Starting phenix.real_space_refine on Sat Aug 10 20:55:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx8_18701/08_2024/8qx8_18701.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx8_18701/08_2024/8qx8_18701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx8_18701/08_2024/8qx8_18701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx8_18701/08_2024/8qx8_18701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx8_18701/08_2024/8qx8_18701.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qx8_18701/08_2024/8qx8_18701.cif" } resolution = 4.6 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= 0.009 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 18919 2.51 5 N 5296 2.21 5 O 5784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 30086 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 7530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 7530 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1078} Chain breaks: 19 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1554 Unresolved non-hydrogen angles: 1999 Unresolved non-hydrogen dihedrals: 1290 Unresolved non-hydrogen chiralities: 169 Planarities with less than four sites: {'GLN:plan1': 19, 'ASP:plan': 21, 'TYR:plan': 15, 'ASN:plan1': 27, 'TRP:plan': 7, 'HIS:plan': 15, 'PHE:plan': 22, 'GLU:plan': 25, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 780 Chain: "D" Number of atoms: 4939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4939 Classifications: {'peptide': 613} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 21, 'TRANS': 591} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 5966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5966 Classifications: {'peptide': 728} Link IDs: {'PTRANS': 18, 'TRANS': 709} Chain breaks: 3 Chain: "A" Number of atoms: 6264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 969, 6264 Classifications: {'peptide': 969} Incomplete info: {'truncation_to_alanine': 453} Link IDs: {'PTRANS': 35, 'TRANS': 933} Chain breaks: 3 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1616 Unresolved non-hydrogen angles: 2051 Unresolved non-hydrogen dihedrals: 1339 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 9, 'TYR:plan': 19, 'ASN:plan1': 28, 'TRP:plan': 1, 'ASP:plan': 35, 'PHE:plan': 30, 'GLU:plan': 43, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 859 Chain: "E" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1077 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 210} Link IDs: {'PTRANS': 3, 'TRANS': 212} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 779 Unresolved non-hydrogen angles: 992 Unresolved non-hydrogen dihedrals: 654 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 4, 'TYR:plan': 11, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 16, 'PHE:plan': 16, 'GLU:plan': 20, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 431 Chain: "C" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 4310 Classifications: {'peptide': 800} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 668} Link IDs: {'PTRANS': 17, 'TRANS': 782} Chain breaks: 18 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 2436 Unresolved non-hydrogen angles: 3123 Unresolved non-hydrogen dihedrals: 2040 Unresolved non-hydrogen chiralities: 240 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 16, 'TYR:plan': 21, 'ASN:plan1': 69, 'TRP:plan': 16, 'ASP:plan': 42, 'PHE:plan': 35, 'GLU:plan': 43, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 1241 Time building chain proxies: 18.24, per 1000 atoms: 0.61 Number of scatterers: 30086 At special positions: 0 Unit cell: (136.479, 209.811, 323.883, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 5784 8.00 N 5296 7.00 C 18919 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 897 " - pdb=" SG CYS F 904 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.53 Conformation dependent library (CDL) restraints added in 6.4 seconds 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8602 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 32 sheets defined 50.9% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'F' and resid 75 through 83 removed outlier: 3.967A pdb=" N SER F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 434 Processing helix chain 'F' and resid 436 through 447 Processing helix chain 'F' and resid 462 through 470 Processing helix chain 'F' and resid 471 through 488 removed outlier: 3.624A pdb=" N LEU F 482 " --> pdb=" O SER F 478 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG F 483 " --> pdb=" O LEU F 479 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS F 488 " --> pdb=" O PHE F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 510 removed outlier: 4.135A pdb=" N VAL F 496 " --> pdb=" O ASP F 492 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR F 497 " --> pdb=" O TYR F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 529 removed outlier: 3.775A pdb=" N GLU F 529 " --> pdb=" O GLU F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 544 removed outlier: 4.335A pdb=" N TYR F 539 " --> pdb=" O ASP F 535 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE F 540 " --> pdb=" O ASN F 536 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU F 541 " --> pdb=" O ALA F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 550 Processing helix chain 'F' and resid 556 through 569 Processing helix chain 'F' and resid 574 through 582 removed outlier: 3.685A pdb=" N ASP F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 589 through 601 Processing helix chain 'F' and resid 602 through 613 removed outlier: 3.523A pdb=" N TYR F 608 " --> pdb=" O ASP F 604 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE F 609 " --> pdb=" O LEU F 605 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP F 610 " --> pdb=" O LEU F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 617 through 629 removed outlier: 3.601A pdb=" N VAL F 621 " --> pdb=" O TYR F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 635 Processing helix chain 'F' and resid 645 through 647 No H-bonds generated for 'chain 'F' and resid 645 through 647' Processing helix chain 'F' and resid 648 through 659 removed outlier: 3.679A pdb=" N VAL F 653 " --> pdb=" O ILE F 649 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR F 654 " --> pdb=" O PHE F 650 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 686 removed outlier: 4.104A pdb=" N LYS F 676 " --> pdb=" O ASP F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 713 through 723 removed outlier: 3.778A pdb=" N ASN F 723 " --> pdb=" O LEU F 719 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 736 removed outlier: 3.676A pdb=" N GLU F 736 " --> pdb=" O ASN F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 757 through 770 removed outlier: 4.174A pdb=" N LYS F 770 " --> pdb=" O LEU F 766 " (cutoff:3.500A) Processing helix chain 