Outliers : 4.61 % Allowed : 29.08 % Favored : 66.31 % Cbeta Deviations : 0.05 % 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: 0.47 (0.18), residues: 2182 helix: 1.20 (0.14), residues: 1433 sheet: None (None), residues: 0 loop : -1.43 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1220 HIS 0.003 0.001 HIS B1369 PHE 0.014 0.001 PHE A 126 TYR 0.008 0.001 TYR A 138 ARG 0.004 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 531 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7395 (mm) REVERT: A 460 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 464 GLU cc_start: 0.8749 (tp30) cc_final: 0.8364 (tp30) REVERT: A 590 ASP cc_start: 0.5007 (OUTLIER) cc_final: 0.4459 (m-30) REVERT: A 677 PRO cc_start: 0.7301 (Cg_endo) cc_final: 0.6819 (Cg_exo) REVERT: A 736 HIS cc_start: 0.6537 (t-90) cc_final: 0.6035 (t-90) REVERT: A 810 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: A 1157 GLU cc_start: 0.7831 (mm-30) cc_final: 0.6474 (tp30) REVERT: A 1178 ASN cc_start: 0.8760 (t0) cc_final: 0.8425 (t0) REVERT: A 1182 TRP cc_start: 0.8958 (m100) cc_final: 0.8583 (m100) REVERT: A 1196 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8008 (tm-30) REVERT: B 78 GLN cc_start: 0.9333 (mm110) cc_final: 0.8510 (tm-30) REVERT: B 346 GLU cc_start: 0.7972 (tp30) cc_final: 0.7751 (tp30) REVERT: B 464 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8249 (tm-30) REVERT: B 520 ILE cc_start: 0.8396 (mm) cc_final: 0.8163 (mm) REVERT: B 831 ASP cc_start: 0.7857 (m-30) cc_final: 0.7477 (m-30) REVERT: B 921 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8437 (t0) REVERT: B 986 ASN cc_start: 0.6107 (OUTLIER) cc_final: 0.4854 (t0) REVERT: B 1150 PHE cc_start: 0.9313 (m-80) cc_final: 0.9107 (m-80) REVERT: B 1323 ILE cc_start: 0.8199 (mt) cc_final: 0.7848 (mm) outliers start: 96 outliers final: 85 residues processed: 580 average time/residue: 0.5462 time to fit residues: 512.5714 Evaluate side-chains 610 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 520 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 218 MET Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 945 ASN Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1038 ASN Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1136 ASP Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1204 GLU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1226 ASP Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1226 ASP Chi-restraints excluded: chain B residue 1228 ILE Chi-restraints excluded: chain B residue 1298 CYS Chi-restraints excluded: chain B residue 1311 VAL Chi-restraints excluded: chain B residue 1363 ILE Chi-restraints excluded: chain B residue 1370 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 216 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18302 Z= 0.194 Angle : 0.513 7.389 24688 Z= 0.273 Chirality : 0.034 0.368 2958 Planarity : 0.003 0.050 3068 Dihedral : 5.119 50.216 2352 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.68 % Favored : 94.18 % Rotamer: Outliers : 5.04 % Allowed : 29.13 % Favored : 65.83 % Cbeta Deviations : 0.05 % 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 (0.18), residues: 2182 helix: 1.22 (0.14), residues: 1433 sheet: None (None), residues: 0 loop : -1.42 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.002 0.001 HIS B 720 PHE 0.017 0.001 PHE A 822 TYR 0.008 0.001 TYR A 138 ARG 0.005 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 531 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 460 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 464 GLU cc_start: 0.8752 (tp30) cc_final: 0.8386 (tp30) REVERT: A 590 ASP cc_start: 0.4792 (OUTLIER) cc_final: 0.4272 (m-30) REVERT: A 689 SER cc_start: -0.6253 (OUTLIER) cc_final: -0.6458 (m) REVERT: A 736 HIS cc_start: 0.6370 (t-90) cc_final: 0.5824 (t-90) REVERT: A 810 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7275 (m-80) REVERT: A 955 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7999 (mm-30) REVERT: A 1111 ARG cc_start: 