Starting phenix.real_space_refine on Tue Nov 19 12:38:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/11_2024/6o7t_0644.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/11_2024/6o7t_0644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/11_2024/6o7t_0644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/11_2024/6o7t_0644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/11_2024/6o7t_0644.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/11_2024/6o7t_0644.cif" } resolution = 3.2 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= 0.015 sd= 0.180 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 109 5.16 5 C 12893 2.51 5 N 3198 2.21 5 O 3530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19730 Number of models: 1 Model: "" Number of chains: 15 Chain: "a" Number of atoms: 5358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5358 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 21, 'TRANS': 712} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 621 Unresolved non-hydrogen angles: 779 Unresolved non-hydrogen dihedrals: 525 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 365 Chain: "b" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 279 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 37} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "c" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1414 Classifications: {'peptide': 195} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 192} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "d" Number of atoms: 2181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2181 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PTRANS': 8, 'TRANS': 305} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 6, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 237 Chain: "f" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 467 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "g" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1080 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 149} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "h" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1085 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "i" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1071 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "j" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1035 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "k" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1049 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "l" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1025 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "m" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1050 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "n" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1034 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "o" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1096 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 149} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "e" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 506 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 60} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.28, per 1000 atoms: 0.57 Number of scatterers: 19730 At special positions: 0 Unit cell: (119.78, 106, 135.68, 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 109 16.00 O 3530 8.00 N 3198 7.00 C 12893 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.28 Conformation dependent library (CDL) restraints added in 2.9 seconds 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5078 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 5 sheets defined 72.3% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'a' and resid 28 through 35 removed outlier: 3.940A pdb=" N THR a 32 " --> pdb=" O ASP a 28 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU a 33 " --> pdb=" O SER a 29 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 58 Processing helix chain 'a' and resid 59 through 79 removed outlier: 3.909A pdb=" N VAL a 65 " --> pdb=" O ARG a 61 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN a 68 " --> pdb=" O ASN a 64 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR a 71 " --> pdb=" O ARG a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 93 Processing helix chain 'a' and resid 105 through 145 removed outlier: 3.596A pdb=" N ARG a 112 " --> pdb=" O ASP a 108 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR a 116 " --> pdb=" O ARG a 112 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU a 132 " --> pdb=" O THR a 128 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN a 134 " --> pdb=" O GLN a 130 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN a 140 " --> pdb=" O ASN a 136 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE a 143 " --> pdb=" O GLU a 139 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE a 144 " --> pdb=" O GLN a 140 " (cutoff:3.500A) Processing helix chain 'a' and resid 195 through 207 removed outlier: 3.590A pdb=" N GLN a 201 " --> pdb=" O ALA a 197 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG a 205 " --> pdb=" O GLN a 201 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU a 207 " --> pdb=" O LEU a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 242 through 256 removed outlier: 3.504A pdb=" N LYS a 247 " --> pdb=" O ASP a 243 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU a 256 " --> pdb=" O ILE a 252 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 304 removed outlier: 3.778A pdb=" N ASP a 283 " --> pdb=" O LYS a 279 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR a 290 " --> pdb=" O THR a 286 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE a 302 " --> pdb=" O GLU a 298 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS a 304 " --> pdb=" O TYR a 300 " (cutoff:3.500A) Processing helix chain 'a' and resid 307 through 325 removed outlier: 3.733A pdb=" N GLN a 311 " --> pdb=" O ASP a 307 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP a 312 " --> pdb=" O SER a 308 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL a 313 " --> pdb=" O TRP a 309 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU a 316 " --> pdb=" O ASP a 312 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE a 319 " --> pdb=" O ARG a 315 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE a 320 " --> pdb=" O GLU a 316 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS a 325 " --> pdb=" O GLU a 321 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 359 removed outlier: 3.813A pdb=" N LEU a 349 " --> pdb=" O GLU a 345 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN a 350 " --> pdb=" O LEU a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 387 through 392 Processing helix chain 'a' and resid 410 through 424 Proline residue: a 416 - end of helix removed outlier: 3.659A pdb=" N MET a 422 " --> pdb=" O MET a 418 " (cutoff:3.500A) Processing helix chain 'a' and resid 425 through 442 removed outlier: 3.568A pdb=" N MET a 432 " --> pdb=" O HIS a 428 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER a 438 " --> pdb=" O LEU a 434 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU a 439 " --> pdb=" O ALA a 435 " (cutoff:3.500A) Processing helix chain 'a' and resid 452 through 461 removed outlier: 4.046A pdb=" N MET a 457 " --> pdb=" O GLU a 453 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA a 458 " --> pdb=" O ILE a 454 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY a 461 " --> pdb=" O MET a 457 " (cutoff:3.500A) Processing helix chain 'a' and resid 462 through 479 removed outlier: 3.943A pdb=" N MET a 468 " --> pdb=" O ILE a 464 " (cutoff:3.500A) Processing helix chain 'a' and resid 519 through 523 removed outlier: 3.709A pdb=" N TRP a 522 " --> pdb=" O ASP a 519 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS a 523 " --> pdb=" O TRP a 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 519 through 523' Processing helix chain 'a' and resid 527 through 560 removed outlier: 3.633A pdb=" N PHE a 531 " --> pdb=" O ASN a 527 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS a 547 " --> pdb=" O MET a 543 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE a 554 " --> pdb=" O TYR a 550 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER a 555 " --> pdb=" O SER a 551 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU a 556 " --> pdb=" O TYR a 552 " (cutoff:3.500A) Processing helix chain 'a' and resid 564 through 583 removed outlier: 3.664A pdb=" N ILE a 568 " --> pdb=" O SER a 564 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE a 569 " --> pdb=" O MET a 565 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ILE a 573 " --> pdb=" O ILE a 569 " (cutoff:3.500A) Proline residue: a 574 - end of helix Processing helix chain 'a' and resid 583 through 595 removed outlier: 3.672A pdb=" N CYS a 589 " --> pdb=" O TYR a 585 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL a 591 " --> pdb=" O SER a 587 " (cutoff:3.500A) Processing helix chain 'a' and resid 607 through 613 Processing helix chain 'a' and resid 630 through 655 removed outlier: 4.306A pdb=" N PHE a 636 " --> pdb=" O LYS a 632 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU a 638 " --> pdb=" O