'F' and resid 778 through 792 removed outlier: 3.963A pdb=" N LYS F 792 " --> pdb=" O THR F 788 " (cutoff:3.500A) Processing helix chain 'F' and resid 800 through 812 removed outlier: 3.542A pdb=" N ASP F 805 " --> pdb=" O ASN F 801 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS F 806 " --> pdb=" O GLN F 802 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL F 807 " --> pdb=" O ALA F 803 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS F 812 " --> pdb=" O VAL F 808 " (cutoff:3.500A) Processing helix chain 'F' and resid 819 through 829 removed outlier: 3.683A pdb=" N ILE F 825 " --> pdb=" O GLU F 821 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU F 828 " --> pdb=" O GLN F 824 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER F 829 " --> pdb=" O ILE F 825 " (cutoff:3.500A) Processing helix chain 'F' and resid 829 through 834 removed outlier: 4.602A pdb=" N TYR F 833 " --> pdb=" O SER F 829 " (cutoff:3.500A) Processing helix chain 'F' and resid 835 through 837 No H-bonds generated for 'chain 'F' and resid 835 through 837' Processing helix chain 'F' and resid 839 through 850 removed outlier: 4.077A pdb=" N ILE F 843 " --> pdb=" O THR F 839 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU F 845 " --> pdb=" O ASN F 841 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 846 " --> pdb=" O PHE F 842 " (cutoff:3.500A) Processing helix chain 'F' and resid 853 through 863 removed outlier: 3.685A pdb=" N SER F 861 " --> pdb=" O HIS F 857 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU F 862 " --> pdb=" O ILE F 858 " (cutoff:3.500A) Processing helix chain 'F' and resid 866 through 875 removed outlier: 3.744A pdb=" N LEU F 873 " --> pdb=" O LEU F 869 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR F 875 " --> pdb=" O LEU F 871 " (cutoff:3.500A) Processing helix chain 'F' and resid 885 through 895 removed outlier: 3.650A pdb=" N THR F 890 " --> pdb=" O ILE F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 904 through 914 Processing helix chain 'F' and resid 914 through 922 removed outlier: 3.548A pdb=" N LEU F 918 " --> pdb=" O ASN F 914 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER F 920 " --> pdb=" O ASP F 916 " (cutoff:3.500A) Processing helix chain 'F' and resid 924 through 935 removed outlier: 3.616A pdb=" N THR F 929 " --> pdb=" O GLU F 925 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP F 933 " --> pdb=" O THR F 929 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE F 934 " --> pdb=" O ILE F 930 " (cutoff:3.500A) Processing helix chain 'F' and resid 936 through 941 Processing helix chain 'F' and resid 947 through 961 removed outlier: 3.773A pdb=" N LYS F 957 " --> pdb=" O LYS F 953 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU F 958 " --> pdb=" O TYR F 954 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR F 961 " --> pdb=" O LYS F 957 " (cutoff:3.500A) Processing helix chain 'F' and resid 970 through 980 Processing helix chain 'F' and resid 981 through 983 No H-bonds generated for 'chain 'F' and resid 981 through 983' Processing helix chain 'F' and resid 985 through 995 removed outlier: 3.861A pdb=" N GLY F 995 " --> pdb=" O LEU F 991 " (cutoff:3.500A) Processing helix chain 'F' and resid 999 through 1013 removed outlier: 4.012A pdb=" N GLN F1012 " --> pdb=" O ASP F1008 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP F1013 " --> pdb=" O LEU F1009 " (cutoff:3.500A) Processing helix chain 'F' and resid 1015 through 1026 Processing helix chain 'F' and resid 1028 through 1047 Processing helix chain 'F' and resid 1050 through 1068 Processing helix chain 'F' and resid 1072 through 1090 Processing helix chain 'F' and resid 1096 through 1115 removed outlier: 4.018A pdb=" N LYS F1115 " --> pdb=" O LEU F1111 " (cutoff:3.500A) Processing helix chain 'F' and resid 1124 through 1141 Processing helix chain 'F' and resid 1143 through 1186 removed outlier: 3.775A pdb=" N LEU F1164 " --> pdb=" O LEU F1160 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER F1165 " --> pdb=" O GLU F1161 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU F1166 " --> pdb=" O ARG F1162 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU F1167 " --> pdb=" O SER F1163 " (cutoff:3.500A) Processing helix chain 'F' and resid 1211 through 1221 removed outlier: 3.677A pdb=" N PHE F1215 " --> pdb=" O ASP F1211 " (cutoff:3.500A) Processing helix chain 'F' and resid 1247 through 1252 Processing helix chain 'D' and resid 8 through 26 removed outlier: 4.234A pdb=" N LEU D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR D 13 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN D 14 " --> pdb=" O PHE D 10 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 65 through 70 removed outlier: 3.756A pdb=" N ASP D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 107 removed outlier: 4.075A pdb=" N LEU D 100 " --> pdb=" O PRO D 96 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 removed outlier: 6.112A pdb=" N THR D 125 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP D 128 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 138 removed outlier: 4.498A pdb=" N GLN D 133 " --> pdb=" O THR D 129 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY D 136 " --> pdb=" O TRP D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 154 Processing helix chain 'D' and resid 200 through 224 Processing helix chain 'D' and resid 235 through 252 removed outlier: 3.516A pdb=" N ARG D 239 " --> pdb=" O ASN D 235 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN D 252 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 263 Processing helix chain 'D' and resid 282 through 284 No H-bonds generated for 'chain 'D' and resid 282 through 284' Processing helix chain 'D' and resid 294 through 303 removed outlier: 3.637A pdb=" N LEU D 302 " --> pdb=" O ILE D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 351 removed outlier: 3.563A pdb=" N LEU D 348 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR D 350 " --> pdb=" O LYS D 346 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN D 351 " --> pdb=" O GLU D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 396 removed outlier: 3.641A pdb=" N GLU D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 416 removed outlier: 4.018A pdb=" N LEU D 407 " --> pdb=" O PHE D 403 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 428 removed outlier: 3.571A pdb=" N ILE D 426 " --> pdb=" O ASP D 422 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU D 428 " --> pdb=" O GLU D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 452 removed outlier: 3.717A pdb=" N ILE D 441 " --> pdb=" O ASP D 437 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS D 452 " --> pdb=" O LEU D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 471 removed outlier: 3.967A pdb=" N THR D 465 " --> pdb=" O GLU