Starting phenix.real_space_refine on Tue Dec 12 12:18:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7u_0645/12_2023/6o7u_0645.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7u_0645/12_2023/6o7u_0645.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7u_0645/12_2023/6o7u_0645.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7u_0645/12_2023/6o7u_0645.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7u_0645/12_2023/6o7u_0645.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7u_0645/12_2023/6o7u_0645.pdb" } resolution = 3.1 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= 0.003 sd= 0.366 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 136 5.16 5 C 13966 2.51 5 N 3411 2.21 5 O 3755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a ARG 9": "NH1" <-> "NH2" Residue "a ARG 129": "NH1" <-> "NH2" Residue "a ARG 151": "NH1" <-> "NH2" Residue "a ARG 246": "NH1" <-> "NH2" Residue "a ARG 258": "NH1" <-> "NH2" Residue "a ARG 261": "NH1" <-> "NH2" Residue "a ARG 497": "NH1" <-> "NH2" Residue "a ARG 606": "NH1" <-> "NH2" Residue "a ARG 703": "NH1" <-> "NH2" Residue "c PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 18": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 84": "NH1" <-> "NH2" Residue "d ARG 92": "NH1" <-> "NH2" Residue "d ARG 181": "NH1" <-> "NH2" Residue "d ARG 218": "NH1" <-> "NH2" Residue "d TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 117": "NH1" <-> "NH2" Residue "l TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 125": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 21268 Number of models: 1 Model: "" Number of chains: 15 Chain: "a" Number of atoms: 5665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5665 Classifications: {'peptide': 713} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 17, 'TRANS': 695} Chain breaks: 4 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 91 Chain: "b" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 330 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 43} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1466 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 2, 'TRANS': 194} Chain: "d" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2720 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 333} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 45 Chain: "e" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 60} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "f" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 463 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "g" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1094 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "h" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1125 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "i" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1125 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "j" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1116 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1132 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "l" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1125 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "m" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1131 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "n" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1131 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "o" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1133 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Time building chain proxies: 11.48, per 1000 atoms: 0.54 Number of scatterers: 21268 At special positions: 0 Unit cell: (118.72, 115.54, 132.5, 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 136 16.00 O 3755 8.00 N 3411 7.00 C 13966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.76 Conformation dependent library (CDL) restraints added in 4.4 seconds 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5102 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 4 sheets defined 76.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'a' and resid 24 through 36 Processing helix chain 'a' and resid 57 through 78 removed outlier: 4.006A pdb=" N PHE a 61 " --> pdb=" O GLN a 57 " (cutoff:3.500A) Processing helix chain 'a' and resid 112 through 118 Processing helix chain 'a' and resid 118 through 164 removed outlier: 3.743A pdb=" N GLU a 122 " --> pdb=" O ASP a 118 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS a 126 " --> pdb=" O GLU a 122 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG a 129 " --> pdb=" O ASP a 125 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER a 139 " --> pdb=" O GLU a 135 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU a 140 " --> pdb=" O SER a 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS a 143 " --> pdb=" O SER a 139 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN a 152 " --> pdb=" O LEU a 148 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL a 153 " --> pdb=" O GLU a 149 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE a 154 " --> pdb=" O GLN a 150 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS a 157 " --> pdb=" O VAL a 153 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS a 159 " --> pdb=" O PHE a 155 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE a 160 " --> pdb=" O GLU a 156 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE a 161 " --> pdb=" O CYS a 157 " (cutoff:3.500A) Processing helix chain 'a' and resid 248 through 260 Processing helix chain 'a' and resid 296 through 305 removed outlier: 3.707A pdb=" N LYS a 301 " --> pdb=" O LEU a 297 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG a 302 " --> pdb=" O LYS a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 320 through 352 removed outlier: 3.588A pdb=" N THR a 324 " --> pdb=" O GLU a 320 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN a 328 " --> pdb=" O THR a 324 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP a 330 " --> pdb=" O ASN a 326 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP a 331 " --> pdb=" O ARG a 327 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE a 335 " --> pdb=" O ASP a 331 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN a 341 " --> pdb=" O ASP a 337 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU a 348 " --> pdb=" O HIS a 344 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL a 349 " --> pdb=" O THR a 345 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE a 350 " --> pdb=" O GLU a 346 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP a 352 " --> pdb=" O LEU a 348 " (cutoff:3.500A) Processing helix chain 'a' and resid 353 through 372 removed outlier: 3.756A pdb=" N ALA a 359 " --> pdb=" O PRO a 355 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR a 361 " --> pdb=" O TRP a 357 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG a 363 " --> pdb=" O ALA a 359 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR a 366 " --> pdb=" O LYS a 362 " (cutoff:3.500A) Processing helix chain 'a' and resid 388 through 390 No H-bonds generated for 