GLN a 634 " (cutoff:3.500A) Proline residue: a 646 - end of helix removed outlier: 3.902A pdb=" N LEU a 649 " --> pdb=" O ILE a 645 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS a 652 " --> pdb=" O LEU a 648 " (cutoff:3.500A) Proline residue: a 653 - end of helix Processing helix chain 'a' and resid 710 through 730 removed outlier: 3.638A pdb=" N HIS a 718 " --> pdb=" O HIS a 714 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE a 720 " --> pdb=" O VAL a 716 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU a 721 " --> pdb=" O ILE a 717 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU a 724 " --> pdb=" O ILE a 720 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN a 725 " --> pdb=" O GLU a 721 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL a 727 " --> pdb=" O CYS a 723 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER a 728 " --> pdb=" O LEU a 724 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR a 730 " --> pdb=" O CYS a 726 " (cutoff:3.500A) Processing helix chain 'a' and resid 731 through 733 No H-bonds generated for 'chain 'a' and resid 731 through 733' Processing helix chain 'a' and resid 734 through 753 removed outlier: 4.268A pdb=" N LEU a 746 " --> pdb=" O ALA a 742 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR a 752 " --> pdb=" O SER a 748 " (cutoff:3.500A) Processing helix chain 'a' and resid 755 through 759 removed outlier: 3.871A pdb=" N PHE a 759 " --> pdb=" O GLN a 756 " (cutoff:3.500A) Processing helix chain 'a' and resid 765 through 786 removed outlier: 4.304A pdb=" N VAL a 771 " --> pdb=" O VAL a 767 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE a 774 " --> pdb=" O THR a 770 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TRP a 777 " --> pdb=" O LEU a 773 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA a 779 " --> pdb=" O ALA a 775 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU a 780 " --> pdb=" O MET a 776 " (cutoff:3.500A) Processing helix chain 'a' and resid 787 through 803 removed outlier: 3.771A pdb=" N HIS a 801 " --> pdb=" O SER a 797 " (cutoff:3.500A) Processing helix chain 'b' and resid 220 through 250 removed outlier: 3.665A pdb=" N LEU b 233 " --> pdb=" O VAL b 229 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU b 234 " --> pdb=" O SER b 230 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA b 240 " --> pdb=" O ILE b 236 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU b 247 " --> pdb=" O TRP b 243 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP b 248 " --> pdb=" O ILE b 244 " (cutoff:3.500A) Processing helix chain 'c' and resid 24 through 39 removed outlier: 3.599A pdb=" N VAL c 29 " --> pdb=" O VAL c 25 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 45 removed outlier: 3.699A 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 89 removed outlier: 3.753A pdb=" N TRP c 59 " --> pdb=" O SER c 55 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU c 66 " --> pdb=" O LEU c 62 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE c 81 " --> pdb=" O TRP c 77 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER c 84 " --> pdb=" O PHE c 80 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY c 88 " --> pdb=" O SER c 84 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 97 removed outlier: 3.631A pdb=" N THR c 97 " --> pdb=" O PRO c 94 " (cutoff:3.500A) Processing helix chain 'c' and resid 104 through 123 removed outlier: 3.652A pdb=" N GLU c 108 " --> pdb=" O ILE c 104 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL c 110 " --> pdb=" O PHE c 106 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA c 111 " --> pdb=" O CYS c 107 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE c 117 " --> pdb=" O TYR c 113 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA c 118 " --> pdb=" O GLY c 114 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 168 removed outlier: 3.596A pdb=" N ASN c 156 " --> pdb=" O VAL c 152 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 206 removed outlier: 4.261A pdb=" N VAL c 186 " --> pdb=" O VAL c 182 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY c 191 " --> pdb=" O ILE c 187 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER c 192 " --> pdb=" O GLU c 188 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU c 204 " --> pdb=" O ILE c 200 " (cutoff:3.500A) Processing helix chain 'd' and resid 10 through 21 Processing helix chain 'd' and resid 27 through 32 removed outlier: 3.848A pdb=" N ILE d 31 " --> pdb=" O ASN d 27 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 27 through 32' Processing helix chain 'd' and resid 38 through 47 Processing helix chain 'd' and resid 64 through 85 removed outlier: 3.547A pdb=" N ILE d 68 " --> pdb=" O THR d 64 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU d 79 " --> pdb=" O LYS d 75 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP d 85 " --> pdb=" O ASN d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 115 removed outlier: 3.503A pdb=" N THR d 99 " --> pdb=" O MET d 95 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY d 101 " --> pdb=" O TYR d 97 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP d 105 " --> pdb=" O GLY d 101 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU d 109 " --> pdb=" O ASP d 105 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE d 111 " --> pdb=" O VAL d 107 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR d 112 " --> pdb=" O ALA d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 119 through 127 removed outlier: 3.937A pdb=" N ARG d 126 " --> pdb=" O GLU d 122 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS d 127 " --> pdb=" O ILE d 123 " (cutoff:3.500A) Processing helix chain 'd' and resid 144 through 152 removed outlier: 3.795A pdb=" N TYR d 149 " --> pdb=" O LEU d 145 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU d 150 " --> pdb=" O GLU d 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 177 through 194 removed outlier: 3.864A pdb=" N ALA d 187 " --> pdb=" O LYS d 183 " (cutoff:3.500A) Processing helix chain 'd' and resid 201 through 228 removed outlier: 4.005A pdb=" N GLU d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N CYS d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU d 212 " --> pdb=" O MET d 208 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN d 222 " --> pdb=" O ARG d 218 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA d 224 " --> pdb=" O SER d 220 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU d 228 " --> pdb=" O ALA d 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 258 removed outlier: 3.825A pdb=" N HIS d 255 " --> pdb=" O LEU d 251 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN d 258 " --> pdb=" O PHE d 254 " (cutoff:3.500A) Processing helix chain 'd' and resid 261 through 269 removed outlier: 3.514A pdb=" N VAL d 265 " --> pdb=" O ASP d 261 " (cutoff:3.500A) Processing helix chain 'd' and resid 288 through 298 removed outlier: 3.918A pdb=" N ASP d 298 " --> pdb=" O GLU d 294 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 332 removed outlier: 4.278A pdb=" N TRP d 310 " --> pdb=" O ILE d 306 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG d 321 " --> pdb=" O GLU d 317 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE d 323 " --> pdb=" O GLU d 319 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR d 324 " --> pdb=" O VAL d 320 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 33 removed outlier: 3.548A pdb=" N VAL f 22 " --> pdb=" O ALA f 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 47 through 70 removed outlier: 4.229A pdb=" N HIS f 53 " --> pdb=" O PRO f 49 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR f 54 " --> pdb=" O ALA f 50 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL f 55 " --> pdb=" O VAL f 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 8 through 43 removed outlier: 4.206A pdb=" N PHE g 12 " --> pdb=" O TYR g 8 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLY g 13 " --> pdb=" O ALA g 9 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE g 21 " --> pdb=" O CYS g 17 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR g 24 " --> pdb=" O ALA g 20 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA g 41 " --> pdb=" O VAL g 37 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 50 removed outlier: 3.664A pdb=" N LEU g 49 " --> pdb=" O ARG g 46 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU g 50 " --> pdb=" O PRO g 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 46 through 50' Processing helix chain 'g' and resid 54 through 76 removed outlier: 3.760A pdb=" N ILE g 63 " --> pdb=" O MET g 59 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 119 removed outlier: 4.127A pdb=" N SER g 100 " --> pdb=" O SER g 96 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA g 103 " --> pdb=" O LEU g 99 " (cutoff:3.500A) Processing helix chain 'g' and resid 124 through 152 removed outlier: 4.361A pdb=" N GLY g 128 " --> pdb=" O ARG g 124 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE g 130 " --> pdb=" O PHE g 126 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU g 131 " --> pdb=" O VAL g 127 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE g 135 " --> pdb=" O LEU g 131 