D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 482 Processing helix chain 'D' and resid 510 through 518 removed outlier: 3.606A pdb=" N ILE D 514 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 560 removed outlier: 3.871A pdb=" N LEU D 560 " --> pdb=" O LEU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 569 removed outlier: 3.620A pdb=" N ASN D 569 " --> pdb=" O ILE D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 596 Processing helix chain 'D' and resid 650 through 668 removed outlier: 3.934A pdb=" N ILE D 654 " --> pdb=" O THR D 650 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 658 " --> pdb=" O ILE D 654 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS D 659 " --> pdb=" O ALA D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 688 Processing helix chain 'B' and resid 3 through 7 removed outlier: 3.541A pdb=" N PHE B 6 " --> pdb=" O ASN B 3 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP B 7 " --> pdb=" O PRO B 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3 through 7' Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 294 through 298 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 322 through 330 removed outlier: 3.775A pdb=" N LEU B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 353 through 364 Processing helix chain 'B' and resid 376 through 393 removed outlier: 3.670A pdb=" N VAL B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 387 " --> pdb=" O CYS B 383 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 388 " --> pdb=" O ASN B 384 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 removed outlier: 3.600A pdb=" N ILE B 407 " --> pdb=" O GLU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.502A pdb=" N ARG B 415 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 433 removed outlier: 3.885A pdb=" N LYS B 430 " --> pdb=" O ILE B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 451 removed outlier: 3.797A pdb=" N PHE B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 444 " --> pdb=" O TYR B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 493 through 501 removed outlier: 3.936A pdb=" N LEU B 501 " --> pdb=" O ARG B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 516 Processing helix chain 'B' and resid 521 through 530 Processing helix chain 'B' and resid 533 through 545 removed outlier: 3.871A pdb=" N SER B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 558 removed outlier: 4.314A pdb=" N LYS B 553 " --> pdb=" O SER B 549 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 569 Processing helix chain 'B' and resid 574 through 584 removed outlier: 3.870A pdb=" N ASP B 578 " --> pdb=" O ALA B 574 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 600 removed outlier: 4.051A pdb=" N GLN B 600 " --> pdb=" O GLN B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 605 No H-bonds generated for 'chain 'B' and resid 603 through 605' Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 621 through 647 removed outlier: 3.918A pdb=" N ARG B 646 " --> pdb=" O SER B 642 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE B 647 " --> pdb=" O LEU B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 665 removed outlier: 3.664A pdb=" N LYS B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 665 " --> pdb=" O SER B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 680 removed outlier: 4.071A pdb=" N LYS B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B 678 " --> pdb=" O GLU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 688 removed outlier: 3.689A pdb=" N LEU B 686 " --> pdb=" O SER B 682 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N HIS B 688 " --> pdb=" O LYS B 684 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 682 through 688' Processing helix chain 'B' and resid 689 through 695 Processing helix chain 'B' and resid 701 through 707 removed outlier: 3.875A pdb=" N ALA B 707 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 726 removed outlier: 4.349A pdb=" N THR B 721 " --> pdb=" O MET B 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 364 through 376 removed outlier: 3.735A pdb=" N GLN A 370 " --> pdb=" O PRO A 366 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N HIS A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 395 Processing helix chain 'A' and resid 399 through 408 removed outlier: 4.421A pdb=" N GLN A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.504A pdb=" N ILE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 447 removed outlier: 4.127A pdb=" N ASN A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.537A pdb=" N LEU A 461 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 476 removed outlier: 3.609A pdb=" N ASP A 471 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE A 473 " --> pdb=" O GLY A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 506 through 517 removed outlier: 3.547A pdb=" N SER A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 521 removed outlier: 4.155A pdb=" N ARG A 521 " --> pdb=" O ASP A 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 518 through 521' Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.650A pdb=" N LYS A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 543 removed outlier: 4.526A pdb=" N VAL A 538 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 557 Processing helix chain 'A' and resid 564 through 575 removed outlier: 6.149A pdb=" N LYS A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LYS A 573 " --> pdb=" O THR A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 591 Processing helix chain 'A' and resid 622 through 631 removed outlier: 3.716A pdb=" N PHE A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 667 removed outlier: 3.585A pdb=" N VAL A 667 " --> pdb=" O SER A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.819A pdb=" N PHE A 673 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 675 " --> pdb=" O PHE A 671 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 686 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 690 removed outlier: 3.899A pdb=" N PHE A 690 " --> pdb=" O TYR A 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 687 through 690' Processing helix chain 'A' and resid 692 through 708 Processing helix chain 'A' and resid 713 through 734 removed outlier: 4.303A pdb=" N ASP A 718 " --> pdb=" O PRO A 714 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ASP A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 775 Processing helix chain 'A' and resid 781 through 796 Processing helix chain 'A' and resid 799 through 808 removed outlier: 4.019A pdb=" N LYS A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 823 removed outlier: 3.857A pdb=" N SER A 821 " --> pdb=" O GLN A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 833 Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 843 through 850 Processing helix