'chain 'a' and resid 388 through 390' Processing helix chain 'a' and resid 391 through 406 removed outlier: 4.064A pdb=" N LYS a 400 " --> pdb=" O GLN a 396 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP a 401 " --> pdb=" O ASP a 397 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU a 404 " --> pdb=" O LYS a 400 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU a 406 " --> pdb=" O TYR a 402 " (cutoff:3.500A) Processing helix chain 'a' and resid 433 through 444 removed outlier: 4.118A pdb=" N TYR a 443 " --> pdb=" O ILE a 439 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY a 444 " --> pdb=" O VAL a 440 " (cutoff:3.500A) Processing helix chain 'a' and resid 456 through 469 Proline residue: a 462 - end of helix removed outlier: 3.653A pdb=" N MET a 468 " --> pdb=" O MET a 464 " (cutoff:3.500A) Processing helix chain 'a' and resid 471 through 488 removed outlier: 4.030A pdb=" N LEU a 485 " --> pdb=" O MET a 481 " (cutoff:3.500A) Processing helix chain 'a' and resid 488 through 494 removed outlier: 3.939A pdb=" N ALA a 494 " --> pdb=" O ARG a 490 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 507 Processing helix chain 'a' and resid 507 through 525 removed outlier: 3.643A pdb=" N LEU a 512 " --> pdb=" O ARG a 508 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU a 513 " --> pdb=" O TYR a 509 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER a 518 " --> pdb=" O MET a 514 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR a 520 " --> pdb=" O ALA a 516 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 569 removed outlier: 3.747A pdb=" N TRP a 568 " --> pdb=" O ASP a 565 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS a 569 " --> pdb=" O PHE a 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 565 through 569' Processing helix chain 'a' and resid 573 through 598 removed outlier: 3.566A pdb=" N PHE a 577 " --> pdb=" O ASN a 573 " (cutoff:3.500A) Processing helix chain 'a' and resid 598 through 608 removed outlier: 3.819A pdb=" N TYR a 602 " --> pdb=" O PHE a 598 " (cutoff:3.500A) Processing helix chain 'a' and resid 610 through 626 removed outlier: 5.111A pdb=" N ILE a 619 " --> pdb=" O ILE a 615 " (cutoff:3.500A) Proline residue: a 620 - end of helix removed outlier: 3.555A pdb=" N PHE a 624 " --> pdb=" O PRO a 620 " (cutoff:3.500A) Processing helix chain 'a' and resid 628 through 642 removed outlier: 3.579A pdb=" N VAL a 637 " --> pdb=" O SER a 633 " (cutoff:3.500A) Processing helix chain 'a' and resid 654 through 664 removed outlier: 3.935A pdb=" N PHE a 662 " --> pdb=" O LEU a 658 " (cutoff:3.500A) Processing helix chain 'a' and resid 675 through 689 removed outlier: 4.078A pdb=" N VAL a 681 " --> pdb=" O ALA a 677 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL a 682 " --> pdb=" O LYS a 678 " (cutoff:3.500A) Processing helix chain 'a' and resid 689 through 703 removed outlier: 3.656A pdb=" N LEU a 695 " --> pdb=" O VAL a 691 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LYS a 698 " --> pdb=" O LEU a 694 " (cutoff:3.500A) Proline residue: a 699 - end of helix Processing helix chain 'a' and resid 704 through 707 removed outlier: 3.538A pdb=" N LYS a 707 " --> pdb=" O ARG a 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 704 through 707' Processing helix chain 'a' and resid 767 through 791 removed outlier: 4.056A pdb=" N HIS a 774 " --> pdb=" O ASP a 770 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE a 787 " --> pdb=" O CYS a 783 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR a 790 " --> pdb=" O CYS a 786 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA a 791 " --> pdb=" O ILE a 787 " (cutoff:3.500A) Processing helix chain 'a' and resid 794 through 815 removed outlier: 3.776A pdb=" N SER a 800 " --> pdb=" O LEU a 796 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP a 811 " --> pdb=" O SER a 807 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET a 813 " --> pdb=" O VAL a 809 " (cutoff:3.500A) Processing helix chain 'a' and resid 826 through 847 removed outlier: 3.882A pdb=" N VAL a 833 " --> pdb=" O ALA a 829 " (cutoff:3.500A) Processing helix chain 'a' and resid 852 through 866 Processing helix chain 'a' and resid 884 through 888 removed outlier: 3.656A pdb=" N ALA a 887 " --> pdb=" O SER a 884 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE a 888 " --> pdb=" O PHE a 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 884 through 888' Processing helix chain 'b' and resid 222 through 246 removed outlier: 3.705A pdb=" N ILE b 228 " --> pdb=" O LEU b 224 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL b 229 " --> pdb=" O MET b 225 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA b 231 " --> pdb=" O LEU b 227 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU b 234 " --> pdb=" O SER b 230 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN b 246 " --> pdb=" O SER b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 250 through 254 removed outlier: 3.588A pdb=" N ALA b 253 " --> pdb=" O THR b 250 " (cutoff:3.500A) Processing helix chain 'c' and resid 18 through 39 Processing helix chain 'c' and resid 41 through 45 removed outlier: 3.694A pdb=" N ILE c 45 " --> pdb=" O GLY c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 54 Processing helix chain 'c' and resid 55 through 90 removed outlier: 3.904A pdb=" N TRP c 59 " --> pdb=" O SER c 55 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL c 72 " --> pdb=" O VAL c 68 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY c 74 " --> pdb=" O LEU c 70 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP c 77 " --> pdb=" O VAL c 73 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER c 85 " --> pdb=" O ILE c 81 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET c 86 " --> pdb=" O THR c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 97 removed outlier: 3.635A pdb=" N ILE c 96 " --> pdb=" O ALA c 93 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR c 97 " --> pdb=" O PRO c 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 93 through 97' Processing helix chain 'c' and resid 98 through 100 No H-bonds generated for 'chain 'c' and resid 98 through 100' Processing helix chain 'c' and resid 101 through 123 removed outlier: 3.588A pdb=" N CYS c 107 " --> pdb=" O SER c 103 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL c 110 " --> pdb=" O PHE c 106 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA c 111 " --> pdb=" O CYS c 107 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE c 112 " --> pdb=" O GLU c 108 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY c 114 " --> pdb=" O VAL c 110 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL c 120 " --> pdb=" O ILE c 116 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 177 removed outlier: 3.793A pdb=" N LEU c 145 " --> pdb=" O THR c 141 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL c 152 " --> pdb=" O ALA c 148 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER c 155 " --> pdb=" O THR c 151 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA c 170 " --> pdb=" O THR c 166 