0.8607 (mtp180) cc_final: 0.8084 (tpt-90) REVERT: A 1157 GLU cc_start: 0.7838 (mm-30) cc_final: 0.6480 (tp30) REVERT: A 1178 ASN cc_start: 0.8756 (t0) cc_final: 0.8424 (t0) REVERT: A 1182 TRP cc_start: 0.8870 (m100) cc_final: 0.8511 (m100) REVERT: A 1196 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 1329 GLU cc_start: 0.7340 (mp0) cc_final: 0.5750 (tp30) REVERT: B 78 GLN cc_start: 0.9350 (mm110) cc_final: 0.8519 (tm-30) REVERT: B 346 GLU cc_start: 0.8096 (tp30) cc_final: 0.7878 (tp30) REVERT: B 464 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7885 (tm-30) REVERT: B 520 ILE cc_start: 0.8385 (mm) cc_final: 0.8159 (mm) REVERT: B 622 SER cc_start: 0.3423 (OUTLIER) cc_final: 0.3139 (p) REVERT: B 831 ASP cc_start: 0.7993 (m-30) cc_final: 0.7748 (m-30) REVERT: B 921 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8435 (t0) REVERT: B 986 ASN cc_start: 0.6391 (OUTLIER) cc_final: 0.5211 (t0) REVERT: B 1186 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7172 (mtp85) REVERT: B 1323 ILE cc_start: 0.8195 (mt) cc_final: 0.7840 (mm) outliers start: 105 outliers final: 87 residues processed: 589 average time/residue: 0.5570 time to fit residues: 531.9867 Evaluate side-chains 617 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 522 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 945 ASN Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1038 ASN Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1136 ASP Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1204 GLU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1226 ASP Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1298 CYS Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1186 ARG Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1226 ASP Chi-restraints excluded: chain B residue 1228 ILE Chi-restraints excluded: chain B residue 1298 CYS Chi-restraints excluded: chain B residue 1311 VAL Chi-restraints excluded: chain B residue 1363 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 123 optimal weight: 0.3980 chunk 158 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 182 optimal weight: 0.1980 chunk 121 optimal weight: 0.9990 chunk 215 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 683 ASN A 921 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18302 Z= 0.200 Angle : 0.517 7.440 24688 Z= 0.275 Chirality : 0.035 0.369 2958 Planarity : 0.003 0.051 3068 Dihedral : 4.984 49.914 2350 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.19 % Favored : 93.68 % Rotamer: Outliers : 5.23 % Allowed : 29.37 % Favored : 65.40 % Cbeta Deviations : 0.05 % 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: 0.54 (0.18), residues: 2182 helix: 1.26 (0.14), residues: 1435 sheet: None (None), residues: 0 loop : -1.43 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 470 HIS 0.002 0.001 HIS B 720 PHE 0.019 0.001 PHE A 126 TYR 0.008 0.001 TYR A 138 ARG 0.007 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 524 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: A 460 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8208 (tm-30) REVERT: A 464 GLU cc_start: 0.8748 (tp30) cc_final: 0.8381 (tp30) REVERT: A 590 ASP cc_start: 0.4796 (OUTLIER) cc_final: 0.4276 (m-30) REVERT: A 689 SER cc_start: -0.6260 (OUTLIER) cc_final: -0.6465 (m) REVERT: A 736 HIS cc_start: 0.6253 (t-90) cc_final: 0.5886 (t-90) REVERT: A 810 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: A 955 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8020 (mm-30) REVERT: A 1157 GLU cc_start: 0.7617 (mm-30) cc_final: 0.6311 (tp30) REVERT: A 1178 ASN cc_start: 0.8744 (t0) cc_final: 0.8446 (t0) REVERT: A 1182 TRP cc_start: 0.8871 (m100) cc_final: 0.8524 (m100) REVERT: A 1329 GLU cc_start: 0.7351 (mp0) cc_final: 0.5715 (tp30) REVERT: B 78 GLN cc_start: 0.9347 (mm110) cc_final: 0.8509 (tm-30) REVERT: B 346 GLU cc_start: 0.8108 (tp30) cc_final: 0.7894 (tp30) REVERT: B 520 ILE cc_start: 0.8372 (mm) cc_final: 0.8119 (mm) REVERT: B 622 SER cc_start: 0.3422 (OUTLIER) cc_final: 0.3133 (p) REVERT: B 831 ASP cc_start: 0.8029 (m-30) cc_final: 0.7702 (m-30) REVERT: B 921 ASN cc_start: 0.9210 (OUTLIER) cc_final: 0.8435 (t0) REVERT: B 986 ASN cc_start: 0.6732 (OUTLIER) cc_final: 0.5498 (t0) REVERT: B 1186 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7168 (mtp85) REVERT: B 1201 TYR cc_start: 0.9231 (t80) cc_final: 0.8839 (t80) REVERT: B 1323 ILE cc_start: 0.8188 (mt) cc_final: 0.7834 (mm) outliers start: 109 outliers final: 93 residues processed: 584 average time/residue: 0.5584 time to fit residues: 528.6518 Evaluate side-chains 618 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 516 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 531 ASP Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 945 ASN Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1038 ASN Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1136 ASP Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1204 GLU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1226 ASP Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1298 CYS Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 949 ILE Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1092 LEU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1152 THR Chi-restraints excluded: chain B residue 1186 ARG Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1226 ASP Chi-restraints excluded: chain B residue 1228 ILE Chi-restraints excluded: chain B residue 1298 CYS Chi-restraints excluded: chain B residue 1311 VAL Chi-restraints excluded: chain B residue 1363 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18302 Z= 0.217 Angle : 0.533 7.544 24688 Z= 0.283 Chirality : 0.035 0.367 2958 Planarity : 0.003 0.053 3068 Dihedral : 5.011 49.802 2350 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.19 % Favored : 93.68 % Rotamer: Outliers : 5.23 % Allowed : 29.80 % Favored : 64.97 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.18), residues: 2182 helix: 1.22 (0.14), residues: 1436 sheet: None (None), residues: 0 loop : -1.51 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 470 HIS 0.002 0.001 HIS B 720 PHE 0.020 0.001 PHE A 126 TYR 0.010 0.001 TYR B1062 ARG 0.008 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 526 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8015 (tm-30) REVERT: A 389 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: A 460 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8209 (tm-30) REVERT: A 464 GLU cc_start: 0.8747 (tp30) cc_final: 0.8378 (tp30) REVERT: A 590 ASP cc_start: 0.4945 (OUTLIER) cc_final: 0.4430 (m-30) REVERT: A 640 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7648 (mm-30) REVERT: A 689 SER cc_start: -0.6266 (OUTLIER) cc_final: -0.6470 (m) REVERT: A 736 HIS cc_start: 0.6266 (t-90) cc_final: 0.5924 (t-90) REVERT: A 810 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.6809 (m-80) REVERT: A 855 ASP cc_start: 0.8704 (m-30) cc_final: 0.8471 (m-30) REVERT: A 955 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: A 1104 LEU cc_start: 0.8500 (pt) cc_final: 0.8239 (pp) REVERT: A 1157 GLU cc_start: 0.7628 (mm-30) cc_final: 0.6323 (tp30) REVERT: A 1178 ASN cc_start: 0.8751 (t0) cc_final: 0.8459 (t0) REVERT: A 1182 TRP cc_start: 0.8867 (m100) cc_final: 0.8533 (m100) REVERT: A 1329 GLU cc_start: 0.7421 (mp0) cc_final: 0.5679 (tp30) REVERT: B 78 GLN cc_start: 0.9358 (mm110) cc_final: 0.8523 (tm-30) REVERT: B 183 ASP cc_start: 0.8192 (t70) cc_final: 0.7955 (t0) REVERT: B 346 GLU cc_start: 0.8117 (tp30) cc_final: 0.7909 (tp30) REVERT: B 356 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8038 (mtm-85) REVERT: B 520 ILE cc_start: 0.8361 (mm) cc_final: 0.8105 (mm) REVERT: B 831 ASP cc_start: 0.8049 (m-30) cc_final: 0.7725 (m-30) REVERT: B 921 ASN cc_start: 0.9223 (OUTLIER) cc_final: 0.8445 (t0) REVERT: B 986 ASN cc_start: 0.6998 (OUTLIER) cc_final: 0.5926 (t0) REVERT: B 1186 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.7176 (mtp85) REVERT: B 1201 TYR cc_start: 0.9238 (t80) cc_final: 0.8863 (t80) REVERT: B 1323 ILE cc_start: 0.7993 (mt) cc_final: 0.7652 (mm) outliers start: 109 outliers final: 92 residues processed: 586 average time/residue: 0.5689 time to fit residues: 541.7640 Evaluate side-chains 623 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 522 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 945 ASN Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1038 ASN Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1136 ASP Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1204 GLU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1217 ASN Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1226 ASP Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1298 CYS Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 586 PHE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1152 THR Chi-restraints excluded: chain B residue 1186 ARG Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1226 ASP Chi-restraints excluded: chain B residue 1228 ILE Chi-restraints excluded: chain B residue 1298 CYS Chi-restraints excluded: chain B residue 1311 VAL Chi-restraints excluded: chain B residue 1363 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 121 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 181 optimal weight: 0.4980 chunk 190 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18302 Z= 0.217 Angle : 0.539 9.941 24688 Z= 0.285 Chirality : 0.035 0.370 2958 Planarity : 0.004 0.056 3068 Dihedral : 5.025 49.606 2350 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.51 % Favored : 93.35 % Rotamer: Outliers : 5.28 % Allowed : 29.99 % Favored : 64.73 % Cbeta Deviations : 0.05 % 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: 0.47 (0.18), residues: 2182 helix: 1.23 (0.14), residues: 1443 sheet: None (None), residues: 0 loop : -1.54 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 470 HIS 0.008 0.001 HIS B1369 PHE 0.020 0.001 PHE A 126 TYR 0.009 0.001 TYR A 138 ARG 0.006 0.000 ARG A 433 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 529 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8022 (tm-30) REVERT: A 389 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: A 460 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8203 (tm-30) REVERT: A 464 GLU cc_start: 0.8745 (tp30) cc_final: 0.8374 (tp30) REVERT: A 590 ASP cc_start: 0.5036 (OUTLIER) cc_final: 0.4559 (m-30) REVERT: A 689 SER cc_start: -0.6268 (OUTLIER) cc_final: -0.6474 (m) REVERT: A 736 HIS cc_start: 0.6284 (t-90) cc_final: 0.5957 (t-90) REVERT: A 810 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: A 855 ASP cc_start: 0.8637 (m-30) cc_final: 0.8409 (m-30) REVERT: A 955 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8070 (mm-30) REVERT: A 1104 LEU cc_start: 0.8483 (pt) cc_final: 0.8226 (pp) REVERT: A 1157 GLU cc_start: 0.7632 (mm-30) cc_final: 0.6325 (tp30) REVERT: A 1178 ASN cc_start: 0.8734 (t0) cc_final: 0.8438 (t0) REVERT: A 1182 TRP cc_start: 0.8782 (m100) cc_final: 0.8441 (m100) REVERT: A 1329 GLU cc_start: 0.7349 (mp0) cc_final: 0.5465 (tp30) REVERT: B 78 GLN cc_start: 0.9354 (mm110) cc_final: 0.8546 (tm-30) REVERT: B 183 ASP cc_start: 0.8200 (t70) cc_final: 0.7962 (t0) REVERT: B 346 GLU cc_start: 0.8131 (tp30) cc_final: 0.7928 (tp30) REVERT: B 356 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8040 (mtm-85) REVERT: B 520 ILE cc_start: 0.8356 (mm) cc_final: 0.8101 (mm) REVERT: B 831 ASP cc_start: 0.8044 (m-30) cc_final: 0.7715 (m-30) REVERT: B 921 ASN cc_start: 0.9227 (OUTLIER) cc_final: 0.8448 (t0) REVERT: B 986 ASN cc_start: 0.7180 (OUTLIER) cc_final: 0.6104 (t0) REVERT: B 1186 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7171 (mtp85) REVERT: B 1201 TYR cc_start: 0.9240 (t80) cc_final: 0.8869 (t80) REVERT: B 1323 ILE cc_start: 0.7988 (mt) cc_final: 0.7649 (mm) outliers start: 110 outliers final: 96 residues processed: 590 average time/residue: 0.5687 time to fit residues: 540.1934 Evaluate side-chains 622 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 