chain 'A' and resid 854 through 864 Processing helix chain 'A' and resid 869 through 916 removed outlier: 3.702A pdb=" N ILE A 873 " --> pdb=" O HIS A 869 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 900 " --> pdb=" O GLU A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 953 Processing helix chain 'A' and resid 958 through 960 No H-bonds generated for 'chain 'A' and resid 958 through 960' Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.656A pdb=" N LEU A 966 " --> pdb=" O SER A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1003 Processing helix chain 'A' and resid 1012 through 1019 Processing helix chain 'E' and resid 780 through 789 Processing helix chain 'E' and resid 801 through 813 removed outlier: 4.225A pdb=" N ASP E 805 " --> pdb=" O SER E 801 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP E 813 " --> pdb=" O GLU E 809 " (cutoff:3.500A) Processing helix chain 'E' and resid 820 through 832 Processing helix chain 'E' and resid 839 through 852 Processing helix chain 'E' and resid 855 through 869 Processing helix chain 'E' and resid 875 through 880 Processing helix chain 'E' and resid 892 through 896 Processing helix chain 'E' and resid 902 through 909 Processing helix chain 'E' and resid 915 through 923 Processing helix chain 'E' and resid 924 through 926 No H-bonds generated for 'chain 'E' and resid 924 through 926' Processing helix chain 'E' and resid 929 through 942 removed outlier: 3.590A pdb=" N ASN E 942 " --> pdb=" O LEU E 938 " (cutoff:3.500A) Processing helix chain 'E' and resid 948 through 958 Processing helix chain 'E' and resid 964 through 1010 removed outlier: 4.036A pdb=" N ILE E 968 " --> pdb=" O PRO E 964 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU E 970 " --> pdb=" O GLN E 966 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU E 971 " --> pdb=" O THR E 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 337 through 348 removed outlier: 4.325A pdb=" N ASN C 344 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU C 345 " --> pdb=" O SER C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 362 through 380 removed outlier: 3.566A pdb=" N TYR C 376 " --> pdb=" O SER C 372 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 392 Processing helix chain 'C' and resid 399 through 411 removed outlier: 3.512A pdb=" N GLN C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 424 Processing helix chain 'C' and resid 431 through 457 removed outlier: 3.899A pdb=" N VAL C 435 " --> pdb=" O SER C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 489 Processing helix chain 'C' and resid 496 through 504 removed outlier: 3.564A pdb=" N GLN C 500 " --> pdb=" O GLU C 496 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS C 504 " --> pdb=" O GLN C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 518 removed outlier: 3.575A pdb=" N LEU C 511 " --> pdb=" O ARG C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 532 removed outlier: 3.560A pdb=" N SER C 526 " --> pdb=" O LYS C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 544 Processing helix chain 'C' and resid 547 through 561 removed outlier: 6.404A pdb=" N LEU C 555 " --> pdb=" O TYR C 551 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE C 556 " --> pdb=" O LYS C 552 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 557 " --> pdb=" O TYR C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 573 removed outlier: 3.511A pdb=" N SER C 567 " --> pdb=" O GLU C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 596 Processing helix chain 'C' and resid 603 through 620 Processing helix chain 'C' and resid 625 through 639 removed outlier: 3.566A pdb=" N TYR C 629 " --> pdb=" O ASN C 625 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP C 639 " --> pdb=" O MET C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 657 Processing helix chain 'C' and resid 662 through 674 Processing helix chain 'C' and resid 675 through 686 removed outlier: 3.692A pdb=" N ILE C 680 " --> pdb=" O THR C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 699 Processing helix chain 'C' and resid 701 through 711 Processing helix chain 'C' and resid 718 through 733 Processing helix chain 'C' and resid 740 through 752 Processing helix chain 'C' and resid 757 through 762 Processing helix chain 'C' and resid 770 through 814 Processing helix chain 'C' and resid 832 through 836 removed outlier: 3.895A pdb=" N ILE C 835 " --> pdb=" O PHE C 832 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS C 836 " --> pdb=" O LEU C 833 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 832 through 836' Processing helix chain 'C' and resid 850 through 859 Processing helix chain 'C' and resid 862 through 869 Processing helix chain 'C' and resid 880 through 888 Processing helix chain 'C' and resid 895 through 900 Processing helix chain 'C' and resid 911 through 915 Processing sheet with id=AA1, first strand: chain 'F' and resid 70 through 74 Processing sheet with id=AA2, first strand: chain 'F' and resid 89 through 92 Processing sheet with id=AA3, first strand: chain 'F' and resid 147 through 151 removed outlier: 6.460A pdb=" N ILE F 157 " --> pdb=" O HIS F 189 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N HIS F 189 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE F 159 " --> pdb=" O VAL F 187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 200 through 204 removed outlier: 6.450A pdb=" N ALA F 210 " --> pdb=" O PHE F 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 220 through 226 removed outlier: 5.740A pdb=" N LEU F 222 " --> pdb=" O LYS F 239 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LYS F 239 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN F 224 " --> pdb=" O SER F 237 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N SER F 237 " --> pdb=" O ASN F 224 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR F 226 " --> pdb=" O TYR F 235 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N TYR F 235 " --> pdb=" O TYR F 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 268 through 271 Processing sheet with id=AA7, first strand: chain 'F' and resid 306 through 310 removed outlier: 4.351A pdb=" N ILE F 325 " --> pdb=" O SER F 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 1237 through 1238 Processing sheet with id=AA9, first strand: chain 'D' and resid 57 through 62 removed outlier: 6.078A pdb=" N GLU D 30 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS D 59 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 84 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS D 112 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N CYS D 116 " --> pdb=" O ILE D 87 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR D 115 " --> pdb=" O TYR D 164 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 229 through 233 Processing sheet with id=AB2, first