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE c 172 " --> pdb=" O ALA c 168 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA c 175 " --> pdb=" O ALA c 171 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 192 removed outlier: 4.130A pdb=" N VAL c 186 " --> pdb=" O VAL c 182 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ILE c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU c 188 " --> pdb=" O ILE c 184 " (cutoff:3.500A) Processing helix chain 'c' and resid 192 through 206 removed outlier: 4.023A pdb=" N LEU c 196 " --> pdb=" O SER c 192 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA c 206 " --> pdb=" O GLY c 202 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 9 removed outlier: 4.017A pdb=" N ILE d 8 " --> pdb=" O TYR d 5 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP d 9 " --> pdb=" O PHE d 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 5 through 9' Processing helix chain 'd' and resid 10 through 22 removed outlier: 3.533A pdb=" N GLY d 15 " --> pdb=" O GLY d 11 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN d 22 " --> pdb=" O ARG d 18 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 35 removed outlier: 3.631A pdb=" N LEU d 33 " --> pdb=" O GLN d 29 " (cutoff:3.500A) Processing helix chain 'd' and resid 38 through 47 Processing helix chain 'd' and resid 64 through 86 removed outlier: 3.515A pdb=" N ILE d 68 " --> pdb=" O THR d 64 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN d 69 " --> pdb=" O THR d 65 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN d 86 " --> pdb=" O TYR d 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 89 through 111 removed outlier: 4.323A pdb=" N GLY d 101 " --> pdb=" O TYR d 97 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP d 105 " --> pdb=" O GLY d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 136 through 141 removed outlier: 3.523A pdb=" N LEU d 139 " --> pdb=" O LEU d 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER d 140 " --> pdb=" O PRO d 137 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL d 141 " --> pdb=" O THR d 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 136 through 141' Processing helix chain 'd' and resid 145 through 150 Processing helix chain 'd' and resid 158 through 162 removed outlier: 3.600A pdb=" N PHE d 162 " --> pdb=" O ALA d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 200 removed outlier: 3.784A pdb=" N ILE d 177 " --> pdb=" O ASP d 173 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU d 178 " --> pdb=" O ASP d 174 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE d 179 " --> pdb=" O MET d 175 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE d 200 " --> pdb=" O VAL d 196 " (cutoff:3.500A) Processing helix chain 'd' and resid 202 through 227 removed outlier: 3.991A pdb=" N CYS d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET d 208 " --> pdb=" O ALA d 204 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU d 211 " --> pdb=" O CYS d 207 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU d 215 " --> pdb=" O LEU d 211 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 239 Processing helix chain 'd' and resid 248 through 258 removed outlier: 5.360A pdb=" N PHE d 254 " --> pdb=" O PRO d 250 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS d 255 " --> pdb=" O LEU d 251 " (cutoff:3.500A) Processing helix chain 'd' and resid 261 through 267 removed outlier: 3.538A pdb=" N VAL d 265 " --> pdb=" O ASP d 261 " (cutoff:3.500A) Processing helix chain 'd' and resid 283 through 298 removed outlier: 3.786A pdb=" N ASP d 298 " --> pdb=" O GLU d 294 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 330 removed outlier: 4.318A pdb=" N TRP d 310 " --> pdb=" O ILE d 306 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER d 315 " --> pdb=" O ALA d 311 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 23 removed outlier: 4.122A pdb=" N VAL e 10 " --> pdb=" O THR e 6 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET e 17 " --> pdb=" O VAL e 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 54 removed outlier: 4.376A pdb=" N SER e 35 " --> pdb=" O ALA e 31 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE e 38 " --> pdb=" O ARG e 34 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU e 39 " --> pdb=" O SER e 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 33 removed outlier: 3.635A pdb=" N LEU f 24 " --> pdb=" O GLY f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 71 removed outlier: 3.689A pdb=" N VAL f 51 " --> pdb=" O ASP f 47 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR f 54 " --> pdb=" O ALA f 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU f 57 " --> pdb=" O HIS f 53 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA f 58 " --> pdb=" O THR f 54 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE f 71 " --> pdb=" O VAL f 67 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 43 removed outlier: 4.144A pdb=" N GLY g 13 " --> pdb=" O ALA g 9 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE g 21 " --> pdb=" O CYS g 17 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N THR g 24 " --> pdb=" O ALA g 20 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER g 35 " --> pdb=" O GLY g 31 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY g 38 " --> pdb=" O LYS g 34 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 45 No H-bonds generated for 'chain 'g' and resid 44 through 45' Processing helix chain 'g' and resid 46 through 50 removed outlier: 3.638A pdb=" N LEU g 49 " --> pdb=" O ARG g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 54 through 76 removed outlier: 3.524A pdb=" N VAL g 70 " --> pdb=" O TYR g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 122 removed outlier: 3.823A pdb=" N VAL g 97 " --> pdb=" O ALA g 93 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP g 113 " --> pdb=" O GLY g 109 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA g 114 " --> pdb=" O ILE g 110 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER g 120 " --> pdb=" O VAL g 116 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN g 121 " --> pdb=" O ARG g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 124 through 153 removed outlier: 4.121A pdb=" N GLY g 128 " --> pdb=" O ARG g 124 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE g 135 " --> pdb=" O LEU g 131 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU g 139 " --> pdb=" O PHE g 135 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY g 140 " --> pdb=" O ALA g 136 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU g 141 " --> pdb=" O GLU g 137 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL g 146 " --> pdb=" O TYR g 142 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG g 153 " --> pdb=" O LEU g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 43 removed outlier: 3.925A pdb=" N GLY h 13 " --> pdb=" O ALA h 9 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA h 20 " --> pdb=" O GLY h 16 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE h 21 " --> pdb=" O CYS h 17 