517 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 682 ASP Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 945 ASN Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 962 ASP Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1038 ASN Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1136 ASP Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1204 GLU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1217 ASN Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1226 ASP Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1298 CYS Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 858 ASN Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain B residue 1040 THR Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1152 THR Chi-restraints excluded: chain B residue 1186 ARG Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1226 ASP Chi-restraints excluded: chain B residue 1228 ILE Chi-restraints excluded: chain B residue 1298 CYS Chi-restraints excluded: chain B residue 1311 VAL Chi-restraints excluded: chain B residue 1363 ILE Chi-restraints excluded: chain B residue 1370 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.6980 chunk 212 optimal weight: 0.9980 chunk 129 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 chunk 177 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 137 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 945 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18302 Z= 0.195 Angle : 0.537 9.674 24688 Z= 0.281 Chirality : 0.035 0.371 2958 Planarity : 0.003 0.059 3068 Dihedral : 4.985 49.409 2350 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.23 % Favored : 93.63 % Rotamer: Outliers : 4.80 % Allowed : 30.71 % Favored : 64.49 % Cbeta Deviations : 0.05 % 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: 0.51 (0.18), residues: 2182 helix: 1.28 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -1.59 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 470 HIS 0.010 0.001 HIS B1369 PHE 0.015 0.001 PHE A 822 TYR 0.009 0.001 TYR B1062 ARG 0.008 0.000 ARG A 433 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 534 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8023 (tm-30) REVERT: A 389 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7523 (m-80) REVERT: A 460 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8193 (tm-30) REVERT: A 464 GLU cc_start: 0.8743 (tp30) cc_final: 0.8368 (tp30) REVERT: A 590 ASP cc_start: 0.5025 (OUTLIER) cc_final: 0.4565 (m-30) REVERT: A 689 SER cc_start: -0.6282 (OUTLIER) cc_final: -0.6489 (m) REVERT: A 736 HIS cc_start: 0.6287 (t-90) cc_final: 0.5975 (t-90) REVERT: A 810 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.6728 (m-80) REVERT: A 955 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8100 (mm-30) REVERT: A 1104 LEU cc_start: 0.8460 (pt) cc_final: 0.8200 (pp) REVERT: A 1178 ASN cc_start: 0.9002 (t0) cc_final: 0.8713 (t0) REVERT: A 1182 TRP cc_start: 0.8871 (m100) cc_final: 0.8539 (m100) REVERT: A 1329 GLU cc_start: 0.7434 (mp0) cc_final: 0.5559 (tp30) REVERT: B 78 GLN cc_start: 0.9350 (mm110) cc_final: 0.8529 (tm-30) REVERT: B 183 ASP cc_start: 0.8196 (t70) cc_final: 0.7960 (t0) REVERT: B 346 GLU cc_start: 0.8133 (tp30) cc_final: 0.7932 (tp30) REVERT: B 356 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8025 (mtm-85) REVERT: B 520 ILE cc_start: 0.8355 (mm) cc_final: 0.8096 (mm) REVERT: B 831 ASP cc_start: 0.8045 (m-30) cc_final: 0.7715 (m-30) REVERT: B 921 ASN cc_start: 0.9220 (OUTLIER) cc_final: 0.8439 (t0) REVERT: B 986 ASN cc_start: 0.7248 (OUTLIER) cc_final: 0.6135 (t0) REVERT: B 1186 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7143 (mtp85) REVERT: B 1201 TYR cc_start: 0.9233 (t80) cc_final: 0.8870 (t80) REVERT: B 1323 ILE cc_start: 0.7982 (mt) cc_final: 0.7649 (mm) outliers start: 100 outliers final: 88 residues processed: 588 average time/residue: 0.5668 time to fit residues: 533.5525 Evaluate side-chains 621 residues out of total 2084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 