strand: chain 'D' and resid 274 through 275 removed outlier: 6.591A pdb=" N ASP D 275 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL D 644 " --> pdb=" O ASP D 275 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU D 279 " --> pdb=" O LEU D 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 274 through 275 removed outlier: 6.591A pdb=" N ASP D 275 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL D 644 " --> pdb=" O ASP D 275 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA D 641 " --> pdb=" O ILE D 674 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE D 676 " --> pdb=" O ALA D 641 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL D 643 " --> pdb=" O ILE D 676 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 9 through 10 removed outlier: 4.095A pdb=" N GLU B 9 " --> pdb=" O TYR B 16 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR B 16 " --> pdb=" O GLU B 9 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 35 through 36 removed outlier: 6.986A pdb=" N ILE B 50 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS B 62 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL B 52 " --> pdb=" O LEU B 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 74 through 76 removed outlier: 3.781A pdb=" N LYS B 74 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.900A pdb=" N TYR B 132 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 174 through 177 Processing sheet with id=AB9, first strand: chain 'B' and resid 194 through 197 removed outlier: 3.975A pdb=" N LYS B 194 " --> pdb=" O TYR B 206 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 236 through 237 removed outlier: 3.782A pdb=" N CYS B 245 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 279 through 282 removed outlier: 4.279A pdb=" N LEU B 290 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 12 through 15 removed outlier: 3.759A pdb=" N ILE A 347 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 45 through 49 removed outlier: 3.897A pdb=" N HIS A 66 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.733A pdb=" N GLU A 93 " --> pdb=" O GLN A 76 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 91 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 118 " --> pdb=" O VAL A 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 134 through 136 Processing sheet with id=AC7, first strand: chain 'A' and resid 181 through 184 Processing sheet with id=AC8, first strand: chain 'A' and resid 263 through 268 removed outlier: 4.340A pdb=" N ARG A 265 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 301 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN A 314 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 303 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AD1, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AD2, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AD3, first strand: chain 'C' and resid 214 through 215 Processing sheet with id=AD4, first strand: chain 'C' and resid 264 through 265 removed outlier: 3.844A pdb=" N THR C 279 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N SER C 282 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL C 288 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 839 through 841 removed outlier: 3.522A pdb=" N ILE C 839 " --> pdb=" O PHE C 847 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS C 845 " --> pdb=" O PHE C 841 " (cutoff:3.500A) 1522 hydrogen bonds defined for protein. 4368 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: 11.86 Time building geometry restraints manager: 13.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10276 1.34 - 1.46: 3641 1.46 - 1.58: 16406 1.58 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 30445 Sorted by residual: bond pdb=" N ILE C 819 " pdb=" CA ILE C 819 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.35e+00 bond pdb=" N ILE C 118 " pdb=" CA ILE C 118 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.20e-02 6.94e+03 8.91e+00 bond pdb=" N LEU A 410 " pdb=" CA LEU A 410 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.14e-02 7.69e+03 8.35e+00 bond pdb=" N LEU C 820 " pdb=" CA LEU C 820 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.23e-02 6.61e+03 8.31e+00 bond pdb=" N LEU C 145 " pdb=" CA LEU C 145 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.18e-02 7.18e+03 8.01e+00 ... (remaining 30440 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.06: 380 106.06 - 113.07: 16997 113.07 - 120.08: 9604 120.08 - 127.09: 14369 127.09 - 134.10: 191 Bond angle restraints: 41541 Sorted by residual: angle pdb=" N PRO A 781 " pdb=" CA PRO A 781 " pdb=" CB PRO A 781 " ideal model delta sigma weight residual 102.35 110.37 -8.02 7.10e-01 1.98e+00 1.28e+02 angle pdb=" N PRO A 854 " pdb=" CA PRO A 854 " pdb=" CB PRO A 854 " ideal model delta sigma weight residual 103.15 110.57 -7.42 9.70e-01 1.06e+00 5.85e+01 angle pdb=" N PRO D 79 " pdb=" CA PRO D 79 " pdb=" CB PRO D 79 " ideal model delta sigma weight residual 103.25 111.16 -7.91 1.05e+00 9.07e-01 5.68e+01 angle pdb=" N PRO D 72 " pdb=" CA PRO D 72 " pdb=" CB PRO D 72 " ideal model delta sigma weight residual 103.20 110.12 -6.92 9.50e-01 1.11e+00 5.31e+01 angle pdb=" N PRO A 798 " pdb=" CA PRO A 798 " pdb=" CB PRO A 798 " ideal model delta sigma weight residual 103.25 110.26 -7.01 1.05e+00 9.07e-01 4.46e+01 ... (remaining 41536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 16814 17.41 - 34.83: 1260 34.83 - 52.24: 210 52.24 - 69.66: 38 69.66 - 87.07: 17 Dihedral angle restraints: 18339 sinusoidal: 5250 harmonic: 13089 Sorted by residual: dihedral pdb=" CA THR D 287 " pdb=" C THR D 287 " pdb=" N PRO D 288 " pdb=" CA PRO D 288 " ideal model delta harmonic sigma weight residual 180.00 150.45 29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CB CYS F 897 " pdb=" SG CYS F 897 " pdb=" SG CYS F 904 " pdb=" CB CYS F 904 " ideal model delta sinusoidal sigma weight residual -86.00 -131.01 45.01 1 1.00e+01 1.00e-02 2.81e+01 dihedral pdb=" CA TYR F 793 " pdb=" C TYR F 793 " pdb=" N PRO F 794 " pdb=" CA PRO F 794 " ideal model delta harmonic sigma weight residual 180.00 157.84 22.16 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 18336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4299 0.058 - 0.116: 749 0.116 - 0.174: 53 0.174 - 0.232: 8 0.232 - 0.290: 6 Chirality restraints: 5115 Sorted by residual: chirality pdb=" CB ILE F1228 " pdb=" CA ILE F1228 " pdb=" CG1 ILE F1228 " pdb=" CG2 ILE F1228 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA PRO A 798 " pdb=" N PRO A 798 " pdb=" C PRO A 798 " pdb=" CB PRO A 798 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA PRO D 79 " pdb=" N PRO D 79 " pdb=" C PRO D 79 " pdb=" CB PRO D 79 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 5112 not shown) Planarity restraints: 5462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 