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR h 24 " --> pdb=" O ALA h 20 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER h 35 " --> pdb=" O GLY h 31 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY h 38 " --> pdb=" O LYS h 34 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE h 39 " --> pdb=" O SER h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 46 through 50 removed outlier: 3.766A pdb=" N LEU h 49 " --> pdb=" O ARG h 46 " (cutoff:3.500A) Processing helix chain 'h' and resid 54 through 76 removed outlier: 4.079A pdb=" N ILE h 63 " --> pdb=" O MET h 59 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA h 64 " --> pdb=" O ALA h 60 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE h 65 " --> pdb=" O GLY h 61 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL h 70 " --> pdb=" O TYR h 66 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 117 removed outlier: 4.006A pdb=" N SER h 100 " --> pdb=" O SER h 96 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA h 103 " --> pdb=" O LEU h 99 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG h 117 " --> pdb=" O ASP h 113 " (cutoff:3.500A) Processing helix chain 'h' and resid 124 through 155 removed outlier: 4.294A pdb=" N GLY h 128 " --> pdb=" O ARG h 124 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE h 135 " --> pdb=" O LEU h 131 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU h 139 " --> pdb=" O PHE h 135 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY h 140 " --> pdb=" O ALA h 136 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG h 153 " --> pdb=" O LEU h 149 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR h 155 " --> pdb=" O ASN h 151 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 43 removed outlier: 4.418A pdb=" N PHE i 12 " --> pdb=" O TYR i 8 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY i 13 " --> pdb=" O ALA i 9 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE i 21 " --> pdb=" O CYS i 17 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N THR i 24 " --> pdb=" O ALA i 20 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER i 35 " --> pdb=" O GLY i 31 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY i 38 " --> pdb=" O LYS i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 50 removed outlier: 3.736A pdb=" N LEU i 50 " --> pdb=" O PRO i 47 " (cutoff:3.500A) Processing helix chain 'i' and resid 54 through 75 removed outlier: 3.772A pdb=" N ILE i 63 " --> pdb=" O MET i 59 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA i 64 " --> pdb=" O ALA i 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL i 70 " --> pdb=" O TYR i 66 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU i 73 " --> pdb=" O VAL i 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS i 75 " --> pdb=" O SER i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 78 No H-bonds generated for 'chain 'i' and resid 76 through 78' Processing helix chain 'i' and resid 83 through 119 removed outlier: 3.574A pdb=" N VAL i 97 " --> pdb=" O ALA i 93 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER i 100 " --> pdb=" O SER i 96 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA i 103 " --> pdb=" O LEU i 99 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL i 111 " --> pdb=" O ALA i 107 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA i 114 " --> pdb=" O ILE i 110 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 152 removed outlier: 4.421A pdb=" N GLY i 128 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU i 139 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY i 140 " --> pdb=" O ALA i 136 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 43 removed outlier: 4.429A pdb=" N PHE j 12 " --> pdb=" O TYR j 8 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY j 13 " --> pdb=" O ALA j 9 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE j 21 " --> pdb=" O CYS j 17 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE j 23 " --> pdb=" O SER j 19 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) Processing helix chain 'j' and resid 54 through 76 removed outlier: 3.723A pdb=" N ILE j 63 " --> pdb=" O MET j 59 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA j 64 " --> pdb=" O ALA j 60 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 117 removed outlier: 3.573A pdb=" N VAL j 97 " --> pdb=" O ALA j 93 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER j 100 " --> pdb=" O SER j 96 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA j 103 " --> pdb=" O LEU j 99 " (cutoff:3.500A) Processing helix chain 'j' and resid 122 through 124 No H-bonds generated for 'chain 'j' and resid 122 through 124' Processing helix chain 'j' and resid 125 through 152 removed outlier: 3.664A pdb=" N LEU j 139 " --> pdb=" O PHE j 135 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY j 140 " --> pdb=" O ALA j 136 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY j 143 " --> pdb=" O LEU j 139 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 42 removed outlier: 4.427A pdb=" N PHE k 12 " --> pdb=" O TYR k 8 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY k 13 " --> pdb=" O ALA k 9 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA k 20 " --> pdb=" O GLY k 16 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE k 21 " --> pdb=" O CYS k 17 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR k 24 " --> pdb=" O ALA k 20 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER k 35 " --> pdb=" O GLY k 31 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY k 38 " --> pdb=" O LYS k 34 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE k 39 " --> pdb=" O SER k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 76 removed outlier: 3.526A pdb=" N ALA k 60 " --> pdb=" O PRO k 56 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE k 63 " --> pdb=" O MET k 59 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA k 64 " --> pdb=" O ALA k 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL k 70 " --> pdb=" O TYR k 66 " (cutoff:3.500A) Processing helix chain 'k' and resid 83 through 119 removed outlier: 3.814A pdb=" N SER k 100 " --> pdb=" O SER k 96 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY k 118 " --> pdb=" O ALA k 114 " (cutoff:3.500A) Processing helix chain 'k' and resid 122 through 124 No H-bonds generated for 'chain 'k' and resid 122 through 124' Processing helix chain 'k' and resid 125 through 151 removed outlier: 3.518A pdb=" N ILE k 130 " --> pdb=" O PHE k 126 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU k 131 " --> pdb=" O VAL k 127 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE k 135 " --> pdb=" O LEU k 131 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU k 139 " --> pdb=" O PHE k 135 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY k 140 " --> pdb=" O ALA k 136 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY k 143 " --> pdb=" O LEU k 139 " (cutoff:3.500A) Processing helix chain 'k' and resid 152 through 154 No H-bonds generated for 'chain 'k' and resid 152 through 154' Processing helix chain 'l' and resid 9 through 43 