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY g 140 " --> pdb=" O ALA g 136 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 42 removed outlier: 4.357A pdb=" N PHE h 12 " --> pdb=" O TYR h 8 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY h 13 " --> pdb=" O ALA h 9 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE h 21 " --> pdb=" O CYS h 17 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR h 24 " --> pdb=" O ALA h 20 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER h 35 " --> pdb=" O GLY h 31 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR h 42 " --> pdb=" O GLY h 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 54 through 74 removed outlier: 3.501A pdb=" N ALA h 64 " --> pdb=" O ALA h 60 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 119 removed outlier: 3.740A pdb=" N SER h 100 " --> pdb=" O SER h 96 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY h 112 " --> pdb=" O ILE h 108 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA h 114 " --> pdb=" O ILE h 110 " (cutoff:3.500A) Processing helix chain 'h' and resid 120 through 121 No H-bonds generated for 'chain 'h' and resid 120 through 121' Processing helix chain 'h' and resid 122 through 124 No H-bonds generated for 'chain 'h' and resid 122 through 124' Processing helix chain 'h' and resid 125 through 153 removed outlier: 4.007A pdb=" N LEU h 131 " --> pdb=" O VAL h 127 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU h 139 " --> pdb=" O PHE h 135 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY h 140 " --> pdb=" O ALA h 136 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU h 141 " --> pdb=" O GLU h 137 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU h 149 " --> pdb=" O ILE h 145 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG h 153 " --> pdb=" O LEU h 149 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 18 removed outlier: 4.431A pdb=" N PHE i 12 " --> pdb=" O TYR i 8 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY i 13 " --> pdb=" O ALA i 9 " (cutoff:3.500A) Processing helix chain 'i' and resid 18 through 44 removed outlier: 3.592A pdb=" N PHE i 23 " --> pdb=" O SER i 19 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR i 24 " --> pdb=" O ALA i 20 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS i 34 " --> pdb=" O TYR i 30 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY i 38 " --> pdb=" O LYS i 34 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL i 44 " --> pdb=" O CYS i 40 " (cutoff:3.500A) Processing helix chain 'i' and resid 54 through 74 removed outlier: 3.683A pdb=" N ILE i 63 " --> pdb=" O MET i 59 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU i 73 " --> pdb=" O VAL i 69 " (cutoff:3.500A) Processing helix chain 'i' and resid 84 through 118 removed outlier: 4.639A pdb=" N GLN i 90 " --> pdb=" O THR i 86 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER i 100 " --> pdb=" O SER i 96 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE i 108 " --> pdb=" O ALA i 104 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE i 110 " --> pdb=" O PHE i 106 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG i 117 " --> pdb=" O ASP i 113 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY i 118 " --> pdb=" O ALA i 114 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 151 removed outlier: 3.504A pdb=" N LEU i 131 " --> pdb=" O VAL i 127 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE i 132 " --> pdb=" O GLY i 128 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU i 139 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY i 140 " --> pdb=" O ALA i 136 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN i 151 " --> pdb=" O ALA i 147 " (cutoff:3.500A) Processing helix chain 'j' and resid 13 through 37 removed outlier: 3.769A pdb=" N ALA j 20 " --> pdb=" O GLY j 16 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE j 21 " --> pdb=" O CYS j 17 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR j 32 " --> pdb=" O ALA j 28 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS j 34 " --> pdb=" O TYR j 30 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER j 35 " --> pdb=" O GLY j 31 " (cutoff:3.500A) Processing helix chain 'j' and resid 54 through 75 removed outlier: 3.569A pdb=" N ALA j 64 " --> pdb=" O ALA j 60 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU j 73 " --> pdb=" O VAL j 69 " (cutoff:3.500A) Processing helix chain 'j' and resid 76 through 78 No H-bonds generated for 'chain 'j' and resid 76 through 78' Processing helix chain 'j' and resid 83 through 115 removed outlier: 3.602A pdb=" N SER j 100 " --> pdb=" O SER j 96 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA j 103 " --> pdb=" O LEU j 99 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA j 114 " --> pdb=" O ILE j 110 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY j 115 " --> pdb=" O VAL j 111 " (cutoff:3.500A) Processing helix chain 'j' and resid 125 through 156 removed outlier: 3.745A pdb=" N MET j 129 " --> pdb=" O LEU j 125 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE j 130 " --> pdb=" O PHE j 126 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU j 131 " --> pdb=" O VAL j 127 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE j 135 " --> pdb=" O LEU j 131 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA j 136 " --> pdb=" O ILE j 132 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY j 143 " --> pdb=" O LEU j 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU j 144 " --> pdb=" O GLY j 140 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL j 146 " --> pdb=" O TYR j 142 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU j 149 " --> pdb=" O ILE j 145 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR j 155 " --> pdb=" O ASN j 151 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN j 156 " --> pdb=" O SER j 152 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 34 removed outlier: 4.351A pdb=" N PHE k 12 " --> pdb=" O TYR k 8 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY k 13 " --> pdb=" O ALA k 9 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE k 21 " --> pdb=" O CYS k 17 " (cutoff:3.500A) Processing helix chain 'k' and resid 35 through 37 No H-bonds generated for 'chain 'k' and resid 35 through 37' Processing helix chain 'k' and resid 38 through 46 removed outlier: 3.825A pdb=" N LEU k 45 " --> pdb=" O ALA k 41 " (cutoff:3.500A) Processing helix chain 'k' and resid 47 through 52 removed outlier: 3.638A pdb=" N LEU k 50 " --> pdb=" O PRO k 47 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE k 51 " --> pdb=" O ASP k 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS k 52 " --> pdb=" O LEU k 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 47 through 52' Processing helix chain 'k' and resid 53 through 75 removed outlier: 3.746A pdb=" N VAL k 57 " --> pdb=" O ASN k 53 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL k 70 " --> pdb=" O TYR k 66 " (cutoff:3.500A) Processing helix chain 'k' and resid 76 through 78 No H-bonds generated for 'chain 'k' and resid 76 through 78' Processing helix chain 'k' and resid 84 through 118 removed outlier: 4.810A pdb=" N GLY k 94 " --> pdb=" O GLN k 90 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL k 97 " --> pdb=" O ALA k 93 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP k 113 " --> pdb=" O GLY k 109 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA k 114 " --> pdb=" O ILE k 110 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL k 116 " --> pdb=" O GLY k 112 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY k 118 " --> pdb=" O ALA k 114 " (cutoff:3.500A) Processing helix chain 'k' and resid 119 through 122 Processing helix chain 'k' and resid 127 through 155 removed outlier: 3.546A pdb=" N ILE k 132 " --> pdb=" O GLY k 128 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE k 135 " --> pdb=" O LEU k 131 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL k 138 " --> pdb=" O ILE k 134 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU k 139 " --> pdb=" O PHE k 135 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY k 140 " --> pdb=" O ALA k 136 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU k 141 " --> pdb=" O GLU k 137 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY k 143 " --> pdb=" O LEU k 139 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL k 146 " --> pdb=" O TYR k 142 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU k 149 " --> pdb=" O ILE k 145 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR k 155 " --> pdb=" O ASN k 151 " (cutoff:3.500A) Processing helix chain 'l' and resid 8 through 40 removed outlier: 4.227A pdb=" N PHE l 12 " --> pdb=" O TYR l 8 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY l 13 " --> pdb=" O ALA l 9 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE l 21 " --> pdb=" O CYS l 17 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY l 38 " --> pdb=" O LYS l 34 " (cutoff:3.500A) Processing helix chain 'l' and resid 46 through 50 removed outlier: 3.654A pdb=" N LEU l 49 " --> pdb=" O ARG l 46 " (cutoff:3.500A) removed outlier: 4.093A 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 75 removed outlier: 3.889A pdb=" N MET l 59 " --> pdb=" O VAL l 55 