287 " 0.043 5.00e-02 4.00e+02 6.46e-02 6.68e+00 pdb=" N PRO D 288 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 288 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 288 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP F 693 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO F 694 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO F 694 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 694 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 688 " -0.014 2.00e-02 2.50e+03 1.52e-02 3.47e+00 pdb=" CG HIS B 688 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS B 688 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 688 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS B 688 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B 688 " -0.004 2.00e-02 2.50e+03 ... (remaining 5459 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5084 2.76 - 3.29: 30449 3.29 - 3.83: 48122 3.83 - 4.36: 48652 4.36 - 4.90: 83435 Nonbonded interactions: 215742 Sorted by model distance: nonbonded pdb=" O PHE C 832 " pdb=" NE2 HIS C 848 " model vdw 2.225 3.120 nonbonded pdb=" OG1 THR D 7 " pdb=" OE2 GLU D 176 " model vdw 2.227 3.040 nonbonded pdb=" OH TYR D 460 " pdb=" O THR D 489 " model vdw 2.236 3.040 nonbonded pdb=" O GLN A 43 " pdb=" OG1 THR A 44 " model vdw 2.243 3.040 nonbonded pdb=" O LEU F 871 " pdb=" OH TYR F 882 " model vdw 2.244 3.040 ... (remaining 215737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.990 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 84.030 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 : 0.002 0.038 30445 Z= 0.154 Angle : 0.579 8.325 41541 Z= 0.345 Chirality : 0.042 0.290 5115 Planarity : 0.003 0.065 5462 Dihedral : 13.355 87.075 9734 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.28 % Favored : 90.39 % Rotamer: Outliers : 0.09 % Allowed : 0.34 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -0.10 (0.14), residues: 4331 helix: 2.15 (0.12), residues: 2002 sheet: -1.63 (0.26), residues: 416 loop : -2.27 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 471 HIS 0.017 0.001 HIS B 688 PHE 0.020 0.001 PHE F 735 TYR 0.020 0.001 TYR B 735 ARG 0.004 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 107 time to evaluate : 3.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 501 MET cc_start: 0.8326 (tmm) cc_final: 0.7970 (tmm) REVERT: F 1227 MET cc_start: 0.8570 (tpp) cc_final: 0.8249 (tpp) REVERT: D 390 ASP cc_start: 0.8723 (m-30) cc_final: 0.8368 (m-30) REVERT: D 687 MET cc_start: 0.7902 (mmm) cc_final: 0.7466 (mmp) REVERT: B 224 MET cc_start: 0.8263 (ttm) cc_final: 0.7861 (tpp) REVERT: B 559 MET cc_start: 0.8251 (tmm) cc_final: 0.8021 (tmm) REVERT: B 720 TYR cc_start: 0.7777 (t80) cc_final: 0.7493 (t80) outliers start: 2 outliers final: 1 residues processed: 109 average time/residue: 0.3496 time to fit residues: 68.9103 Evaluate side-chains 97 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 372 optimal weight: 0.9980 chunk 334 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 345 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 257 optimal weight: 0.7980 chunk 400 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN D 186 ASN B 294 GLN B 550 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30445 Z= 0.182 Angle : 0.516 7.850 41541 Z= 0.282 Chirality : 0.042 0.233 5115 Planarity : 0.003 0.062 5462 Dihedral : 4.101 50.117 4578 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.72 % Favored : 90.12 % Rotamer: Outliers : 0.09 % Allowed : 6.38 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 4331 helix: 2.01 (0.12), residues: 2091 sheet: -1.80 (0.25), residues: 426 loop : -2.34 (0.15), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 517 HIS 0.012 0.001 HIS B 688 PHE 0.015 0.001 PHE F 735 TYR 0.029 0.001 TYR F 834 ARG 0.005 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 501 MET cc_start: 0.8385 (tmm) cc_final: 0.8054 (tmm) REVERT: F 1227 MET cc_start: 0.8578 (tpp) cc_final: 0.8219 (tpp) REVERT: D 192 MET cc_start: 0.8381 (tpt) cc_final: 0.7889 (tpp) REVERT: D 390 ASP cc_start: 0.8751 (m-30) cc_final: 0.8406 (m-30) REVERT: B 224 MET cc_start: 0.8211 (ttm) cc_final: 0.7669 (tpp) REVERT: B 559 MET cc_start: 0.8178 (tmm) cc_final: 0.7971 (tmm) REVERT: B 569 MET cc_start: 0.8535 (mmp) cc_final: 0.8256 (mmp) REVERT: A 344 MET cc_start: 0.8193 (mmt) cc_final: 0.7673 (mmm) outliers start: 2 outliers final: 1 residues processed: 108 average time/residue: 0.3415 time to fit residues: 67.2599 Evaluate side-chains 100 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 222 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 333 optimal weight: 0.6980 chunk 272 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 401 optimal weight: 0.0970 chunk 433 optimal weight: 1.9990 chunk 357 optimal weight: 5.9990 chunk 397 optimal weight: 1.9990 chunk 136 optimal weight: 0.0270 chunk 321 optimal weight: 2.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN D 433 GLN B 294 GLN B 550 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30445 Z= 0.143 Angle : 0.498 7.681 41541 Z= 0.268 Chirality : 0.041 0.245 5115 Planarity : 0.003 0.064 5462 Dihedral : 3.970 41.189 4578 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.28 % Favored : 90.56 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 4331 helix: 2.07 (0.12), residues: 2096 sheet: -1.81 (0.25), residues: 428 loop : -2.32 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D 517 HIS 0.009 0.001 HIS B 688 PHE 0.015 0.001 PHE B 719 TYR 0.013 0.001 TYR F 834 ARG 0.005 0.000 ARG D 512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 501 MET cc_start: 0.8424 (tmm) cc_final: 0.8025 (tmm) REVERT: F 865 TYR cc_start: 0.8219 (m-10) cc_final: 0.7677 (m-80) REVERT: F 1227 MET cc_start: 0.8556 (tpp) cc_final: 0.8206 (tpp) REVERT: D 192 MET cc_start: 0.8458 (tpt) cc_final: 0.8190 (mmm) REVERT: D 390 ASP cc_start: 0.8736 (m-30) cc_final: 0.8390 (m-30) REVERT: B 224 MET cc_start: 0.8294 (ttm) cc_final: 0.7822 (tpp) REVERT: B 559 MET cc_start: 0.8188 (tmm) cc_final: 0.7947 (tmm) REVERT: B 569 MET cc_start: 0.8590 (mmp) cc_final: 0.8313 (mmp) REVERT: A 433 MET cc_start: 0.8558 (mpp) cc_final: 0.8234 (mmt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3282 time to fit residues: 66.5865 Evaluate side-chains 100 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 396 optimal weight: 0.7980 chunk 301 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 191 optimal weight: 0.9980 chunk 269 optimal weight: 0.4980 chunk 402 optimal weight: 9.9990 chunk 426 optimal weight: 0.4980 chunk 210 optimal weight: 0.8980 chunk 381 optimal weight: 10.0000 chunk 114 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN B 294 GLN B 299 ASN B 550 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30445 Z= 0.135 Angle : 0.492 6.933 41541 Z= 0.263 Chirality : 0.041 0.261 5115 Planarity : 0.003 0.057 5462 Dihedral : 3.933 46.296 4578 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.42 % Favored : 90.42 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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 (0.14), residues: 4331 helix: 2.20 (0.12), residues: 2084 sheet: -1.77 (0.25), residues: 428 loop : -2.32 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 517 HIS 0.015 0.001 HIS B 688 PHE 0.018 0.001 PHE F 442 TYR 0.011 0.001 TYR D 164 ARG 0.005 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 501 MET cc_start: 0.8424 (tmm) cc_final: 0.7996 (tmm) REVERT: F 1227 MET cc_start: 0.8512 (tpp) cc_final: 0.8172 (tpp) REVERT: D 687 MET cc_start: 0.8085 (mmp) cc_final: 0.7825 (mmp) REVERT: B 224 MET cc_start: 0.8288 (ttm) cc_final: 0.7841 (tpp) REVERT: B 474 MET cc_start: 0.8395 (tmm) cc_final: 0.8180 (tmm) REVERT: B 569 MET cc_start: 0.8669 (mmp) cc_final: 0.8361 (mmp) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3759 time to fit residues: 72.6077 Evaluate side-chains 97 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 355 optimal weight: 6.9990 chunk 241 optimal weight: 0.0030 chunk 6 optimal weight: 9.9990 chunk 317 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 chunk 363 optimal weight: 20.0000 chunk 294 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 217 optimal weight: 0.6980 chunk 382 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 overall best weight: 2.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1246 HIS D 153 GLN B 294 GLN ** B 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 878 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 30445 Z= 0.429 Angle : 0.693 10.510 41541 Z= 0.380 Chirality : 0.045 0.300 5115 Planarity : 0.004 0.060 5462 Dihedral : 4.887 46.717 4578 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.24 % Favored : 87.58 % Rotamer: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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 (0.14), residues: 4331 helix: 1.53 (0.12), residues: 2104 sheet: -2.08 (0.25), residues: 420 loop : -2.53 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 517 HIS 0.014 0.002 HIS B 688 PHE 0.022 0.002 PHE D 488 TYR 0.017 0.002 TYR F 493 ARG 0.006 0.001 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 501 MET cc_start: 0.8493 (tmm) cc_final: 0.8044 (tmm) REVERT: F 865 TYR cc_start: 0.8540 (m-80) cc_final: 0.8210 (m-80) REVERT: F 1227 MET cc_start: 0.8689 (tpp) cc_final: 0.8366 (tpp) REVERT: D 457 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7202 (mm-30) REVERT: D 471 TRP cc_start: 0.8650 (m100) cc_final: 0.8145 (m100) REVERT: B 224 MET cc_start: 0.8370 (ttm) cc_final: 0.8019 (tpp) REVERT: A 344 MET cc_start: 0.8274 (mmt) cc_final: 0.7840 (mmm) REVERT: C 909 ASP cc_start: 0.9369 (m-30) cc_final: 0.9104 (m-30) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3402 time to fit residues: 67.5221 Evaluate side-chains 103 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 4.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 143 optimal weight: 0.9980 chunk 383 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 250 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 426 optimal weight: 4.9990 chunk 354 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 141 optimal weight: 0.1980 chunk 224 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN B 294 GLN B 550 GLN B 653 ASN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30445 Z= 0.193 Angle : 0.541 7.561 41541 Z= 0.292 Chirality : 0.043 0.258 5115 Planarity : 0.003 0.056 5462 Dihedral : 4.514 50.271 4578 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.67 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -0.33 (0.14), residues: 4331 helix: 1.95 (0.12), residues: 2096 sheet: -2.18 (0.25), residues: 423 loop : -2.48 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 517 HIS 0.012 0.001 HIS B 688 PHE 0.018 0.001 PHE F 442 TYR 0.013 0.001 TYR D 164 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 3.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 501 MET cc_start: 0.8418 (tmm) cc_final: 0.7912 (tmm) REVERT: F 865 TYR cc_start: 0.8562 (m-80) cc_final: 0.8292 (m-80) REVERT: F 1227 MET cc_start: 0.8640 (tpp) cc_final: 0.8309 (tpp) REVERT: D 192 MET cc_start: 0.8428 (mmm) cc_final: 0.8027 (tpp) REVERT: D 415 MET cc_start: 0.8657 (tmm) cc_final: 0.8405 (tmm) REVERT: D 457 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8001 (mm-30) REVERT: D 687 MET cc_start: 0.8750 (mmp) cc_final: 0.8470 (mmp) REVERT: B 224 MET cc_start: 0.8363 (ttm) cc_final: 0.8040 (tpp) REVERT: B 474 MET cc_start: 0.8506 (tmm) cc_final: 0.8116 (tmm) REVERT: A 433 MET cc_start: 0.8889 (mmp) cc_final: 0.8597 (mmm) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3337 time to fit residues: 64.7546 Evaluate side-chains 98 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 411 optimal weight: 8.9990 chunk 48 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 311 optimal weight: 0.0270 chunk 241 optimal weight: 0.2980 chunk 359 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 425 optimal weight: 8.9990 chunk 266 optimal weight: 1.9990 chunk 259 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN B 294 GLN B 550 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30445 Z= 0.175 Angle : 0.529 8.723 41541 Z= 0.285 Chirality : 0.042 0.218 5115 Planarity : 0.003 0.061 5462 Dihedral : 4.373 50.321 4578 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.74 % Favored : 89.08 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: -0.23 (0.14), residues: 4331 helix: 2.05 (0.12), residues: 2097 sheet: -2.11 (0.24), residues: 430 loop : -2.47 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 517 HIS 0.011 0.001 HIS B 688 PHE 0.018 0.001 PHE D 221 TYR 0.016 0.001 TYR B 720 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 501 MET cc_start: 0.8428 (tmm) cc_final: 0.7903 (tmm) REVERT: F 865 TYR cc_start: 0.8545 (m-80) cc_final: 0.8319 (m-80) REVERT: F 1227 MET cc_start: 0.8638 (tpp) cc_final: 0.8315 (tpp) REVERT: D 415 MET cc_start: 0.8632 (tmm) cc_final: 0.8403 (tmm) REVERT: D 457 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8009 (mm-30) REVERT: D 687 MET cc_start: 0.8587 (mmp) cc_final: 0.8349 (mmp) REVERT: B 224 MET cc_start: 0.8339 (ttm) cc_final: 0.8002 (mtp) REVERT: A 344 MET cc_start: 0.8009 (mmt) cc_final: 0.7714 (mmm) REVERT: A 433 MET cc_start: 0.8982 (mmp) cc_final: 0.8613 (mmp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3484 time to fit residues: 67.4037 Evaluate side-chains 94 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 262 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 253 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 83 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 270 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 334 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN B 294 GLN B 550 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30445 Z= 0.166 Angle : 0.535 8.869 41541 Z= 0.286 Chirality : 0.042 0.213 5115 Planarity : 0.003 0.056 5462 Dihedral : 4.262 34.746 4578 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.09 % Favored : 89.73 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -0.19 (0.14), residues: 4331 helix: 2.09 (0.12), residues: 2098 sheet: -2.06 (0.25), residues: 428 loop : -2.48 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP D 517 HIS 0.010 0.001 HIS B 688 PHE 0.025 0.001 PHE F 735 TYR 0.012 0.001 TYR D 513 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 3.