removed outlier: 3.999A pdb=" N GLY l 13 " --> pdb=" O ALA l 9 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE l 21 " --> pdb=" O CYS l 17 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE l 23 " --> pdb=" O SER l 19 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR l 24 " --> pdb=" O ALA l 20 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER l 35 " --> pdb=" O GLY l 31 " (cutoff:3.500A) Processing helix chain 'l' and resid 46 through 50 removed outlier: 3.529A pdb=" N LEU l 49 " --> pdb=" O ARG l 46 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU l 50 " --> pdb=" O PRO l 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 46 through 50' Processing helix chain 'l' and resid 54 through 74 removed outlier: 3.996A pdb=" N ILE l 63 " --> pdb=" O MET l 59 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA l 64 " --> pdb=" O ALA l 60 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE l 65 " --> pdb=" O GLY l 61 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY l 67 " --> pdb=" O ILE l 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL l 70 " --> pdb=" O TYR l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 75 through 78 removed outlier: 3.540A pdb=" N LEU l 78 " --> pdb=" O CYS l 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 75 through 78' Processing helix chain 'l' and resid 83 through 117 removed outlier: 3.875A pdb=" N SER l 100 " --> pdb=" O SER l 96 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA l 103 " --> pdb=" O LEU l 99 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP l 113 " --> pdb=" O GLY l 109 " (cutoff:3.500A) Processing helix chain 'l' and resid 122 through 124 No H-bonds generated for 'chain 'l' and resid 122 through 124' Processing helix chain 'l' and resid 125 through 152 removed outlier: 3.748A pdb=" N PHE l 135 " --> pdb=" O LEU l 131 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU l 139 " --> pdb=" O PHE l 135 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY l 140 " --> pdb=" O ALA l 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 40 removed outlier: 4.393A pdb=" N PHE m 12 " --> pdb=" O TYR m 8 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY m 13 " --> pdb=" O ALA m 9 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA m 20 " --> pdb=" O GLY m 16 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE m 21 " --> pdb=" O CYS m 17 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR m 24 " --> pdb=" O ALA m 20 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY m 27 " --> pdb=" O PHE m 23 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR m 30 " --> pdb=" O LEU m 26 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER m 35 " --> pdb=" O GLY m 31 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY m 38 " --> pdb=" O LYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 50 Processing helix chain 'm' and resid 54 through 76 removed outlier: 3.959A pdb=" N ILE m 63 " --> pdb=" O MET m 59 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA m 64 " --> pdb=" O ALA m 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL m 70 " --> pdb=" O TYR m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 117 removed outlier: 3.839A pdb=" N SER m 100 " --> pdb=" O SER m 96 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA m 103 " --> pdb=" O LEU m 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP m 113 " --> pdb=" O GLY m 109 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA m 114 " --> pdb=" O ILE m 110 " (cutoff:3.500A) Processing helix chain 'm' and resid 122 through 124 No H-bonds generated for 'chain 'm' and resid 122 through 124' Processing helix chain 'm' and resid 125 through 152 removed outlier: 3.623A pdb=" N PHE m 135 " --> pdb=" O LEU m 131 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU m 139 " --> pdb=" O PHE m 135 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY m 140 " --> pdb=" O ALA m 136 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU m 141 " --> pdb=" O GLU m 137 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY m 143 " --> pdb=" O LEU m 139 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 43 removed outlier: 4.175A pdb=" N GLY n 13 " --> pdb=" O ALA n 9 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE n 21 " --> pdb=" O CYS n 17 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR n 24 " --> pdb=" O ALA n 20 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER n 35 " --> pdb=" O GLY n 31 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY n 38 " --> pdb=" O LYS n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 46 through 50 removed outlier: 3.560A pdb=" N LEU n 49 " --> pdb=" O ARG n 46 " (cutoff:3.500A) Processing helix chain 'n' and resid 54 through 76 removed outlier: 3.916A pdb=" N ILE n 63 " --> pdb=" O MET n 59 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA n 64 " --> pdb=" O ALA n 60 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 120 removed outlier: 4.015A pdb=" N SER n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA n 103 " --> pdb=" O LEU n 99 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP n 113 " --> pdb=" O GLY n 109 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA n 114 " --> pdb=" O ILE n 110 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER n 120 " --> pdb=" O VAL n 116 " (cutoff:3.500A) Processing helix chain 'n' and resid 124 through 152 removed outlier: 4.503A pdb=" N GLY n 128 " --> pdb=" O ARG n 124 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU n 139 " --> pdb=" O PHE n 135 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY n 140 " --> pdb=" O ALA n 136 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 48 removed outlier: 4.373A pdb=" N PHE o 18 " --> pdb=" O TYR o 14 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY o 19 " --> pdb=" O ALA o 15 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU o 29 " --> pdb=" O ALA o 25 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER o 30 " --> pdb=" O ALA o 26 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER o 41 " --> pdb=" O GLY o 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY o 44 " --> pdb=" O LYS o 40 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE o 48 " --> pdb=" O GLY o 44 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 56 removed outlier: 3.515A pdb=" N LEU o 55 " --> pdb=" O LYS o 52 " (cutoff:3.500A) Processing helix chain 'o' and resid 60 through 82 removed outlier: 3.527A pdb=" N SER o 66 " --> pdb=" O PRO o 62 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU o 69 " --> pdb=" O MET o 65 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA o 70 " --> pdb=" O SER o 66 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE o 71 " --> pdb=" O GLY o 67 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL o 76 " --> pdb=" O TYR o 72 " (cutoff:3.500A) Processing helix chain 'o' and resid 91 through 128 removed outlier: 3.576A pdb=" N VAL o 105 " --> pdb=" O CYS o 101 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE o 107 " --> pdb=" O LEU o 103 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA o 108 " --> pdb=" O CYS o 104 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP o 121 " --> pdb=" O GLY o 117 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL o 122 " --> pdb=" O MET o 118 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL o 124 " --> pdb=" O GLY o 120 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET o 128 " --> pdb=" O VAL o 124 " (cutoff:3.500A) Processing helix chain 'o' and resid 133 through 162 removed outlier: 4.382A pdb=" N LEU o 147 " --> pdb=" O PHE o 143 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLY o 148 " --> pdb=" O SER o 144 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU o 149 " --> pdb=" O GLU o 145 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY o 151 " --> pdb=" O LEU o 147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'a' and resid 267 through 270 removed outlier: 3.519A pdb=" N PHE a 269 " --> pdb=" O CYS a 286 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY a 242 " --> pdb=" O PHE a 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 540 through 541 Processing sheet with id=AA4, first strand: chain 'a' and resid 552 through 553 1429 hydrogen bonds defined for protein. 4236 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: 6.69 Time building geometry restraints manager: 9.21 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: 6321 1.34 - 1.46: 4361 1.46 - 1.58: 10800 1.58 - 1.70: 1 1.70 - 1.82: 205 Bond restraints: 21688 Sorted by residual: bond pdb=" C ALA g 9 " pdb=" N PRO g 10 " ideal model delta sigma weight residual 1.334 1.372 -0.038 8.40e-03 1.42e+04 2.07e+01 bond pdb=" CB THR i 24 " pdb=" CG2 THR i 24 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.11e+00 bond pdb=" CA VAL g 55 " pdb=" C VAL g 55 " ideal model delta sigma weight residual 1.520 1.538 -0.019 8.80e-03 1.29e+04 4.45e+00 bond pdb=" C VAL a 691 " pdb=" N PRO a 692 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.00e+00 bond pdb=" CB THR g 24 " pdb=" CG2 THR g 24 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.93e+00 ... (remaining 21683 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.61: 366 105.61 - 112.74: 11133 112.74 - 119.87: 8275 119.87 - 127.00: 9514 127.00 - 134.13: 179 Bond angle restraints: 29467 Sorted by residual: angle pdb=" C ILE l 54 " pdb=" N VAL l 55 " pdb=" CA VAL l 55 " ideal model delta sigma weight residual 120.24 125.38 -5.14 6.30e-01 2.52e+00 6.66e+01 angle pdb=" C ILE m 54 " pdb=" N VAL m 55 " pdb=" CA VAL m 55 " ideal model delta sigma weight residual 120.24 123.89 -3.65 6.30e-01 2.52e+00 3.36e+01 angle pdb=" N VAL f 39 " pdb=" CA VAL f 39 " pdb=" C VAL f 39 " ideal model delta sigma weight residual 113.53 108.13 5.40 9.80e-01 1.04e+00 3.04e+01 angle pdb=" C ILE g 54 " pdb=" N VAL g 55 " pdb=" CA VAL g 55 " ideal model delta sigma weight residual 120.24 123.62 -3.38 6.30e-01 2.52e+00 2.87e+01 angle pdb=" C GLN i 156 " pdb=" N ASP i 157 " pdb=" CA ASP i 157 " ideal model delta sigma weight residual 121.54 131.29 -9.75 1.91e+00 2.74e-01 2.60e+01 ... (remaining 29462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.21: 11951 15.21 - 30.41: 506 30.41 - 45.61: 102 45.61 - 60.82: 10 60.82 - 76.02: 13 Dihedral angle restraints: 12582 sinusoidal: 4552 harmonic: 8030 Sorted by residual: dihedral pdb=" CA TYR d 249 " pdb=" C TYR d 249 " pdb=" N PRO d 250 " pdb=" CA PRO d 250 " ideal model delta harmonic sigma weight residual -180.00 -150.87 -29.13 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA LEU d 172 " pdb=" C LEU d 172 " pdb=" N ASP d 173 " pdb=" CA ASP d 173 " ideal model delta harmonic sigma weight residual 180.00 155.98 24.02 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA SER d 59 " pdb=" C SER d 59 " pdb=" N SER d 60 " pdb=" CA SER d 60 " ideal model delta harmonic sigma weight residual 180.00 156.44 23.56 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 12579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3055 0.073 - 0.146: 461 0.146 - 0.219: 28 0.219 - 0.293: 6 0.293 - 0.366: 1 Chirality restraints: 3551 Sorted by residual: chirality pdb=" CB ILE a 528 " pdb=" CA ILE a 528 " pdb=" CG1 ILE a 528 " pdb=" CG2 ILE a 528 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CG LEU c 199 " pdb=" CB LEU c 199 " pdb=" CD1 LEU c 199 " pdb=" CD2 LEU c 199 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CB ILE a 25 " pdb=" CA ILE a 25 " pdb=" CG1 ILE a 25 " pdb=" CG2 ILE a 25 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 3548 not shown) Planarity restraints: 3641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 693 " 0.017 2.00e-02 2.50e+03 1.84e-02 8.50e+00 pdb=" CG TRP a 693 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP a 693 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP a 693 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP a 693 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP a 693 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP a 693 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 693 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 693 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP a 693 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP c 77 " 0.017 2.00e-02 2.50e+03 1.83e-02 8.35e+00 pdb=" CG TRP c 77 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP c 77 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP c 77 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP c 77 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP c 77 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP c 77 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 77 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 77 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP c 77 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE d 192 " -0.019 2.00e-02 2.50e+03 2.13e-02 7.92e+00 pdb=" CG PHE d 192 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE d 192 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE d 192 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE d 192 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE d 192 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE d 192 " -0.001 2.00e-02 2.50e+03 ... (remaining 3638 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 6110 2.82 - 3.34: 20102 3.34 - 3.86: 36565 3.86 - 4.38: 43475 4.38 - 4.90: 74398 Nonbonded interactions: 180650 Sorted by model distance: nonbonded pdb=" O GLY h 31 " pdb=" OG SER h 35 " model vdw 2.294 2.440 nonbonded pdb=" O ALA a 453 " pdb=" OG1 THR a 457 " model vdw 2.324 2.440 nonbonded pdb=" O GLY k 31 " pdb=" OG SER k 35 " model vdw 2.324 2.440 nonbonded pdb=" OG SER d 315 " pdb=" OH TYR d 345 " model vdw 2.330 2.440 nonbonded pdb=" O GLY g 31 " pdb=" OG SER g 35 " model vdw 2.332 2.440 ... (remaining 180645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'g' selection = (chain 'h' and resid 4 through 156) selection = (chain 'i' and resid 4 through 156) selection = (chain 'j' and resid 4 through 156) selection = (chain 'k' and resid 4 through 156) selection = (chain 'l' and resid 4 through 156) selection = (chain 'm' and