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE l 65 " --> pdb=" O GLY l 61 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL l 70 " --> pdb=" O TYR l 66 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU l 73 " --> pdb=" O VAL l 69 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS l 75 " --> pdb=" O SER l 71 " (cutoff:3.500A) Processing helix chain 'l' and resid 76 through 78 No H-bonds generated for 'chain 'l' and resid 76 through 78' Processing helix chain 'l' and resid 84 through 119 removed outlier: 4.439A pdb=" N GLN l 90 " --> pdb=" O THR l 86 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER l 100 " --> pdb=" O SER l 96 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA l 114 " --> pdb=" O ILE l 110 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 154 removed outlier: 4.033A pdb=" N GLY l 128 " --> pdb=" O ARG l 124 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU l 139 " --> pdb=" O PHE l 135 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLY l 140 " --> pdb=" O ALA l 136 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU l 150 " --> pdb=" O VAL l 146 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG l 153 " --> pdb=" O LEU l 149 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA l 154 " --> pdb=" O LEU l 150 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 42 removed outlier: 4.098A pdb=" N PHE m 12 " --> pdb=" O TYR m 8 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY m 13 " --> pdb=" O ALA m 9 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE m 21 " --> pdb=" O CYS m 17 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY m 38 " --> pdb=" O LYS m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 54 through 76 removed outlier: 3.654A pdb=" N ILE m 63 " --> pdb=" O MET m 59 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA m 64 " --> pdb=" O ALA m 60 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL m 70 " --> pdb=" O TYR m 66 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 122 removed outlier: 3.531A pdb=" N ILE m 108 " --> pdb=" O ALA m 104 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE m 110 " --> pdb=" O PHE m 106 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP m 113 " --> pdb=" O GLY m 109 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA m 114 " --> pdb=" O ILE m 110 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG m 117 " --> pdb=" O ASP m 113 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY m 118 " --> pdb=" O ALA m 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN m 121 " --> pdb=" O ARG m 117 " (cutoff:3.500A) Processing helix chain 'm' and resid 125 through 151 removed outlier: 3.609A pdb=" N LEU m 131 " --> pdb=" O VAL m 127 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE m 132 " --> pdb=" O GLY m 128 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU m 137 " --> pdb=" O LEU m 133 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU m 139 " --> pdb=" O PHE m 135 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY m 140 " --> pdb=" O ALA m 136 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY m 143 " --> pdb=" O LEU m 139 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU m 149 " --> pdb=" O ILE m 145 " (cutoff:3.500A) Processing helix chain 'm' and resid 152 through 154 No H-bonds generated for 'chain 'm' and resid 152 through 154' Processing helix chain 'n' and resid 9 through 40 removed outlier: 3.995A pdb=" N GLY n 13 " --> pdb=" O ALA n 9 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE n 21 " --> pdb=" O CYS n 17 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL n 37 " --> pdb=" O ALA n 33 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 78 removed outlier: 3.594A pdb=" N VAL n 70 " --> pdb=" O TYR n 66 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER n 77 " --> pdb=" O LEU n 73 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 116 removed outlier: 4.482A pdb=" N VAL n 97 " --> pdb=" O ALA n 93 " (cutoff:3.500A) Processing helix chain 'n' and resid 117 through 124 removed outlier: 3.686A pdb=" N SER n 120 " --> pdb=" O ARG n 117 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN n 121 " --> pdb=" O GLY n 118 " (cutoff:3.500A) Proline residue: n 123 - end of helix Processing helix chain 'n' and resid 125 through 133 removed outlier: 4.071A pdb=" N ILE n 130 " --> pdb=" O PHE n 126 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU n 131 " --> pdb=" O VAL n 127 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE n 132 " --> pdb=" O GLY n 128 " (cutoff:3.500A) Processing helix chain 'n' and resid 134 through 151 removed outlier: 3.709A pdb=" N LEU n 139 " --> pdb=" O PHE n 135 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY n 140 " --> pdb=" O ALA n 136 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 154 No H-bonds generated for 'chain 'n' and resid 152 through 154' Processing helix chain 'o' and resid 16 through 46 removed outlier: 3.536A pdb=" N LEU o 29 " --> pdb=" O ALA o 25 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER o 30 " --> pdb=" O ALA o 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 60 through 80 removed outlier: 3.922A pdb=" N ILE o 68 " --> pdb=" O VAL o 64 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU o 69 " --> pdb=" O MET o 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA o 70 " --> pdb=" O SER o 66 " (cutoff:3.500A) Processing helix chain 'o' and resid 91 through 124 removed outlier: 3.534A pdb=" N GLY o 95 " --> pdb=" O THR o 91 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N VAL o 122 " --> pdb=" O MET o 118 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL o 124 " --> pdb=" O GLY o 120 " (cutoff:3.500A) Processing helix chain 'o' and resid 133 through 162 removed outlier: 3.686A pdb=" N LEU o 139 " --> pdb=" O VAL o 135 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE o 143 " --> pdb=" O LEU o 139 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU o 147 " --> pdb=" O PHE o 143 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLY o 148 " --> pdb=" O SER o 144 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU o 149 " --> pdb=" O GLU o 145 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR o 160 " --> pdb=" O LEU o 156 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 24 removed outlier: 4.149A pdb=" N VAL e 10 " --> pdb=" O THR e 6 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE e 23 " --> pdb=" O VAL e 19 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 54 removed outlier: 4.332A pdb=" N SER e 35 " --> pdb=" O ALA e 31 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR e 36 " --> pdb=" O VAL e 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'a' and resid 40 through 41 Processing sheet with id=AA3, first strand: chain 'a' and resid 187 through 191 removed outlier: 3.687A pdb=" N PHE a 239 " --> pdb=" O PHE a 212 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE a 212 " --> pdb=" O PHE a 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 494 through 495 Processing sheet with id=AA5, first strand: chain 'a' and resid 506 through 507 1353 hydrogen bonds defined for protein. 4014 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: 6.27 Time building geometry restraints manager: 5.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4753 1.33 - 1.45: 4541 1.45 - 1.58: 10630 1.58 - 1.70: 0 1.70 - 1.82: 166 Bond restraints: 20090 Sorted by residual: bond pdb=" CB VAL n 97 " pdb=" CG2 VAL n 97 " ideal model delta sigma weight residual 1.521 1.384 0.137 3.30e-02 9.18e+02 1.72e+01 bond pdb=" CB THR k 24 " pdb=" CG2 THR k 24 " ideal model delta sigma weight residual 1.521 1.397 0.124 3.30e-02 9.18e+02 1.40e+01 bond pdb=" CG1 ILE n 21 " pdb=" CD1 ILE n 21 " ideal model delta sigma weight residual 1.513 1.387 0.126 3.90e-02 6.57e+02 1.05e+01 bond pdb=" CB VAL o 105 " pdb=" CG2 VAL o 105 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.87e+00 bond pdb=" CB THR i 24 " pdb=" CG2 THR i 24 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.80e+00 ... (remaining 20085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 26340 2.82 - 5.65: 910 5.65 - 8.47: 137 8.47 - 11.29: 32 11.29 - 14.11: 13 Bond angle restraints: 27432 Sorted by residual: angle pdb=" C GLN j 156 " pdb=" N ASP j 157 " pdb=" CA ASP j 157 " ideal model delta sigma weight residual 121.54 131.50 -9.96 1.91e+00 2.74e-01 2.72e+01 angle pdb=" CG1 VAL n 97 " pdb=" CB VAL n 97 " pdb=" CG2 VAL n 97 " ideal model delta sigma weight residual 110.80 99.47 11.33 2.20e+00 2.07e-01 2.65e+01 angle pdb=" N ILE k 22 " pdb=" CA ILE k 22 " pdb=" C ILE k 22 " ideal model delta sigma weight residual 110.53 115.29 -4.76 9.40e-01 1.13e+00 2.56e+01 angle pdb=" N VAL a 651 " pdb=" CA VAL a 651 " pdb=" C VAL a 651 " ideal model delta sigma weight residual 110.62 115.72 -5.10 1.02e+00 9.61e-01 2.50e+01 angle pdb=" N LEU k 95 " pdb=" CA LEU k 95 " pdb=" C LEU k 95 " ideal model delta sigma weight residual 111.36 106.07 5.29 1.09e+00 8.42e-01 2.35e+01 ... (remaining 27427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 10643 15.22 - 30.45: 630 30.45 - 45.67: 174 45.67 - 60.90: 24 60.90 - 76.12: 7 Dihedral angle restraints: 11478 sinusoidal: 3487 harmonic: 7991 Sorted by residual: dihedral pdb=" CA ILE a 482 " pdb=" C ILE a 482 " pdb=" N PHE a 483 " pdb=" CA PHE a 483 " ideal model delta harmonic sigma weight residual 180.00 -151.04 -28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA GLN m 90 " pdb=" C GLN m 90 " pdb=" N LEU m 91 " pdb=" CA LEU m 91 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA ASP a 481 " pdb=" C ASP a 481 " pdb=" N ILE a 482 " pdb=" CA ILE a 482 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 11475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 3224 0.137 - 0.275: 156 0.275 - 0.412: 4 0.412 - 0.549: 2 0.549 - 0.687: 4 Chirality restraints: 3390 Sorted by residual: chirality pdb=" CB ILE m 22 " pdb=" CA ILE m 22 " pdb=" CG1 ILE m 22 " pdb=" CG2 ILE m 22 " both_signs ideal model delta sigma weight residual False 2.64 1.96 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CB ILE k 22 " pdb=" CA ILE k 22 " pdb=" CG1 ILE k 22 " pdb=" CG2 ILE k 22 " both_signs ideal model delta sigma weight residual False 2.64 1.96 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CB VAL h 138 " pdb=" CA VAL h 138 " pdb=" CG1 VAL h 138 " pdb=" CG2 VAL h 138 " both_signs ideal model delta sigma weight residual False -2.63 -2.01 -0.61 2.00e-01 2.50e+01 9.45e+00 ... (remaining 3387 not shown) Planarity restraints: 3431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE m 89 " -0.028 2.00e-02 2.50e+03 5.52e-02 3.04e+01 pdb=" C ILE m 89 " 0.095 2.00e-02 2.50e+03 pdb=" O ILE m 89 " -0.035 2.00e-02 2.50e+03 pdb=" N GLN m 90 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL j 97 " -0.026 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C VAL j 97 " 0.088 2.00e-02 2.50e+03 pdb=" O VAL j 97 " -0.032 2.00e-02 2.50e+03 pdb=" N GLY j 98 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE h 15 " -0.025 2.00e-02 2.50e+03 5.08e-02 2.59e+01 pdb=" C ILE h 15 " 0.088 2.00e-02 2.50e+03 pdb=" O ILE h 15 " -0.033 2.00e-02 2.50e+03 pdb=" N GLY h 16 " -0.030 2.00e-02 2.50e+03 ... (remaining 3428 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4333 2.77 - 3.30: 18904 3.30 - 3.83: 33285 3.83 - 4.37: 39553 4.37 - 4.90: 66621 Nonbonded interactions: 162696 Sorted by model distance: nonbonded pdb=" O TRP a 777 " pdb=" OG1 THR a 781 " model vdw 2.236 3.040 nonbonded pdb=" O ALA a 407 " pdb=" OG1 THR a 411 " model vdw 2.238 3.040 nonbonded pdb=" OH TYR n 66 " pdb=" OE2 GLU n 137 " model vdw 2.241 3.040 nonbonded pdb=" O LEU c 51 " pdb=" OH TYR c 143 " model vdw 2.250 3.040 nonbonded pdb=" O GLY i 31 " pdb=" OG SER i 35 " model vdw 2.255 3.040 ... (remaining 162691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'g' and (resid 2 through 20 or (resid 21 through 22 and (name N or name C \ A or name C or name O or name CB )) or resid 23 through 33 or (resid 34 through \ 35 and (name N or name CA or name C or name O or name CB )) or resid 36 or (resi \ d 37 and (name N or name CA or name C or name O or name CB )) or resid 38 or (re \ sid 39 through 53 and (name N or name CA or name C or name O or name CB )) or re \ sid 54 through 55 or (resid 56 and (name N or name CA or name C or name O or nam \ e CB )) or resid 57 or (resid 58 and (name N or name CA or name C or name O or n \ ame CB )) or resid 59 through 62 or (resid 63 through 65 and (name N or name CA \ or name C or name O or name CB )) or resid 66 through 105 or (resid 106 through \ 107 and (name N or name CA or name C or name O or name CB )) or resid 108 throug \ h 109 or (resid 110 through 111 and (name N or name CA or name C or name O or na \ me CB )) or resid 112 or (resid 113 through 114 and (name N or name CA or name C \ or name O or name CB )) or resid 115 or (resid 116 through 117 and (name N or n \ ame CA or name C or name O or name CB )) or resid 118 or (resid 119 through 127 \ and (name N or name CA or name C or name O or name CB )) or resid 128 or (resid \ 129 through 132 and (name N or name CA or name C or name O or name CB )) or resi \ d 133 through 144 or (resid 145 and (name N or name CA or name C or name O or na \ me CB )) or resid 146 through 154 or (resid 155 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'h' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 20 or (resid 21 through 22 and (nam \ e N or name CA or name C or name O or name CB )) or resid 23 through 33 or (resi \ d 34 through 35 and (name N or name CA or name C or name O or name CB )) or resi \ d 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or re \ sid 38 or (resid 39 through 53 and (name N or name CA or name C or name O or nam \ e CB )) or resid 54 through 55 or (resid 56 and (name N or name CA or name C or \ name O or name CB )) or resid 57 or (resid 58 and (name N or name CA or name C o \ r name O or name CB )) or resid 59 through 62 or (resid 63 through 65 and (name \ N or name CA or name C or name O or name CB )) or resid 66 through 105 or (resid \ 106 through 107 and (name N or name CA or name C or name O or name CB )) or res \ id 108 through 109 or (resid 110 through 111 and (name N or name CA or name C or \ name O or name CB )) or resid 112 or (resid 113 through 114 and (name N or name \ CA or name C or name O or name CB )) or resid 115 or (resid 116 through 117 and \ (name N or name CA or name C or name O or name CB )) or (resid 118 through 127 \ and (name N or name CA or name C or name O or name CB )) or resid 128 or (resid \ 129 through 132 and (name N or name CA or name C or name O or name CB )) or resi \ d 133 through 144 or (resid 145 and (name N or name CA or name C or name O or na \ me CB )) or resid 146 through 154 or (resid 155 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'i' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 20 or (resid 21 through 22 and (nam \ e N or name CA or name C or name O or name CB )) or resid 23 through 33 or (resi \ d 34 through 35 and (name N or name CA or name C or name O or name CB )) or resi \ d 36 or (resid 37 and (name N or name CA or name C or name O or name CB )) or (r \ esid 38 through 53 and (name N or name CA or name C or name O or name CB )) or r \ esid 54 through 55 or (resid 56 and (name N or name CA or name C or name O or na \ me CB )) or resid 57 or (resid 58 and (name N or name CA or name C or name O or \ name CB )) or resid 59 through 62 or (resid 63 through 65 and (name N or name CA \ or name C or name O or name CB )) or resid 66 through 105 or (resid 106 through \ 107 and (name N or name CA or name C or name O or name CB )) or resid 108 throu \ gh 109 or (resid 110 through 111 and (name N or name CA or name C or name O or n \ ame CB )) or resid 112 or (resid 113 through 114 and (name N or name CA or name \ C or name O or name CB )) or resid 115 or (resid 116 through 117 and (name N or \ name CA or name C or name O or name CB )) or (resid 118 through 127 and (name N \ or name CA or name C or name O or name CB )) or resid 128 or (resid 129 through \ 132 and (name N or name CA or name C or name O or name CB )) or resid 133 throug \ h 144 or (resid 145 and (name N or name CA or name C or name O or name CB )) or \ resid 146 through 155)) selection = (chain 'j' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 21 or (resid 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 through 33 or (resid 34 throug \ h 35 and (name N or name CA or name C or name O or name CB )) or resid 36 or (re \ sid 37 and (name N or name CA or name C or name O or name CB )) or resid 38 thro \ ugh 105 or (resid 106 through 107 and (name N or name CA or name C or name O or \ name CB )) or resid 108 through 109 or (resid 110 through 111 and (name N or nam \ e CA or name C or name O or name CB )) or resid 112 or (resid 113 through 114 an \ d (name N or name CA or name C or name O or name CB )) or (resid 115 through 127 \ and (name N or name CA or name C or name O or name CB )) or resid 128 or (resid \ 129 through 132 and (name N or name CA or name C or name O or name CB )) or res \ id 133 through 144 or (resid 145 and (name N or name CA or name C or name O or n \ ame CB )) or resid 146 through 154 or (resid 155 and (name N or name CA or name \ C or name O or name CB )))) selection = (chain 'k' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 21 or (resid 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 through 34 or (resid 35 and (n \ ame N or name CA or name C or name O or name CB )) or (resid 36 through 53 and ( \ name N or name CA or name C or name O or name CB )) or resid 54 through 55 or (r \ esid 56 and (name N or name CA or name C or name O or name CB )) or resid 57 or \ (resid 58 and (name N or name CA or name C or name O or name CB )) or resid 59 t \ hrough 62 or (resid 63 through 65 and (name N or name CA or name C or name O or \ name CB )) or resid 66 through 105 or (resid 106 through 107 and (name N or name \ CA or name C or name O or name CB )) or resid 108 through 109 or (resid 110 thr \ ough 111 and (name N or name CA or name C or name O or name CB )) or resid 112 o \ r (resid 113 through 114 and (name N or name CA or name C or name O or name CB ) \ ) or (resid 115 through 127 and (name N or name CA or name C or name O or name C \ B )) or resid 128 or (resid 129 through 132 and (name N or name CA or name C or \ name O or name CB )) or resid 133 through 144 or (resid 145 and (name N or name \ CA or name C or name O or name CB )) or resid 146 through 