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 501 MET cc_start: 0.8510 (tmm) cc_final: 0.7971 (tmm) REVERT: F 865 TYR cc_start: 0.8441 (m-80) cc_final: 0.8235 (m-80) REVERT: F 1227 MET cc_start: 0.8621 (tpp) cc_final: 0.8300 (tpp) REVERT: D 415 MET cc_start: 0.8638 (tmm) cc_final: 0.8400 (tmm) REVERT: D 457 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7972 (mm-30) REVERT: D 657 MET cc_start: 0.7184 (mmt) cc_final: 0.6842 (tpp) REVERT: D 687 MET cc_start: 0.8569 (mmp) cc_final: 0.8347 (mmp) REVERT: A 433 MET cc_start: 0.8919 (mmp) cc_final: 0.8594 (mmm) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.3247 time to fit residues: 64.1329 Evaluate side-chains 97 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 386 optimal weight: 7.9990 chunk 407 optimal weight: 0.9980 chunk 371 optimal weight: 30.0000 chunk 396 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 172 optimal weight: 0.0030 chunk 311 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 357 optimal weight: 4.9990 chunk 374 optimal weight: 10.0000 chunk 394 optimal weight: 3.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1224 HIS D 153 GLN B 294 GLN B 550 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30445 Z= 0.357 Angle : 0.642 10.189 41541 Z= 0.351 Chirality : 0.044 0.209 5115 Planarity : 0.004 0.068 5462 Dihedral : 4.763 40.112 4578 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.42 % Favored : 87.35 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 4331 helix: 1.76 (0.12), residues: 2099 sheet: -2.30 (0.24), residues: 425 loop : -2.58 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 517 HIS 0.010 0.001 HIS B 688 PHE 0.022 0.002 PHE D 488 TYR 0.016 0.002 TYR B 568 ARG 0.009 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 501 MET cc_start: 0.8508 (tmm) cc_final: 0.7968 (tmm) REVERT: F 865 TYR cc_start: 0.8456 (m-80) cc_final: 0.8187 (m-80) REVERT: F 1227 MET cc_start: 0.8701 (tpp) cc_final: 0.8388 (tpp) REVERT: D 192 MET cc_start: 0.8562 (tpt) cc_final: 0.8167 (mmm) REVERT: D 415 MET cc_start: 0.8625 (tmm) cc_final: 0.8385 (tmm) REVERT: D 457 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7495 (mm-30) REVERT: B 224 MET cc_start: 0.8545 (ttm) cc_final: 0.8156 (tpp) REVERT: A 344 MET cc_start: 0.8221 (mmt) cc_final: 0.7871 (mmm) REVERT: A 433 MET cc_start: 0.8944 (mmp) cc_final: 0.8626 (mmp) REVERT: C 909 ASP cc_start: 0.9373 (m-30) cc_final: 0.9120 (m-30) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3413 time to fit residues: 67.0613 Evaluate side-chains 98 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 3.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 260 optimal weight: 0.6980 chunk 418 optimal weight: 7.9990 chunk 255 optimal weight: 0.6980 chunk 198 optimal weight: 0.5980 chunk 291 optimal weight: 0.9990 chunk 439 optimal weight: 0.8980 chunk 404 optimal weight: 0.1980 chunk 349 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 270 optimal weight: 0.9980 chunk 214 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 153 GLN B 294 GLN B 550 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30445 Z= 0.154 Angle : 0.551 8.656 41541 Z= 0.292 Chirality : 0.043 0.233 5115 Planarity : 0.003 0.067 5462 Dihedral : 4.432 38.763 4578 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.16 % Favored : 89.63 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: -0.30 (0.14), residues: 4331 helix: 2.00 (0.12), residues: 2100 sheet: -2.21 (0.24), residues: 429 loop : -2.51 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 517 HIS 0.010 0.001 HIS B 688 PHE 0.017 0.001 PHE F 735 TYR 0.023 0.001 TYR B 150 ARG 0.005 0.000 ARG D 555 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8662 Ramachandran restraints generated. 4331 Oldfield, 0 Emsley, 4331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 501 MET cc_start: 0.8494 (tmm) cc_final: 0.7939 (tmm) REVERT: F 1227 MET cc_start: 0.8654 (tpp) cc_final: 0.8325 (tpp) REVERT: D 192 MET cc_start: 0.8337 (tpt) cc_final: 0.7502 (tpp) REVERT: D 251 HIS cc_start: 0.8922 (m170) cc_final: 0.8716 (m170) REVERT: D 415 MET cc_start: 0.8654 (tmm) cc_final: 0.8392 (tmm) REVERT: D 457 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7520 (mm-30) REVERT: D 657 MET cc_start: 0.6865 (mmt) cc_final: 0.6549 (tpp) REVERT: B 224 MET cc_start: 0.8490 (ttm) cc_final: 0.8072 (tpp) REVERT: A 433 MET cc_start: 0.8868 (mmp) cc_final: 0.8562 (mmp) REVERT: C 909 ASP cc_start: 0.9358 (m-30) cc_final: 0.9086 (m-30) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3323 time to fit residues: 65.0409 Evaluate side-chains 97 residues out of total 4149 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 3.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 3.9990 chunk 372 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 322 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 350 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 359 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1224 HIS D 153 GLN B 294 GLN B 550 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.059252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.049860 restraints weight = 234870.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.049608 restraints weight = 310662.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.049574 restraints weight = 278309.032| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30445 Z= 0.296 Angle : 0.607 9.165 41541 Z= 0.329 Chirality : 0.044 0.232 5115 Planarity : 0.004 0.062 5462 Dihedral : 4.667 40.876 4578 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.24 % Favored : 87.51 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.78 % 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: -0.45 (0.14), residues: 4331 helix: 1.89 (0.12), residues: 2101 sheet: -2.31 (0.24), residues: 427 loop : -2.58 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 517 HIS 0.017 0.001 HIS B 688 PHE 0.019 0.002 PHE D 488 TYR 0.015 0.002 TYR A 29 ARG 0.005 0.000 ARG D 555 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4049.86 seconds wall clock time: 75 minutes 21.25 seconds (4521.25 seconds total)