resid 4 through 156) selection = (chain 'n' and resid 4 through 156) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.840 Check model and map are aligned: 0.250 Set scattering table: 0.180 Process input model: 59.110 Find NCS groups from input model: 1.230 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 21688 Z= 0.367 Angle : 0.977 15.771 29467 Z= 0.533 Chirality : 0.053 0.366 3551 Planarity : 0.007 0.062 3641 Dihedral : 9.818 76.024 7480 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.12), residues: 2794 helix: -2.27 (0.09), residues: 2042 sheet: -2.75 (0.73), residues: 45 loop : -3.15 (0.18), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP a 693 HIS 0.023 0.003 HIS a 789 PHE 0.049 0.003 PHE d 192 TYR 0.039 0.002 TYR a 605 ARG 0.012 0.001 ARG d 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 435 time to evaluate : 2.565 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 437 average time/residue: 0.4050 time to fit residues: 260.6622 Evaluate side-chains 277 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 2.419 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 140 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 160 optimal weight: 0.9990 chunk 249 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 117 ASN a 353 GLN a 437 GLN a 626 GLN a 680 GLN a 767 ASN a 775 GLN a 817 ASN b 246 ASN c 100 ASN d 10 ASN d 128 HIS d 283 ASN ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 333 ASN e 55 GLN ** g 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN j 53 ASN k 53 ASN k 151 ASN ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 122 GLN ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 121 GLN ** o 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21688 Z= 0.187 Angle : 0.543 11.336 29467 Z= 0.279 Chirality : 0.039 0.195 3551 Planarity : 0.004 0.044 3641 Dihedral : 4.647 24.623 3008 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.66 % Allowed : 6.14 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.15), residues: 2794 helix: -0.49 (0.11), residues: 2064 sheet: -2.56 (0.72), residues: 44 loop : -2.56 (0.20), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP a 693 HIS 0.007 0.001 HIS a 789 PHE 0.029 0.001 PHE c 80 TYR 0.013 0.001 TYR a 525 ARG 0.006 0.000 ARG d 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 298 time to evaluate : 2.352 Fit side-chains outliers start: 37 outliers final: 15 residues processed: 324 average time/residue: 0.3569 time to fit residues: 177.5669 Evaluate side-chains 281 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 266 time to evaluate : 2.539 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1990 time to fit residues: 9.0000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 170 optimal weight: 0.0670 chunk 68 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 200 optimal weight: 0.3980 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 617 ASN ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 246 ASN d 164 ASN ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 333 ASN ** g 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 82 GLN ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21688 Z= 0.187 Angle : 0.515 10.517 29467 Z= 0.263 Chirality : 0.039 0.160 3551 Planarity : 0.004 0.043 3641 Dihedral : 4.338 23.491 3008 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.26 % Allowed : 7.84 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2794 helix: 0.32 (0.12), residues: 2064 sheet: -2.33 (0.73), residues: 44 loop : -2.22 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 693 HIS 0.005 0.001 HIS a 864 PHE 0.029 0.001 PHE c 80 TYR 0.012 0.001 TYR a 525 ARG 0.005 0.000 ARG o 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 276 time to evaluate : 2.461 Fit side-chains outliers start: 28 outliers final: 9 residues processed: 293 average time/residue: 0.3208 time to fit residues: 144.9937 Evaluate side-chains 269 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 260 time to evaluate : 1.812 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2512 time to fit residues: 6.0596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 2.9990 chunk 188 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 265 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 353 GLN ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 246 ASN c 132 ASN d 164 ASN ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 333 ASN g 156 GLN h 90 GLN i 121 GLN k 53 ASN ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 21688 Z= 0.280 Angle : 0.549 11.833 29467 Z= 0.278 Chirality : 0.040 0.145 3551 Planarity : 0.004 0.043 3641 Dihedral : 4.307 23.471 3008 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.84 % Allowed : 8.56 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2794 helix: 0.63 (0.12), residues: 2069 sheet: -2.06 (0.76), residues: 44 loop : -2.06 (0.21), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a 693 HIS 0.007 0.001 HIS a 864 PHE 0.032 0.001 PHE c 80 TYR 0.015 0.001 TYR a 525 ARG 0.005 0.000 ARG o 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 263 time to evaluate : 2.441 Fit side-chains outliers start: 41 outliers final: 20 residues processed: 290 average time/residue: 0.3730 time to fit residues: 165.3669 Evaluate side-chains 267 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 247 time to evaluate : 2.517 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1992 time to fit residues: 10.9818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 0.5980 chunk 150 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 226 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 238 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 569 HIS ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 246 ASN c 132 ASN d 258 GLN ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 333 ASN g 156 GLN k 53 ASN ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 21688 Z= 0.244 Angle : 0.517 9.328 29467 Z= 0.265 Chirality : 0.040 0.141 3551 Planarity : 0.003 0.043 3641 Dihedral : 4.219 23.056 3008 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.17 % Allowed : 9.28 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.16), residues: 2794 helix: 0.87 (0.12), residues: 2067 sheet: -1.78 (0.75), residues: 45 loop : -1.92 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 693 HIS 0.006 0.001 HIS a 864 PHE 0.028 0.001 PHE c 80 TYR 0.012 0.001 TYR a 525 ARG 0.006 0.000 ARG o 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 262 time to evaluate : 2.383 Fit side-chains outliers start: 26 outliers final: 7 residues processed: 278 average time/residue: 0.3881 time to fit residues: 163.1426 Evaluate side-chains 249 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 242 time to evaluate : 2.440 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3493 time to fit residues: 7.1660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 0.7980 chunk 239 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 132 ASN ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 53 ASN ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 