154 or (resid 155 and \ (name N or name CA or name C or name O or name CB )))) selection = (chain 'l' and (resid 2 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB )) or resid 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or (resid 38 through 53 and (name N or name CA or nam \ e C or name O or name CB )) or resid 54 through 55 or (resid 56 and (name N or n \ ame CA or name C or name O or name CB )) or resid 57 through 62 or (resid 63 thr \ ough 65 and (name N or name CA or name C or name O or name CB )) or resid 66 thr \ ough 115 or (resid 116 through 117 and (name N or name CA or name C or name O or \ name CB )) or (resid 118 through 127 and (name N or name CA or name C or name O \ or name CB )) or (resid 128 through 132 and (name N or name CA or name C or nam \ e O or name CB )) or resid 133 through 144 or (resid 145 and (name N or name CA \ or name C or name O or name CB )) or resid 146 through 154 or (resid 155 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'm' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 21 or (resid 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 through 34 or (resid 35 and (n \ ame N or name CA or name C or name O or name CB )) or resid 36 or (resid 37 and \ (name N or name CA or name C or name O or name CB )) or (resid 38 through 53 and \ (name N or name CA or name C or name O or name CB )) or resid 54 through 55 or \ (resid 56 and (name N or name CA or name C or name O or name CB )) or resid 57 o \ r (resid 58 and (name N or name CA or name C or name O or name CB )) or resid 59 \ through 62 or (resid 63 through 65 and (name N or name CA or name C or name O o \ r name CB )) or resid 66 through 105 or (resid 106 through 107 and (name N or na \ me CA or name C or name O or name CB )) or resid 108 through 109 or (resid 110 t \ hrough 111 and (name N or name CA or name C or name O or name CB )) or resid 112 \ or (resid 113 through 114 and (name N or name CA or name C or name O or name CB \ )) or (resid 115 through 127 and (name N or name CA or name C or name O or name \ CB )) or resid 128 or (resid 129 through 132 and (name N or name CA or name C o \ r name O or name CB )) or resid 133 through 144 or (resid 145 and (name N or nam \ e CA or name C or name O or name CB )) or resid 146 through 154 or (resid 155 an \ d (name N or name CA or name C or name O or name CB )))) selection = (chain 'n' and (resid 2 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 20 or (resid 21 through 22 and (nam \ e N or name CA or name C or name O or name CB )) or resid 23 through 34 or (resi \ d 35 and (name N or name CA or name C or name O or name CB )) or resid 36 throug \ h 55 or (resid 56 and (name N or name CA or name C or name O or name CB )) or re \ sid 57 or (resid 58 and (name N or name CA or name C or name O or name CB )) or \ resid 59 through 62 or (resid 63 through 65 and (name N or name CA or name C or \ name O or name CB )) or resid 66 through 105 or (resid 106 through 107 and (name \ N or name CA or name C or name O or name CB )) or resid 108 through 109 or (res \ id 110 through 111 and (name N or name CA or name C or name O or name CB )) or ( \ resid 112 through 132 and (name N or name CA or name C or name O or name CB )) o \ r resid 133 through 154 or (resid 155 and (name N or name CA or name C or name O \ or name CB )))) } 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: 1.340 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: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 43.750 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 0.009 0.137 20090 Z= 0.604 Angle : 1.251 14.115 27432 Z= 0.670 Chirality : 0.069 0.687 3390 Planarity : 0.011 0.085 3431 Dihedral : 11.380 76.120 6400 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.92 % Favored : 95.98 % Rotamer: Outliers : 0.73 % Allowed : 7.52 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.13), residues: 2784 helix: -2.45 (0.10), residues: 1954 sheet: -2.27 (0.73), residues: 34 loop : -3.15 (0.17), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.005 TRP c 77 HIS 0.024 0.003 HIS a 559 PHE 0.058 0.004 PHE d 192 TYR 0.054 0.004 TYR m 142 ARG 0.008 0.001 ARG l 153 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 614 time to evaluate : 2.128 Fit side-chains REVERT: d 27 ASN cc_start: 0.8373 (t160) cc_final: 0.8134 (t0) REVERT: d 75 LYS cc_start: 0.8760 (tmtt) cc_final: 0.8512 (tttm) REVERT: d 178 GLU cc_start: 0.8296 (mp0) cc_final: 0.7997 (mp0) REVERT: d 191 ASP cc_start: 0.8944 (t70) cc_final: 0.8558 (t0) REVERT: g 37 VAL cc_start: 0.9169 (p) cc_final: 0.8954 (t) REVERT: j 15 ILE cc_start: 0.7996 (mm) cc_final: 0.7762 (mm) REVERT: k 129 MET cc_start: 0.7095 (ttt) cc_final: 0.6728 (ttp) REVERT: l 25 SER cc_start: 0.8589 (p) cc_final: 0.8377 (p) REVERT: m 58 ILE cc_start: 0.9001 (tt) cc_final: 0.8759 (tt) REVERT: m 151 ASN cc_start: 0.8525 (t160) cc_final: 0.8101 (t0) REVERT: o 139 LEU cc_start: 0.9179 (tt) cc_final: 0.8533 (tt) REVERT: o 143 PHE cc_start: 0.8195 (m-80) cc_final: 0.7772 (m-80) REVERT: e 43 MET cc_start: 0.8543 (mmm) cc_final: 0.8317 (mmt) outliers start: 13 outliers final: 4 residues processed: 623 average time/residue: 0.2857 time to fit residues: 281.6552 Evaluate side-chains 407 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 403 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 648 LEU Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain k residue 26 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 0.5980 chunk 206 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 159 optimal weight: 7.9990 chunk 247 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 18 GLN a 68 GLN a 79 HIS a 311 GLN a 480 ASN a 547 HIS a 571 ASN a 725 ASN ** c 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 132 ASN c 138 ASN d 10 ASN d 27 ASN d 222 ASN f 35 HIS h 90 GLN k 53 ASN ** k 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 151 ASN l 80 GLN ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 151 ASN ** n 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 83 ASN o 159 ASN e 55 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20090 Z= 0.222 Angle : 0.666 8.086 27432 Z= 0.351 Chirality : 0.041 0.214 3390 Planarity : 0.005 0.058 3431 Dihedral : 5.377 58.367 2962 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.70 % Allowed : 15.32 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.14), residues: 2784 helix: -1.17 (0.11), residues: 1999 sheet: -2.03 (0.90), residues: 26 loop : -2.67 (0.19), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP a 647 HIS 0.012 0.002 HIS a 79 PHE 0.029 0.002 PHE c 80 TYR 0.027 0.002 TYR a 285 ARG 0.005 0.001 ARG d 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 459 time to evaluate : 2.108 Fit side-chains REVERT: a 432 MET cc_start: 0.8626 (ttm) cc_final: 0.8403 (ttt) REVERT: a 649 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8311 (pp) REVERT: c 46 ASN cc_start: 0.7528 (p0) cc_final: 0.7179 (p0) REVERT: d 27 ASN cc_start: 0.8303 (t0) cc_final: 0.8102 (t0) REVERT: d 59 SER cc_start: 0.8700 (OUTLIER) cc_final: 0.8400 (m) REVERT: d 178 GLU cc_start: 0.8251 (mp0) cc_final: 0.8027 (mp0) REVERT: d 191 ASP cc_start: 0.8943 (t70) cc_final: 0.8626 (t0) REVERT: h 129 MET cc_start: 0.7779 (tpp) cc_final: 0.7462 (tpt) REVERT: i 108 ILE cc_start: 0.8432 (pp) cc_final: 0.8055 (mt) REVERT: i 144 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8415 (tp) REVERT: j 12 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7313 (p90) REVERT: j 15 ILE cc_start: 0.7979 (mm) cc_final: 0.7714 (mm) REVERT: k 129 MET cc_start: 0.7113 (ttt) cc_final: 0.6738 (ttp) REVERT: k 130 ILE cc_start: 0.8258 (pp) cc_final: 0.7986 (mt) REVERT: m 151 ASN cc_start: 0.8619 (t0) cc_final: 0.8159 (t0) REVERT: o 9 ILE cc_start: 0.8565 (tp) cc_final: 0.8231 (pt) REVERT: o 139 LEU cc_start: 0.9197 (tt) cc_final: 0.8932 (tt) REVERT: o 143 PHE cc_start: 0.8143 (m-80) cc_final: 0.7714 (m-80) outliers start: 66 outliers final: 32 residues processed: 496 average time/residue: 0.2804 time to fit residues: 221.9982 Evaluate side-chains 434 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 398 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 394 CYS Chi-restraints excluded: chain a residue 472 SER Chi-restraints excluded: chain a residue 480 ASN Chi-restraints excluded: chain a residue 648 LEU Chi-restraints excluded: chain a residue 649 LEU Chi-restraints excluded: chain a residue 748 SER Chi-restraints excluded: chain b residue 220 THR Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 59 SER Chi-restraints excluded: chain d residue 208 MET Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 215 GLU Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain f residue 17 SER Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain h residue 135 PHE Chi-restraints excluded: chain i residue 5 CYS Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 131 LEU Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 12 PHE Chi-restraints excluded: chain k residue 72 VAL Chi-restraints excluded: chain l residue 5 CYS Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain n residue 62 ILE Chi-restraints excluded: chain n residue 108 ILE Chi-restraints excluded: chain o residue 30 SER Chi-restraints excluded: chain o residue 55 LEU Chi-restraints excluded: chain o residue 135 VAL Chi-restraints excluded: chain o residue 149 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 221 optimal weight: 0.7980 chunk 246 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 480 ASN a 571 ASN a 718 HIS ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN ** k 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 82 GLN m 90 GLN n 82 GLN n 90 GLN o 98 HIS o 130 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20090 Z= 0.230 Angle : 0.631 9.883 27432 Z= 0.326 Chirality : 0.041 0.185 3390 Planarity : 0.004 0.061 3431 Dihedral : 4.862 53.214 2958 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.88 % Allowed : 16.67 % Favored : 78.45 % 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: -1.53 (0.15), residues: 2784 helix: -0.39 (0.11), residues: 2006 sheet: -1.52 (0.96), residues: 26 loop : -2.45 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 243 HIS 0.010 0.001 HIS a 718 PHE 0.028 0.002 PHE c 80 TYR 0.019 0.001 TYR o 127 ARG 0.004 0.001 ARG d 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 428 time to evaluate : 2.162 Fit side-chains revert: symmetry clash REVERT: a 432 MET cc_start: 0.8526 (ttm) cc_final: 0.8300 (ttt) REVERT: b 236 ILE cc_start: 0.8533 (pt) cc_final: 0.8245 (mt) REVERT: c 46 ASN cc_start: 0.7455 (p0) cc_final: 0.7104 (p0) REVERT: d 59 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8252 (m) REVERT: d 69 GLN cc_start: 0.8474 (tm-30) cc_final: 0.8261 (tm-30) REVERT: d 178 GLU cc_start: 0.8256 (mp0) cc_final: 0.7914 (mp0) REVERT: g 149 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8474 (mp) REVERT: h 15 ILE cc_start: 0.8678 (pt) cc_final: 0.8038 (mm) REVERT: h 129 MET cc_start: 0.7749 (tpp) cc_final: 0.7459 (tpp) REVERT: i 144 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8358 (tp) REVERT: j 12 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7181 (p90) REVERT: j 15 ILE cc_start: 0.8005 (mm) cc_final: 0.7696 (mm) REVERT: k 129 MET cc_start: 0.7285 (ttt) cc_final: 0.6943 (ttp) REVERT: m 151 ASN cc_start: 0.8629 (t0) cc_final: 0.8206 (t0) REVERT: n 65 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8816 (mp) REVERT: n 129 MET cc_start: 0.7463 (tpt) cc_final: 0.7112 (tpt) REVERT: o 9 ILE cc_start: 0.8634 (tp) cc_final: 0.8428 (tt) REVERT: o 139 LEU cc_start: 0.9171 (tt) cc_final: 0.8938 (tt) REVERT: o 143 PHE cc_start: 0.8212 (m-80) cc_final: 0.7729 (m-80) outliers start: 87 outliers final: 50 residues processed: 478 average time/residue: 0.2790 time to fit residues: 215.4816 Evaluate side-chains 450 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 395 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 62 LEU Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 394 CYS Chi-restraints excluded: chain a residue 472 SER Chi-restraints excluded: chain a residue 480 ASN Chi-restraints excluded: chain a residue 507 THR Chi-restraints excluded: chain a residue 519 ASP Chi-restraints excluded: chain a residue 648 LEU Chi-restraints excluded: chain a residue 730 THR Chi-restraints excluded: chain a residue 732 SER Chi-restraints excluded: chain a residue 748 SER Chi-restraints excluded: chain a residue 781 THR Chi-restraints excluded: chain a residue 797 SER Chi-restraints excluded: chain b residue 220 THR Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 59 SER Chi-restraints excluded: chain d residue 70 GLU Chi-restraints excluded: chain f residue 12 CYS Chi-restraints excluded: chain f residue 17 SER Chi-restraints excluded: chain f residue 67 VAL Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain g residue 149 LEU Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 68 LEU Chi-restraints excluded: chain h residue 135 PHE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 131 LEU Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 12 PHE Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 76 TYR Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 133 LEU Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 76 TYR Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain n residue 62 ILE Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain o residue 135 VAL Chi-restraints excluded: chain o residue 149 LEU Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain e residue 30 GLN Chi-restraints excluded: chain e residue 35 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 0.6980 chunk 186 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 118 optimal weight: 50.0000 chunk 166 optimal weight: 20.0000 chunk 249 optimal weight: 0.7980 chunk 263 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 480 ASN a 718 HIS ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN ** k 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20090 Z= 0.197 Angle : 0.593 10.640 27432 Z= 0.304 Chirality : 0.040 0.178 3390 Planarity : 0.004 0.064 3431 Dihedral : 4.603 47.697 2958 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.38 % Allowed : 16.89 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 2784 helix: 0.12 (0.11), residues: 1995 sheet: -1.07 (1.03), residues: 26 loop : -2.26 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 243 HIS 0.009 0.001 HIS a 718 PHE 0.025 0.001 PHE c 80 TYR 0.020 0.001 TYR o 127 ARG 0.004 0.000 ARG e 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 416 time to evaluate : 2.185 Fit side-chains REVERT: a 395 ASP cc_start: 0.7967 (p0) cc_final: 0.7707 (p0) REVERT: b 236 ILE cc_start: 0.8433 (pt) cc_final: 0.8169 (mt) REVERT: c 21 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8401 (tp) REVERT: c 46 ASN cc_start: 0.7369 (p0) cc_final: 0.7082 (p0) REVERT: d 59 SER cc_start: 0.8441 (t) cc_final: 0.8161 (m) REVERT: d 69 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8290 (tm-30) REVERT: d 178 GLU cc_start: 0.8324 (mp0) cc_final: 0.7967 (mp0) REVERT: d 302 GLN cc_start: 0.8172 (mp10) cc_final: 0.7928 (mp10) REVERT: h 15 ILE cc_start: 0.8615 (pt) cc_final: 0.8128 (mm) REVERT: h 22 ILE cc_start: 0.8958 (mt) cc_final: 0.8720 (mp) REVERT: h 129 MET cc_start: 0.7710 (tpp) cc_final: 0.7476 (tpp) REVERT: i 129 MET cc_start: 0.7945 (ttp) cc_final: 0.7633 (ttt) REVERT: i 144 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8358 (tp) REVERT: j 12 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7410 (p90) REVERT: j 15 ILE cc_start: 0.8036 (mm) cc_final: 0.7736 (mm) REVERT: k 129 MET cc_start: 0.7337 (ttt) cc_final: 0.7059 (ttp) REVERT: m 151 ASN cc_start: 0.8630 (t0) cc_final: 0.8243 (t0) REVERT: n 65 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8699 (mp) REVERT: n 129 MET cc_start: 0.7422 (tpt) cc_final: 0.7080 (tpt) REVERT: o 9 ILE cc_start: 0.8641 (tp) cc_final: 0.8420 (tt) REVERT: o 143 PHE cc_start: 0.8204 (m-80) cc_final: 0.7719 (m-80) REVERT: e 30 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7073 (mm-40) outliers start: 78 outliers final: 51 residues processed: 461 average time/residue: 0.2844 time to fit residues: 211.1708 Evaluate side-chains 443 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 387 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 62 LEU Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain a residue 348 THR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 370 VAL Chi-restraints excluded: chain a residue 394 CYS Chi-restraints excluded: chain a residue 472 SER Chi-restraints excluded: chain a residue 480 ASN Chi-restraints excluded: chain a residue 507 THR Chi-restraints excluded: chain a residue 519 ASP Chi-restraints excluded: chain a residue 648 LEU Chi-restraints excluded: chain a residue 730 THR Chi-restraints excluded: chain a residue 748 SER Chi-restraints excluded: chain a residue 781 THR Chi-restraints excluded: chain a residue 815 LEU Chi-restraints excluded: chain b residue 220 THR Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain c residue 159 CYS Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 70 GLU Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 68 LEU Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 135 PHE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 131 LEU Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 12 PHE Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 76 TYR Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 76 TYR Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain n residue 62 ILE Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain o residue 135 VAL Chi-restraints excluded: chain o residue 149 LEU Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain e residue 30 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 182 optimal weight: 0.0670 chunk 0 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 134 GLN a 381 HIS a 480 ASN a 718 HIS c 61 ASN d 7 ASN ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 90 GLN ** k 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 80 GLN o 130 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 20090 Z= 0.365 Angle : 0.666 9.712 27432 Z= 0.341 Chirality : 0.043 0.222 3390 Planarity : 0.004 0.065 3431 Dihedral : 4.653 40.676 2958 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.33 % Allowed : 18.13 % Favored : 76.54 % 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: -0.78 (0.15), residues: 2784 helix: 