524 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 84 ASN Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 403 SER Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 521 CYS Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 586 PHE Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 665 PHE Chi-restraints excluded: chain A residue 689 SER Chi-restraints excluded: chain A residue 810 PHE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 830 ASP Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 858 ASN Chi-restraints excluded: chain A residue 860 ILE Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain A residue 1025 SER Chi-restraints excluded: chain A residue 1026 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1038 ASN Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain A residue 1136 ASP Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1204 GLU Chi-restraints excluded: chain A residue 1205 SER Chi-restraints excluded: chain A residue 1217 ASN Chi-restraints excluded: chain A residue 1221 VAL Chi-restraints excluded: chain A residue 1226 ASP Chi-restraints excluded: chain A residue 1276 LEU Chi-restraints excluded: chain A residue 1298 CYS Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1357 SER Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1377 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain B residue 84 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 356 ARG Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 533 PHE Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 566 CYS Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 674 ASP Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 726 TYR Chi-restraints excluded: chain B residue 727 SER Chi-restraints excluded: chain B residue 803 LEU Chi-restraints excluded: chain B residue 838 ILE Chi-restraints excluded: chain B residue 921 ASN Chi-restraints excluded: chain B residue 929 ILE Chi-restraints excluded: chain B residue 986 ASN Chi-restraints excluded: chain B residue 1031 SER Chi-restraints excluded: chain B residue 1040 THR Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1125 ASP Chi-restraints excluded: chain B residue 1133 LEU Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain B residue 1139 LEU Chi-restraints excluded: chain B residue 1186 ARG Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1226 ASP Chi-restraints excluded: chain B residue 1228 ILE Chi-restraints excluded: chain B residue 1298 CYS Chi-restraints excluded: chain B residue 1311 VAL Chi-restraints excluded: chain B residue 1363 ILE Chi-restraints excluded: chain B residue 1370 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 26 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 74 optimal weight: 0.0670 chunk 182 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1415 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.181251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154322 restraints weight = 104776.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.159589 restraints weight = 45749.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.162771 restraints weight = 25267.950| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18302 Z= 0.167 Angle : 0.525 9.252 24688 Z= 0.272 Chirality : 0.035 0.372 2958 Planarity : 0.003 0.047 3068 Dihedral : 4.884 49.743 2350 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.73 % Favored : 94.13 % Rotamer: Outliers : 4.22 % Allowed : 31.14 % Favored : 64.64 % Cbeta Deviations : 0.05 % 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: 0.66 (0.19), residues: 2182 helix: 1.39 (0.14), residues: 1445 sheet: None (None), residues: 0 loop : -1.53 (0.24), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 470 HIS 0.013 0.001 HIS B1369 PHE 0.015 0.001 PHE A 822 TYR 0.008 0.001 TYR A 138 ARG 0.005 0.000 ARG A 433 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9341.58 seconds wall clock time: 164 minutes 27.76 seconds (9867.76 seconds total)