122 GLN o 98 HIS o 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 21688 Z= 0.279 Angle : 0.536 11.941 29467 Z= 0.273 Chirality : 0.040 0.189 3551 Planarity : 0.004 0.042 3641 Dihedral : 4.214 23.066 3008 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.26 % Allowed : 9.86 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.16), residues: 2794 helix: 0.93 (0.12), residues: 2076 sheet: -1.69 (0.74), residues: 45 loop : -1.89 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 693 HIS 0.006 0.001 HIS a 864 PHE 0.029 0.001 PHE c 80 TYR 0.014 0.001 TYR a 525 ARG 0.008 0.000 ARG a 508 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 249 time to evaluate : 2.338 Fit side-chains outliers start: 28 outliers final: 14 residues processed: 267 average time/residue: 0.3648 time to fit residues: 148.6584 Evaluate side-chains 253 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 239 time to evaluate : 2.508 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1933 time to fit residues: 8.2703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 223 optimal weight: 0.5980 chunk 148 optimal weight: 0.7980 chunk 265 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 132 ASN ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 53 ASN ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21688 Z= 0.205 Angle : 0.498 11.343 29467 Z= 0.255 Chirality : 0.039 0.242 3551 Planarity : 0.003 0.042 3641 Dihedral : 4.090 23.116 3008 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.99 % Allowed : 10.31 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2794 helix: 1.14 (0.12), residues: 2071 sheet: -1.61 (0.74), residues: 45 loop : -1.78 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 48 HIS 0.004 0.001 HIS a 864 PHE 0.025 0.001 PHE c 80 TYR 0.012 0.001 TYR a 525 ARG 0.006 0.000 ARG o 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 247 time to evaluate : 2.531 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 261 average time/residue: 0.3814 time to fit residues: 151.1521 Evaluate side-chains 252 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 238 time to evaluate : 2.098 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1908 time to fit residues: 8.0324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 208 optimal weight: 0.4980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 ASN c 132 ASN ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 90 GLN ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21688 Z= 0.190 Angle : 0.489 10.399 29467 Z= 0.250 Chirality : 0.038 0.224 3551 Planarity : 0.003 0.042 3641 Dihedral : 4.005 23.298 3008 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.45 % Allowed : 10.98 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.16), residues: 2794 helix: 1.31 (0.12), residues: 2067 sheet: -1.40 (0.76), residues: 45 loop : -1.71 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 48 HIS 0.004 0.001 HIS a 864 PHE 0.024 0.001 PHE c 80 TYR 0.012 0.001 TYR a 525 ARG 0.006 0.000 ARG o 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 243 time to evaluate : 2.519 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 249 average time/residue: 0.3861 time to fit residues: 147.3667 Evaluate side-chains 236 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1883 time to fit residues: 3.7283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 0.7980 chunk 253 optimal weight: 0.9990 chunk 231 optimal weight: 0.9980 chunk 246 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 107 optimal weight: 0.0370 chunk 193 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 132 ASN ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 21688 Z= 0.178 Angle : 0.485 10.746 29467 Z= 0.247 Chirality : 0.038 0.223 3551 Planarity : 0.003 0.041 3641 Dihedral : 3.931 23.284 3008 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.22 % Allowed : 11.70 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.16), residues: 2794 helix: 1.46 (0.12), residues: 2072 sheet: -1.16 (0.77), residues: 45 loop : -1.67 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 48 HIS 0.004 0.001 HIS a 864 PHE 0.024 0.001 PHE c 80 TYR 0.012 0.001 TYR a 525 ARG 0.007 0.000 ARG o 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 240 time to evaluate : 2.435 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 242 average time/residue: 0.3727 time to fit residues: 136.4380 Evaluate side-chains 236 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 2.187 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1851 time to fit residues: 3.7185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 3.9990 chunk 159 optimal weight: 0.0470 chunk 123 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 273 optimal weight: 0.3980 chunk 252 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 133 optimal weight: 0.0470 chunk 173 optimal weight: 3.9990 overall best weight: 1.0980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 132 ASN ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21688 Z= 0.209 Angle : 0.501 11.694 29467 Z= 0.254 Chirality : 0.039 0.226 3551 Planarity : 0.003 0.040 3641 Dihedral : 3.954 23.581 3008 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.13 % Allowed : 11.88 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.16), residues: 2794 helix: 1.48 (0.12), residues: 2072 sheet: -0.97 (0.79), residues: 45 loop : -1.67 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 48 HIS 0.004 0.001 HIS a 864 PHE 0.026 0.001 PHE c 80 TYR 0.011 0.001 TYR a 525 ARG 0.007 0.000 ARG o 161 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 237 time to evaluate : 2.375 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 238 average time/residue: 0.3792 time to fit residues: 136.6604 Evaluate side-chains 236 residues out of total 2289 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 235 time to evaluate : 2.305 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1941 time to fit residues: 3.4739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 201 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 218 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 132 ASN ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.112458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.084247 restraints weight = 22507.481| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 1.19 r_work: 0.2720 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 21688 Z= 0.223 Angle : 0.504 11.146 29467 Z= 0.257 Chirality : 0.039 0.221 3551 Planarity : 0.003 0.040 3641 Dihedral : 3.974 23.742 3008 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.22 % Allowed : 12.10 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.16), residues: 2794 helix: 1.45 (0.12), residues: 2090 sheet: -0.90 (0.79), residues: 45 loop : -1.71 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 48 HIS 0.004 0.001 HIS a 864 PHE 0.026 0.001 PHE c 80 TYR 0.012 0.001 TYR a 525 ARG 0.007 0.000 ARG o 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4388.62 seconds wall clock time: 84 minutes 15.46 seconds (5055.46 seconds total)