0.18 (0.11), residues: 1999 sheet: -0.59 (1.09), residues: 24 loop : -2.26 (0.20), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 243 HIS 0.009 0.001 HIS a 718 PHE 0.028 0.002 PHE c 80 TYR 0.021 0.002 TYR o 127 ARG 0.005 0.001 ARG d 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 395 time to evaluate : 2.237 Fit side-chains REVERT: a 395 ASP cc_start: 0.8043 (p0) cc_final: 0.7744 (p0) REVERT: a 519 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7898 (t70) REVERT: b 236 ILE cc_start: 0.8578 (pt) cc_final: 0.8325 (mt) REVERT: c 46 ASN cc_start: 0.7537 (p0) cc_final: 0.7191 (p0) REVERT: d 59 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8233 (p) REVERT: d 178 GLU cc_start: 0.8303 (mp0) cc_final: 0.7982 (mp0) REVERT: d 302 GLN cc_start: 0.8240 (mp10) cc_final: 0.8013 (mp10) REVERT: h 22 ILE cc_start: 0.8999 (mt) cc_final: 0.8752 (mp) REVERT: h 73 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8612 (mp) REVERT: h 108 ILE cc_start: 0.8766 (pt) cc_final: 0.8518 (pt) REVERT: h 129 MET cc_start: 0.7792 (tpp) cc_final: 0.7460 (tpp) REVERT: i 141 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7389 (tt) REVERT: i 144 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8359 (tp) REVERT: j 12 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7074 (p90) REVERT: k 129 MET cc_start: 0.7383 (ttt) cc_final: 0.7093 (ttp) REVERT: k 134 ILE cc_start: 0.8851 (tp) cc_final: 0.8604 (tp) REVERT: m 151 ASN cc_start: 0.8693 (t0) cc_final: 0.8362 (t0) REVERT: n 25 SER cc_start: 0.8066 (m) cc_final: 0.7752 (p) REVERT: n 65 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8841 (mp) REVERT: n 129 MET cc_start: 0.7543 (tpt) cc_final: 0.7157 (tpt) REVERT: o 9 ILE cc_start: 0.8650 (tp) cc_final: 0.8414 (tt) REVERT: o 58 LYS cc_start: 0.8464 (ttmt) cc_final: 0.8055 (ttpt) REVERT: o 128 MET cc_start: 0.8557 (mmm) cc_final: 0.8304 (mmt) REVERT: o 143 PHE cc_start: 0.8176 (m-80) cc_final: 0.7736 (m-80) REVERT: e 30 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7089 (mm-40) outliers start: 95 outliers final: 66 residues processed: 448 average time/residue: 0.3004 time to fit residues: 215.8514 Evaluate side-chains 458 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 384 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 18 GLN Chi-restraints excluded: chain a residue 47 LYS Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain a residue 62 LEU Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain a residue 348 THR Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 370 VAL Chi-restraints excluded: chain a residue 394 CYS Chi-restraints excluded: chain a residue 434 LEU Chi-restraints excluded: chain a residue 448 LYS Chi-restraints excluded: chain a residue 472 SER Chi-restraints excluded: chain a residue 480 ASN Chi-restraints excluded: chain a residue 507 THR Chi-restraints excluded: chain a residue 519 ASP Chi-restraints excluded: chain a residue 624 ASP Chi-restraints excluded: chain a residue 648 LEU Chi-restraints excluded: chain a residue 651 VAL Chi-restraints excluded: chain a residue 730 THR Chi-restraints excluded: chain a residue 732 SER Chi-restraints excluded: chain a residue 748 SER Chi-restraints excluded: chain a residue 757 ILE Chi-restraints excluded: chain a residue 781 THR Chi-restraints excluded: chain a residue 815 LEU Chi-restraints excluded: chain b residue 220 THR Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain c residue 159 CYS Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 59 SER Chi-restraints excluded: chain d residue 70 GLU Chi-restraints excluded: chain d residue 342 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain g residue 149 LEU Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 73 LEU Chi-restraints excluded: chain h residue 135 PHE Chi-restraints excluded: chain h residue 152 SER Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 131 LEU Chi-restraints excluded: chain i residue 141 LEU Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 12 PHE Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain l residue 5 CYS Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain m residue 76 TYR Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain o residue 135 VAL Chi-restraints excluded: chain o residue 149 LEU Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain e residue 30 GLN Chi-restraints excluded: chain e residue 35 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 0.6980 chunk 237 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 154 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 219 optimal weight: 10.0000 chunk 122 optimal weight: 0.0270 chunk 21 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 480 ASN a 718 HIS c 61 ASN ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN k 82 GLN n 151 ASN o 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20090 Z= 0.181 Angle : 0.573 8.976 27432 Z= 0.295 Chirality : 0.039 0.197 3390 Planarity : 0.004 0.065 3431 Dihedral : 4.424 34.720 2958 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.38 % Allowed : 19.14 % Favored : 76.49 % 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: -0.29 (0.16), residues: 2784 helix: 0.54 (0.12), residues: 1999 sheet: -0.27 (1.09), residues: 24 loop : -2.06 (0.20), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 312 HIS 0.009 0.001 HIS a 718 PHE 0.021 0.001 PHE c 80 TYR 0.015 0.001 TYR o 127 ARG 0.009 0.000 ARG j 153 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5568 Ramachandran restraints generated. 2784 Oldfield, 0 Emsley, 2784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 406 time to evaluate : 2.331 Fit side-chains REVERT: a 395 ASP cc_start: 0.7845 (p0) cc_final: 0.7585 (p0) REVERT: c 46 ASN cc_start: 0.7317 (p0) cc_final: 0.7032 (p0) REVERT: d 59 SER cc_start: 0.8505 (t) cc_final: 0.8103 (p) REVERT: d 69 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8301 (tm-30) REVERT: d 178 GLU cc_start: 0.8308 (mp0) cc_final: 0.8012 (mp0) REVERT: d 319 GLU cc_start: 0.7708 (pp20) cc_final: 0.7342 (pp20) REVERT: h 15 ILE cc_start: 0.8578 (pt) cc_final: 0.8185 (mm) REVERT: h 22 ILE cc_start: 0.8926 (mt) cc_final: 0.8663 (mp) REVERT: h 59 MET cc_start: 0.8695 (mtp) cc_final: 0.8282 (mmm) REVERT: h 108 ILE cc_start: 0.8592 (pt) cc_final: 0.8335 (pt) REVERT: h 129 MET cc_start: 0.7793 (tpp) cc_final: 0.7392 (tpp) REVERT: j 12 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7382 (p90) REVERT: k 129 MET cc_start: 0.7365 (ttt) cc_final: 0.7083 (ttp) REVERT: k 134 ILE cc_start: 0.8845 (tp) cc_final: 0.8620 (tp) REVERT: l 100 SER cc_start: 0.8021 (t) cc_final: 0.7790 (t) REVERT: m 151 ASN cc_start: 0.8655 (t0) cc_final: 0.8305 (t0) REVERT: n 65 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8778 (mp) REVERT: n 129 MET cc_start: 0.7418 (tpt) cc_final: 0.7039 (tpt) REVERT: o 9 ILE cc_start: 0.8611 (tp) cc_final: 0.8410 (tt) REVERT: o 58 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8076 (ttpt) REVERT: o 97 MET cc_start: 0.8001 (mmm) cc_final: 0.7283 (mmm) REVERT: o 143 PHE cc_start: 0.8062 (m-80) cc_final: 0.7701 (m-80) REVERT: e 30 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7004 (mm-40) outliers start: 78 outliers final: 53 residues processed: 450 average time/residue: 0.2922 time to fit residues: 212.1807 Evaluate side-chains 440 residues out of total 2270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 384 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 18 GLN Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain a residue 348 THR Chi-restraints excluded: chain a residue 370 VAL Chi-restraints excluded: chain a residue 394 CYS Chi-restraints excluded: chain a residue 448 LYS Chi-restraints excluded: chain a residue 472 SER Chi-restraints excluded: chain a residue 480 ASN Chi-restraints excluded: chain a residue 507 THR Chi-restraints excluded: chain a residue 519 ASP Chi-restraints excluded: chain a residue 556 LEU Chi-restraints excluded: chain a residue 624 ASP Chi-restraints excluded: chain a residue 651 VAL Chi-restraints excluded: chain a residue 730 THR Chi-restraints excluded: chain a residue 748 SER Chi-restraints excluded: chain a residue 815 LEU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain c residue 159 CYS Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 342 ILE Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain g residue 149 LEU Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 69 VAL Chi-restraints excluded: chain h residue 135 PHE Chi-restraints excluded: chain h residue 152 SER Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 108 ILE Chi-restraints excluded: chain i residue 131 LEU Chi-restraints excluded: chain j residue 12 PHE Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain j residue 158 VAL Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain m residue 76 TYR Chi-restraints excluded: chain m residue 133 LEU Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain o residue 135 VAL Chi-restraints excluded: chain o residue 149 LEU Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain e residue 30 GLN Chi-restraints excluded: chain e residue 35 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 192 optimal weight: 0.0570 chunk 149 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: