Starting phenix.real_space_refine on Sat Feb 17 19:46:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/02_2024/6o7t_0644.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/02_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_0644/02_2024/6o7t_0644.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/02_2024/6o7t_0644.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/02_2024/6o7t_0644.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o7t_0644/02_2024/6o7t_0644.pdb" } 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 Residue "a ARG 27": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a ARG 403": "NH1" <-> "NH2" Residue "a PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 117": "NH1" <-> "NH2" Residue "g ARG 124": "NH1" <-> "NH2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "h ARG 117": "NH1" <-> "NH2" Residue "h ARG 153": "NH1" <-> "NH2" Residue "i ARG 117": "NH1" <-> "NH2" Residue "i ARG 153": "NH1" <-> "NH2" Residue "j PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 153": "NH1" <-> "NH2" Residue "k ARG 153": "NH1" <-> "NH2" Residue "l ARG 117": "NH1" <-> "NH2" Residue "l ARG 153": "NH1" <-> "NH2" Residue "m ARG 153": "NH1" <-> "NH2" Residue "n ARG 153": "NH1" <-> "NH2" Residue "o TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 125": "NH1" <-> "NH2" Residue "o TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 11.08, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.56 Conformation dependent library (CDL) restraints added in 4.2 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: 2.12 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: 6.03 Time building geometry restraints manager: 9.17 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: 93.37 - 101.51: 53 101.51 - 109.65: 2756 109.65 - 117.78: 11677 117.78 - 125.92: 12725 125.92 - 134.06: 221 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 2.440 nonbonded pdb=" O ALA a 407 " pdb=" OG1 THR a 411 " model vdw 2.238 2.440 nonbonded pdb=" OH TYR n 66 " pdb=" OE2 GLU n 137 " model vdw 2.241 2.440 nonbonded pdb=" O LEU c 51 " pdb=" OH TYR c 143 " model vdw 2.250 2.440 nonbonded pdb=" O GLY i 31 " pdb=" OG SER i 35 " model vdw 2.255 2.440 ... (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 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.670 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 55.040 Find NCS groups from input model: 1.080 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.420 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 13 poor density : 614 time to evaluate : 2.152 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: 0.2755 time to fit residues: 271.4860 Evaluate side-chains 407 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 403 time to evaluate : 2.144 ------------------------------------------------------------------------------- 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: 0.8980 chunk 206 optimal weight: 0.5980 chunk 114 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 18 GLN a 68 GLN a 79 HIS a 311 GLN a 480 ASN a 547 HIS a 571 ASN c 132 ASN c 138 ASN d 10 ASN d 27 ASN ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 222 ASN f 35 HIS g 90 GLN h 90 GLN ** i 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 90 GLN j 151 ASN k 53 ASN ** k 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 151 ASN l 80 GLN ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20090 Z= 0.208 Angle : 0.653 8.079 27432 Z= 0.344 Chirality : 0.041 0.208 3390 Planarity : 0.005 0.057 3431 Dihedral : 5.335 59.396 2962 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.76 % Allowed : 15.66 % Favored : 80.58 % 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: -2.45 (0.14), residues: 2784 helix: -1.11 (0.11), residues: 1992 sheet: -2.08 (0.89), residues: 26 loop : -2.64 (0.19), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 647 HIS 0.010 0.001 HIS a 559 PHE 0.028 0.002 PHE c 80 TYR 0.027 0.002 TYR a 285 ARG 0.004 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 526 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 459 time to evaluate : 2.379 Fit side-chains REVERT: a 432 MET cc_start: 0.8618 (ttm) cc_final: 0.8394 (ttt) REVERT: a 648 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8595 (tt) REVERT: a 649 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8342 (pp) REVERT: c 46 ASN cc_start: 0.7479 (p0) cc_final: 0.7167 (p0) REVERT: d 20 TYR cc_start: 0.8657 (m-80) cc_final: 0.8444 (m-10) REVERT: d 178 GLU cc_start: 0.8170 (mp0) cc_final: 0.7818 (mp0) REVERT: d 191 ASP cc_start: 0.8946 (t70) cc_final: 0.8632 (t0) REVERT: h 129 MET cc_start: 0.7773 (tpp) cc_final: 0.7441 (tpt) REVERT: i 108 ILE cc_start: 0.8371 (pp) cc_final: 0.8045 (mt) REVERT: i 141 LEU cc_start: 0.8010 (tt) cc_final: 0.7664 (tt) REVERT: i 144 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8348 (tp) REVERT: j 12 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7354 (p90) REVERT: j 15 ILE cc_start: 0.7917 (mm) cc_final: 0.7642 (mm) REVERT: k 129 MET cc_start: 0.7117 (ttt) cc_final: 0.6748 (ttp) REVERT: k 130 ILE cc_start: 0.8248 (pp) cc_final: 0.8005 (mt) REVERT: m 151 ASN cc_start: 0.8661 (t160) cc_final: 0.8246 (t0) REVERT: o 9 ILE cc_start: 0.8538 (tp) cc_final: 0.8213 (pt) REVERT: o 139 LEU cc_start: 0.9186 (tt) cc_final: 0.8948 (tt) REVERT: o 143 PHE cc_start: 0.8136 (m-80) cc_final: 0.7727 (m-80) REVERT: e 30 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.6724 (mp10) outliers start: 67 outliers final: 36 residues processed: 498 average time/residue: 0.2757 time to fit residues: 220.4844 Evaluate side-chains 446 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 405 time to evaluate : 2.347 ------------------------------------------------------------------------------- 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 507 THR Chi-restraints excluded: chain a residue 648 LEU Chi-restraints excluded: chain a residue 649 LEU Chi-restraints excluded: chain a residue 730 THR 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 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 f residue 33 THR Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain h residue 2 THR 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 2 THR 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 55 LEU Chi-restraints excluded: chain o residue 135 VAL Chi-restraints excluded: chain o residue 149 LEU Chi-restraints excluded: chain e residue 30 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.0670 chunk 206 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 246 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- 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 a 725 ASN c 138 ASN ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN h 90 GLN ** i 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 GLN k 90 GLN 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20090 Z= 0.234 Angle : 0.623 9.820 27432 Z= 0.321 Chirality : 0.041 0.197 3390 Planarity : 0.004 0.060 3431 Dihedral : 4.871 57.924 2958 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.27 % Allowed : 17.17 % Favored : 77.55 % 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: -1.46 (0.15), residues: 2784 helix: -0.35 (0.11), residues: 1998 sheet: -1.56 (0.95), residues: 26 loop : -2.38 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 243 HIS 0.009 0.001 HIS a 718 PHE 0.028 0.002 PHE c 80 TYR 0.018 0.001 TYR o 127 ARG 0.006 0.001 ARG j 153 *********************** 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 517 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 423 time to evaluate : 2.144 Fit side-chains REVERT: a 432 MET cc_start: 0.8554 (ttm) cc_final: 0.8346 (ttt) REVERT: b 236 ILE cc_start: 0.8527 (pt) cc_final: 0.8232 (mt) REVERT: c 46 ASN cc_start: 0.7346 (p0) cc_final: 0.7067 (p0) REVERT: c 100 ASN cc_start: 0.8169 (t0) cc_final: 0.7960 (t0) REVERT: d 50 ASP cc_start: 0.8011 (t0) cc_final: 0.7611 (t70) REVERT: d 178 GLU cc_start: 0.8181 (mp0) cc_final: 0.7857 (mp0) REVERT: h 15 ILE cc_start: 0.8680 (pt) cc_final: 0.7998 (mm) REVERT: h 129 MET cc_start: 0.7747 (tpp) cc_final: 0.7456 (tpp) REVERT: i 144 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8370 (tp) REVERT: j 12 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7137 (p90) REVERT: k 129 MET cc_start: 0.7292 (ttt) cc_final: 0.6941 (ttp) REVERT: m 151 ASN cc_start: 0.8682 (t160) cc_final: 0.8291 (t0) REVERT: n 65 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8755 (mp) REVERT: n 129 MET cc_start: 0.7471 (tpt) cc_final: 0.7125 (tpt) REVERT: o 9 ILE cc_start: 0.8599 (tp) cc_final: 0.8390 (tt) REVERT: o 139 LEU cc_start: 0.9171 (tt) cc_final: 0.8933 (tt) REVERT: o 143 PHE cc_start: 0.8212 (m-80) cc_final: 0.7726 (m-80) REVERT: e 30 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.6822 (mp10) outliers start: 94 outliers final: 55 residues processed: 475 average time/residue: 0.2741 time to fit residues: 210.6437 Evaluate side-chains 451 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 392 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 196 VAL Chi-restraints excluded: chain a residue 199 LEU Chi-restraints excluded: chain a residue 259 ASN Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 394 CYS Chi-restraints excluded: chain a residue 464 ILE 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 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 109 VAL Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 70 GLU Chi-restraints excluded: chain d residue 134 ASP Chi-restraints excluded: chain f residue 12 CYS Chi-restraints excluded: chain f residue 17 SER Chi-restraints excluded: chain f residue 33 THR 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 h residue 2 THR Chi-restraints excluded: chain h residue 54 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 77 SER Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain m residue 65 ILE 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 n residue 96 SER Chi-restraints excluded: chain o residue 30 SER 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: 0.3980 chunk 186 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 118 optimal weight: 50.0000 chunk 166 optimal weight: 20.0000 chunk 249 optimal weight: 0.2980 chunk 263 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 134 GLN a 480 ASN a 718 HIS d 7 ASN ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN h 90 GLN i 90 GLN l 151 ASN o 130 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 20090 Z= 0.228 Angle : 0.600 10.448 27432 Z= 0.307 Chirality : 0.040 0.164 3390 Planarity : 0.004 0.061 3431 Dihedral : 4.655 55.640 2958 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.11 % Allowed : 17.00 % Favored : 77.89 % 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: -0.90 (0.15), residues: 2784 helix: 0.08 (0.11), residues: 2001 sheet: -1.18 (1.01), residues: 26 loop : -2.25 (0.20), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 243 HIS 0.009 0.001 HIS a 718 PHE 0.026 0.001 PHE c 80 TYR 0.015 0.001 TYR o 127 ARG 0.005 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 500 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 409 time to evaluate : 2.317 Fit side-chains REVERT: a 395 ASP cc_start: 0.8053 (p0) cc_final: 0.7831 (p0) REVERT: a 519 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7928 (t70) REVERT: b 236 ILE cc_start: 0.8489 (pt) cc_final: 0.8212 (mt) REVERT: c 21 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8448 (tp) REVERT: c 46 ASN cc_start: 0.7322 (OUTLIER) cc_final: 0.7008 (p0) REVERT: c 100 ASN cc_start: 0.8377 (t0) cc_final: 0.8139 (t0) REVERT: d 50 ASP cc_start: 0.8181 (t0) cc_final: 0.7886 (t70) REVERT: d 97 TYR cc_start: 0.8606 (m-80) cc_final: 0.8378 (m-80) REVERT: d 178 GLU cc_start: 0.8092 (mp0) cc_final: 0.7827 (mp0) REVERT: d 191 ASP cc_start: 0.9046 (t0) cc_final: 0.8800 (t0) REVERT: h 22 ILE cc_start: 0.8996 (mt) cc_final: 0.8761 (mp) REVERT: h 129 MET cc_start: 0.7726 (tpp) cc_final: 0.7483 (tpp) REVERT: i 144 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8374 (tp) REVERT: j 12 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7151 (p90) REVERT: k 129 MET cc_start: 0.7341 (ttt) cc_final: 0.7063 (ttp) REVERT: k 134 ILE cc_start: 0.8869 (tp) cc_final: 0.8653 (tp) REVERT: m 151 ASN cc_start: 0.8689 (t160) cc_final: 0.8308 (t0) REVERT: n 25 SER cc_start: 0.8073 (m) cc_final: 0.7567 (p) REVERT: n 65 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8728 (mp) REVERT: n 129 MET cc_start: 0.7451 (tpt) cc_final: 0.7105 (tpt) REVERT: o 9 ILE cc_start: 0.8629 (tp) cc_final: 0.8427 (tt) REVERT: o 139 LEU cc_start: 0.9164 (tt) cc_final: 0.8927 (tt) REVERT: o 143 PHE cc_start: 0.8236 (m-80) cc_final: 0.7716 (m-80) REVERT: e 30 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.6880 (mp10) outliers start: 91 outliers final: 62 residues processed: 457 average time/residue: 0.2752 time to fit residues: 202.6197 Evaluate side-chains 457 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 388 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 46 ASN Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 126 THR 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 d residue 134 ASP Chi-restraints excluded: chain f residue 17 SER Chi-restraints excluded: chain f residue 33 THR 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 2 THR 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 135 PHE Chi-restraints excluded: chain h residue 152 SER 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 77 SER Chi-restraints excluded: chain j residue 96 SER Chi-restraints excluded: chain j residue 133 LEU 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 l residue 5 CYS 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 96 SER Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 59 SER 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: 1.9990 chunk 149 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 196 optimal weight: 9.9990 chunk 108 optimal weight: 0.0870 chunk 225 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- 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 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN j 151 ASN ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 80 GLN o 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2952 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= 0.286 Angle : 0.616 10.826 27432 Z= 0.315 Chirality : 0.041 0.274 3390 Planarity : 0.004 0.064 3431 Dihedral : 4.596 51.789 2958 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.89 % Allowed : 18.18 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2784 helix: 0.28 (0.12), residues: 2000 sheet: -1.03 (1.02), residues: 26 loop : -2.15 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 243 HIS 0.009 0.001 HIS a 718 PHE 0.029 0.002 PHE a 636 TYR 0.019 0.001 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 498 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 393 time to evaluate : 2.487 Fit side-chains REVERT: a 395 ASP cc_start: 0.8075 (p0) cc_final: 0.7790 (p0) REVERT: a 519 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8028 (t70) REVERT: b 236 ILE cc_start: 0.8549 (pt) cc_final: 0.8329 (mt) REVERT: c 46 ASN cc_start: 0.7395 (OUTLIER) cc_final: 0.7064 (p0) REVERT: c 100 ASN cc_start: 0.8351 (t0) cc_final: 0.8140 (t0) REVERT: d 50 ASP cc_start: 0.8212 (t0) cc_final: 0.7930 (t70) REVERT: d 97 TYR cc_start: 0.8644 (m-80) cc_final: 0.8393 (m-80) REVERT: d 178 GLU cc_start: 0.8105 (mp0) cc_final: 0.7846 (mp0) REVERT: d 191 ASP cc_start: 0.9042 (t0) cc_final: 0.8814 (t0) REVERT: d 302 GLN cc_start: 0.8258 (mp10) cc_final: 0.7986 (mp10) REVERT: h 22 ILE cc_start: 0.8977 (mt) cc_final: 0.8735 (mp) REVERT: h 108 ILE cc_start: 0.8713 (pt) cc_final: 0.8452 (pt) REVERT: h 129 MET cc_start: 0.7734 (tpp) cc_final: 0.7368 (tpp) REVERT: i 144 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8391 (tp) REVERT: j 12 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7066 (p90) REVERT: k 129 MET cc_start: 0.7353 (ttt) cc_final: 0.7084 (ttp) REVERT: k 134 ILE cc_start: 0.8892 (tp) cc_final: 0.8643 (tp) REVERT: m 151 ASN cc_start: 0.8684 (t160) cc_final: 0.8315 (t0) REVERT: n 25 SER cc_start: 0.8081 (m) cc_final: 0.7595 (p) REVERT: n 65 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8803 (mp) REVERT: n 129 MET cc_start: 0.7519 (tpt) cc_final: 0.7140 (tpt) REVERT: o 9 ILE cc_start: 0.8599 (tp) cc_final: 0.8385 (tt) REVERT: o 139 LEU cc_start: 0.9177 (tt) cc_final: 0.8668 (tt) REVERT: o 143 PHE cc_start: 0.8261 (m-80) cc_final: 0.7720 (m-80) REVERT: e 39 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8391 (mp) outliers start: 105 outliers final: 79 residues processed: 448 average time/residue: 0.2960 time to fit residues: 213.6783 Evaluate side-chains 461 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 376 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 259 ASN 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 434 LEU Chi-restraints excluded: chain a residue 448 LYS Chi-restraints excluded: chain a residue 464 ILE 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 648 LEU 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 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 46 ASN Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 58 VAL Chi-restraints excluded: chain d residue 70 GLU Chi-restraints excluded: chain d residue 134 ASP Chi-restraints excluded: chain d residue 342 ILE Chi-restraints excluded: chain f residue 17 SER Chi-restraints excluded: chain f residue 33 THR 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 99 LEU Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 54 ILE 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 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 77 SER Chi-restraints excluded: chain j residue 96 SER 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 7 VAL Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain k residue 158 VAL Chi-restraints excluded: chain l residue 5 CYS 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 96 SER Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain o residue 110 LEU 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 35 SER Chi-restraints excluded: chain e residue 39 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 381 HIS a 480 ASN a 718 HIS c 61 ASN c 132 ASN ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 151 ASN o 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20090 Z= 0.386 Angle : 0.668 10.969 27432 Z= 0.340 Chirality : 0.044 0.301 3390 Planarity : 0.004 0.067 3431 Dihedral : 4.678 46.466 2958 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 6.23 % Allowed : 18.86 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2784 helix: 0.25 (0.11), residues: 2003 sheet: -0.61 (1.04), residues: 26 loop : -2.11 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 77 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 0.004 0.001 ARG e 63 *********************** 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 488 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 377 time to evaluate : 2.377 Fit side-chains REVERT: a 395 ASP cc_start: 0.8194 (p0) cc_final: 0.7933 (p0) REVERT: a 467 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8667 (mp) REVERT: a 519 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7958 (t70) REVERT: c 46 ASN cc_start: 0.7515 (p0) cc_final: 0.7179 (p0) REVERT: c 100 ASN cc_start: 0.8374 (t0) cc_final: 0.8121 (t0) REVERT: c 201 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8512 (t) REVERT: d 33 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8801 (tt) REVERT: d 50 ASP cc_start: 0.8291 (t0) cc_final: 0.8000 (t70) REVERT: d 178 GLU cc_start: 0.8129 (mp0) cc_final: 0.7871 (mp0) REVERT: g 149 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8560 (mp) REVERT: h 22 ILE cc_start: 0.8977 (mt) cc_final: 0.8729 (mp) REVERT: h 108 ILE cc_start: 0.8813 (pt) cc_final: 0.8569 (pt) REVERT: h 129 MET cc_start: 0.7807 (tpp) cc_final: 0.7483 (tpp) REVERT: i 129 MET cc_start: 0.8069 (ttp) cc_final: 0.7699 (ttt) REVERT: i 144 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8394 (tp) REVERT: j 12 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7067 (p90) REVERT: j 129 MET cc_start: 0.8229 (tpt) cc_final: 0.7447 (tpp) REVERT: k 129 MET cc_start: 0.7448 (ttt) cc_final: 0.7126 (ttp) REVERT: k 134 ILE cc_start: 0.8802 (tp) cc_final: 0.8571 (tp) REVERT: m 151 ASN cc_start: 0.8760 (t160) cc_final: 0.8438 (t0) REVERT: n 25 SER cc_start: 0.8163 (m) cc_final: 0.7700 (p) REVERT: n 129 MET cc_start: 0.7574 (tpt) cc_final: 0.7170 (tpt) REVERT: o 143 PHE cc_start: 0.8348 (m-80) cc_final: 0.7865 (m-80) REVERT: e 30 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7107 (mp10) REVERT: e 39 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8250 (mp) outliers start: 111 outliers final: 79 residues processed: 446 average time/residue: 0.2738 time to fit residues: 195.4547 Evaluate side-chains 454 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 366 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 18 GLN 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 259 ASN 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 434 LEU Chi-restraints excluded: chain a residue 448 LYS Chi-restraints excluded: chain a residue 464 ILE Chi-restraints excluded: chain a residue 467 LEU 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 518 LEU 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 648 LEU Chi-restraints excluded: chain a residue 730 THR 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 797 SER 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 109 VAL Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain c residue 201 VAL Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 58 VAL Chi-restraints excluded: chain d residue 59 SER Chi-restraints excluded: chain d residue 70 GLU Chi-restraints excluded: chain d residue 134 ASP Chi-restraints excluded: chain d residue 342 ILE Chi-restraints excluded: chain f residue 17 SER Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain f residue 64 VAL 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 99 LEU Chi-restraints excluded: chain g residue 134 ILE Chi-restraints excluded: chain g residue 149 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 58 ILE Chi-restraints excluded: chain h residue 73 LEU Chi-restraints excluded: chain h residue 152 SER 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 77 SER Chi-restraints excluded: chain j residue 96 SER 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 k residue 127 VAL Chi-restraints excluded: chain l residue 5 CYS Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 76 TYR Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain n residue 62 ILE Chi-restraints excluded: chain n residue 96 SER Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain o residue 110 LEU Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain o residue 135 VAL Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain e residue 30 GLN Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 39 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 150 optimal weight: 4.9990 chunk 192 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 222 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 263 optimal weight: 0.9990 chunk 164 optimal weight: 0.5980 chunk 160 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 68 GLN a 480 ASN a 718 HIS c 61 ASN d 7 ASN ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN ** h 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 151 ASN o 130 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3266 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= 0.180 Angle : 0.577 12.200 27432 Z= 0.294 Chirality : 0.039 0.234 3390 Planarity : 0.003 0.068 3431 Dihedral : 4.417 40.775 2958 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.87 % Allowed : 21.32 % Favored : 74.80 % 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: -0.10 (0.16), residues: 2784 helix: 0.67 (0.12), residues: 1985 sheet: -0.34 (1.05), residues: 26 loop : -1.90 (0.21), residues: 773 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 0.020 0.001 PHE c 80 TYR 0.018 0.001 TYR g 30 ARG 0.007 0.000 ARG j 153 *********************** REFINEMENT MACRO_CYCLE 7 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 467 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 398 time to evaluate : 2.509 Fit side-chains REVERT: a 395 ASP cc_start: 0.7839 (p0) cc_final: 0.7602 (p0) REVERT: c 46 ASN cc_start: 0.7245 (OUTLIER) cc_final: 0.6987 (p0) REVERT: c 100 ASN cc_start: 0.8289 (t0) cc_final: 0.8043 (t0) REVERT: c 201 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8372 (t) REVERT: d 33 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8697 (tt) REVERT: d 50 ASP cc_start: 0.8201 (t0) cc_final: 0.7946 (t70) REVERT: d 178 GLU cc_start: 0.8112 (mp0) cc_final: 0.7834 (mp0) REVERT: d 302 GLN cc_start: 0.8227 (mp10) cc_final: 0.7994 (mp10) REVERT: d 319 GLU cc_start: 0.7643 (pp20) cc_final: 0.7310 (pp20) REVERT: h 15 ILE cc_start: 0.8532 (pt) cc_final: 0.8161 (mm) REVERT: h 22 ILE cc_start: 0.8886 (mt) cc_final: 0.8620 (mp) REVERT: h 59 MET cc_start: 0.8744 (mtp) cc_final: 0.8538 (mtt) REVERT: h 108 ILE cc_start: 0.8647 (pt) cc_final: 0.8377 (pt) REVERT: h 129 MET cc_start: 0.7793 (tpp) cc_final: 0.7399 (tpp) REVERT: i 129 MET cc_start: 0.8037 (ttp) cc_final: 0.7660 (ttt) REVERT: i 141 LEU cc_start: 0.7870 (tp) cc_final: 0.7613 (tp) REVERT: j 12 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7053 (p90) REVERT: j 129 MET cc_start: 0.8259 (tpt) cc_final: 0.7512 (tpp) REVERT: k 129 MET cc_start: 0.7372 (ttt) cc_final: 0.7101 (ttp) REVERT: k 134 ILE cc_start: 0.8800 (tp) cc_final: 0.8587 (tp) REVERT: m 151 ASN cc_start: 0.8633 (t160) cc_final: 0.8270 (t0) REVERT: n 129 MET cc_start: 0.7431 (tpt) cc_final: 0.7050 (tpt) REVERT: o 139 LEU cc_start: 0.9115 (tt) cc_final: 0.8665 (tt) REVERT: o 143 PHE cc_start: 0.8298 (m-80) cc_final: 0.7755 (m-80) REVERT: e 30 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.6989 (mm-40) outliers start: 69 outliers final: 52 residues processed: 440 average time/residue: 0.2798 time to fit residues: 198.9835 Evaluate side-chains 433 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 376 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 18 GLN 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 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 464 ILE Chi-restraints excluded: chain a residue 472 SER Chi-restraints excluded: chain a residue 480 ASN Chi-restraints excluded: chain a residue 519 ASP Chi-restraints excluded: chain a residue 624 ASP Chi-restraints excluded: chain a residue 651 VAL Chi-restraints excluded: chain a residue 748 SER Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 46 ASN Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain c residue 201 VAL Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 134 ASP Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 342 ILE Chi-restraints excluded: chain f residue 17 SER 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 58 ILE Chi-restraints excluded: chain h residue 73 LEU Chi-restraints excluded: chain h residue 135 PHE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 24 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 96 SER Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain k residue 2 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 m residue 76 TYR Chi-restraints excluded: chain n residue 62 ILE Chi-restraints excluded: chain n residue 96 SER Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 135 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 167 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 206 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN m 82 GLN n 151 ASN o 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3359 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= 0.210 Angle : 0.593 12.062 27432 Z= 0.300 Chirality : 0.040 0.228 3390 Planarity : 0.003 0.073 3431 Dihedral : 4.264 24.598 2956 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.15 % Allowed : 21.21 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2784 helix: 0.81 (0.12), residues: 1986 sheet: -0.13 (1.04), residues: 26 loop : -1.87 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 312 HIS 0.009 0.001 HIS a 718 PHE 0.021 0.001 PHE c 80 TYR 0.018 0.001 TYR o 127 ARG 0.006 0.000 ARG j 153 *********************** REFINEMENT MACRO_CYCLE 8 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 447 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 373 time to evaluate : 2.232 Fit side-chains REVERT: a 395 ASP cc_start: 0.7825 (p0) cc_final: 0.7586 (p0) REVERT: c 46 ASN cc_start: 0.7315 (OUTLIER) cc_final: 0.7041 (p0) REVERT: c 100 ASN cc_start: 0.8284 (t0) cc_final: 0.8040 (t0) REVERT: c 201 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8347 (t) REVERT: d 33 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8697 (tt) REVERT: d 50 ASP cc_start: 0.8201 (t0) cc_final: 0.7953 (t70) REVERT: d 178 GLU cc_start: 0.8123 (mp0) cc_final: 0.7844 (mp0) REVERT: d 302 GLN cc_start: 0.8172 (mp10) cc_final: 0.7930 (mp10) REVERT: d 319 GLU cc_start: 0.7646 (pp20) cc_final: 0.7279 (pp20) REVERT: h 15 ILE cc_start: 0.8533 (pt) cc_final: 0.8147 (mm) REVERT: h 22 ILE cc_start: 0.8895 (mt) cc_final: 0.8613 (mp) REVERT: h 59 MET cc_start: 0.8755 (mtp) cc_final: 0.8194 (mtt) REVERT: h 108 ILE cc_start: 0.8617 (pt) cc_final: 0.8382 (pt) REVERT: h 129 MET cc_start: 0.7796 (tpp) cc_final: 0.7452 (tpp) REVERT: i 129 MET cc_start: 0.8056 (ttp) cc_final: 0.7658 (ttt) REVERT: i 141 LEU cc_start: 0.7877 (tp) cc_final: 0.7602 (tp) REVERT: i 144 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8347 (tp) REVERT: j 12 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7040 (p90) REVERT: j 129 MET cc_start: 0.8086 (tpt) cc_final: 0.7477 (tpp) REVERT: j 157 ASP cc_start: 0.7797 (m-30) cc_final: 0.7352 (t0) REVERT: k 129 MET cc_start: 0.7381 (ttt) cc_final: 0.7114 (ttp) REVERT: k 134 ILE cc_start: 0.8835 (tp) cc_final: 0.8632 (tp) REVERT: m 151 ASN cc_start: 0.8596 (t160) cc_final: 0.8238 (t0) REVERT: n 129 MET cc_start: 0.7461 (tpt) cc_final: 0.7079 (tpt) REVERT: o 139 LEU cc_start: 0.9115 (tt) cc_final: 0.8908 (tt) REVERT: o 143 PHE cc_start: 0.8280 (m-80) cc_final: 0.7746 (m-80) REVERT: e 30 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7027 (mm-40) outliers start: 74 outliers final: 55 residues processed: 421 average time/residue: 0.2718 time to fit residues: 183.6992 Evaluate side-chains 425 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 364 time to evaluate : 2.128 ------------------------------------------------------------------------------- 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 259 ASN 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 434 LEU Chi-restraints excluded: chain a residue 448 LYS Chi-restraints excluded: chain a residue 464 ILE Chi-restraints excluded: chain a residue 472 SER Chi-restraints excluded: chain a residue 480 ASN Chi-restraints excluded: chain a residue 519 ASP 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 30 ILE Chi-restraints excluded: chain c residue 46 ASN Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain c residue 201 VAL Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 134 ASP Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 342 ILE Chi-restraints excluded: chain f residue 17 SER 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 58 ILE Chi-restraints excluded: chain h residue 73 LEU Chi-restraints excluded: chain h residue 135 PHE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 108 ILE 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 96 SER Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain k residue 24 THR Chi-restraints excluded: chain k residue 96 SER Chi-restraints excluded: chain k residue 158 VAL Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 125 LEU Chi-restraints excluded: chain n residue 62 ILE Chi-restraints excluded: chain n residue 96 SER Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 135 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 1.9990 chunk 252 optimal weight: 0.0030 chunk 229 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 overall best weight: 1.1996 ------------------------------------------------------------------------------- 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 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN n 151 ASN o 130 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20090 Z= 0.235 Angle : 0.604 12.163 27432 Z= 0.305 Chirality : 0.041 0.234 3390 Planarity : 0.004 0.076 3431 Dihedral : 4.256 22.992 2956 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.93 % Allowed : 21.38 % Favored : 74.69 % 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: 0.17 (0.16), residues: 2784 helix: 0.88 (0.12), residues: 1987 sheet: -0.07 (1.03), residues: 26 loop : -1.86 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 312 HIS 0.010 0.001 HIS a 718 PHE 0.021 0.001 PHE c 80 TYR 0.015 0.001 TYR g 30 ARG 0.006 0.001 ARG j 153 *********************** REFINEMENT MACRO_CYCLE 9 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 442 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 372 time to evaluate : 2.356 Fit side-chains REVERT: a 395 ASP cc_start: 0.7822 (p0) cc_final: 0.7497 (p0) REVERT: c 46 ASN cc_start: 0.7357 (OUTLIER) cc_final: 0.7032 (p0) REVERT: c 100 ASN cc_start: 0.8301 (t0) cc_final: 0.8060 (t0) REVERT: c 201 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8351 (t) REVERT: d 33 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8733 (tt) REVERT: d 50 ASP cc_start: 0.8223 (t0) cc_final: 0.7965 (t70) REVERT: d 178 GLU cc_start: 0.8128 (mp0) cc_final: 0.7867 (mp0) REVERT: d 302 GLN cc_start: 0.8168 (mp10) cc_final: 0.7927 (mp10) REVERT: d 319 GLU cc_start: 0.7615 (pp20) cc_final: 0.7236 (pp20) REVERT: h 15 ILE cc_start: 0.8546 (pt) cc_final: 0.8152 (mm) REVERT: h 22 ILE cc_start: 0.8896 (mt) cc_final: 0.8614 (mp) REVERT: h 59 MET cc_start: 0.8745 (mtp) cc_final: 0.8369 (mmm) REVERT: h 73 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8635 (mp) REVERT: h 108 ILE cc_start: 0.8657 (pt) cc_final: 0.8405 (pt) REVERT: h 129 MET cc_start: 0.7790 (tpp) cc_final: 0.7461 (tpp) REVERT: i 129 MET cc_start: 0.8067 (ttp) cc_final: 0.7673 (ttt) REVERT: i 141 LEU cc_start: 0.7924 (tp) cc_final: 0.7648 (tp) REVERT: i 144 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8357 (tp) REVERT: j 12 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.6983 (p90) REVERT: j 129 MET cc_start: 0.8019 (tpt) cc_final: 0.7499 (tpp) REVERT: j 157 ASP cc_start: 0.7822 (m-30) cc_final: 0.7373 (t0) REVERT: k 129 MET cc_start: 0.7390 (ttt) cc_final: 0.7124 (ttp) REVERT: m 151 ASN cc_start: 0.8601 (t160) cc_final: 0.8266 (t0) REVERT: n 129 MET cc_start: 0.7503 (tpt) cc_final: 0.7115 (tpt) REVERT: o 139 LEU cc_start: 0.9123 (tt) cc_final: 0.8901 (tt) REVERT: o 143 PHE cc_start: 0.8296 (m-80) cc_final: 0.7812 (m-80) REVERT: e 30 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7047 (mm-40) REVERT: e 39 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8405 (mp) outliers start: 70 outliers final: 58 residues processed: 418 average time/residue: 0.2944 time to fit residues: 196.5516 Evaluate side-chains 432 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 366 time to evaluate : 2.177 ------------------------------------------------------------------------------- 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 259 ASN 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 434 LEU Chi-restraints excluded: chain a residue 448 LYS Chi-restraints excluded: chain a residue 464 ILE 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 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 30 ILE Chi-restraints excluded: chain c residue 46 ASN Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain c residue 197 LEU Chi-restraints excluded: chain c residue 201 VAL Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 134 ASP Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 342 ILE Chi-restraints excluded: chain f residue 17 SER 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 58 ILE Chi-restraints excluded: chain h residue 73 LEU 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 144 LEU Chi-restraints excluded: chain j residue 12 PHE Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 96 SER Chi-restraints excluded: chain j residue 133 LEU 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 k residue 158 VAL Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 125 LEU Chi-restraints excluded: chain m residue 76 TYR Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain n residue 62 ILE Chi-restraints excluded: chain n residue 96 SER Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 105 VAL Chi-restraints excluded: chain o residue 135 VAL Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain e residue 30 GLN Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 39 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 1.9990 chunk 259 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 271 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN n 151 ASN o 130 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20090 Z= 0.301 Angle : 0.638 12.387 27432 Z= 0.321 Chirality : 0.042 0.242 3390 Planarity : 0.004 0.080 3431 Dihedral : 4.330 19.381 2956 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.38 % Allowed : 21.27 % Favored : 74.35 % 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: 0.06 (0.16), residues: 2784 helix: 0.80 (0.12), residues: 1994 sheet: -0.43 (0.97), residues: 30 loop : -1.94 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 312 HIS 0.010 0.001 HIS a 718 PHE 0.023 0.002 PHE c 80 TYR 0.020 0.001 TYR o 127 ARG 0.006 0.001 ARG j 153 ********************** REFINEMENT MACRO_CYCLE 10 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 453 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 375 time to evaluate : 2.481 Fit side-chains REVERT: a 395 ASP cc_start: 0.7842 (p0) cc_final: 0.7529 (p0) REVERT: a 519 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7862 (t70) REVERT: a 613 ILE cc_start: 0.8871 (mt) cc_final: 0.8632 (mt) REVERT: c 46 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7070 (p0) REVERT: c 100 ASN cc_start: 0.8320 (t0) cc_final: 0.8064 (t0) REVERT: c 201 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8331 (t) REVERT: d 33 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8772 (tt) REVERT: d 50 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7974 (t70) REVERT: d 178 GLU cc_start: 0.8139 (mp0) cc_final: 0.7881 (mp0) REVERT: d 302 GLN cc_start: 0.8187 (mp10) cc_final: 0.7942 (mp10) REVERT: h 15 ILE cc_start: 0.8556 (pt) cc_final: 0.8110 (mm) REVERT: h 22 ILE cc_start: 0.8919 (mt) cc_final: 0.8641 (mp) REVERT: h 59 MET cc_start: 0.8746 (mtp) cc_final: 0.8377 (mmm) REVERT: h 73 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8690 (mp) REVERT: h 108 ILE cc_start: 0.8723 (pt) cc_final: 0.8487 (pt) REVERT: h 129 MET cc_start: 0.7792 (tpp) cc_final: 0.7468 (tpp) REVERT: i 129 MET cc_start: 0.8077 (ttp) cc_final: 0.7680 (ttt) REVERT: i 144 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8384 (tp) REVERT: j 12 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7013 (p90) REVERT: j 129 MET cc_start: 0.8070 (tpt) cc_final: 0.7596 (tpp) REVERT: k 129 MET cc_start: 0.7462 (ttt) cc_final: 0.7149 (ttp) REVERT: l 81 LYS cc_start: 0.8779 (mttp) cc_final: 0.8556 (mttt) REVERT: m 151 ASN cc_start: 0.8670 (t160) cc_final: 0.8337 (t0) REVERT: n 65 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8811 (mp) REVERT: n 129 MET cc_start: 0.7570 (tpt) cc_final: 0.7202 (tpt) REVERT: o 139 LEU cc_start: 0.9152 (tt) cc_final: 0.8658 (tt) REVERT: o 143 PHE cc_start: 0.8325 (m-80) cc_final: 0.7739 (m-80) REVERT: e 30 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7047 (mm-40) REVERT: e 39 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8311 (mp) REVERT: e 43 MET cc_start: 0.8167 (mtp) cc_final: 0.7927 (mmm) outliers start: 78 outliers final: 59 residues processed: 423 average time/residue: 0.2765 time to fit residues: 188.0829 Evaluate side-chains 440 residues out of total 2270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 370 time to evaluate : 2.196 ------------------------------------------------------------------------------- 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 259 ASN 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 434 LEU Chi-restraints excluded: chain a residue 448 LYS Chi-restraints excluded: chain a residue 464 ILE 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 651 VAL Chi-restraints excluded: chain a residue 730 THR Chi-restraints excluded: chain a residue 748 SER Chi-restraints excluded: chain a residue 757 ILE 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 30 ILE Chi-restraints excluded: chain c residue 46 ASN Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 126 THR Chi-restraints excluded: chain c residue 197 LEU Chi-restraints excluded: chain c residue 201 VAL Chi-restraints excluded: chain d residue 21 ARG Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain d residue 50 ASP Chi-restraints excluded: chain d residue 134 ASP Chi-restraints excluded: chain d residue 200 ILE Chi-restraints excluded: chain d residue 342 ILE Chi-restraints excluded: chain f residue 17 SER Chi-restraints excluded: chain f residue 33 THR Chi-restraints excluded: chain g residue 42 THR Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 71 SER 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 58 ILE Chi-restraints excluded: chain h residue 73 LEU 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 144 LEU Chi-restraints excluded: chain j residue 12 PHE Chi-restraints excluded: chain j residue 24 THR Chi-restraints excluded: chain j residue 96 SER Chi-restraints excluded: chain j residue 133 LEU 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 k residue 158 VAL Chi-restraints excluded: chain l residue 7 VAL Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain l residue 125 LEU Chi-restraints excluded: chain m residue 76 TYR Chi-restraints excluded: chain m residue 138 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 96 SER Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 87 THR Chi-restraints excluded: chain o residue 105 VAL Chi-restraints excluded: chain o residue 156 LEU Chi-restraints excluded: chain e residue 30 GLN Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 39 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 222 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 ASN n 151 ASN o 130 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.153028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120296 restraints weight = 24112.025| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.85 r_work: 0.3145 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20090 Z= 0.229 Angle : 0.608 12.796 27432 Z= 0.307 Chirality : 0.041 0.227 3390 Planarity : 0.004 0.078 3431 Dihedral : 4.263 18.350 2956 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.87 % Allowed : 22.00 % Favored : 74.13 % 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: 0.22 (0.16), residues: 2784 helix: 0.93 (0.12), residues: 1991 sheet: -0.38 (0.97), residues: 30 loop : -1.87 (0.21), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP d 312 HIS 0.010 0.001 HIS a 718 PHE 0.020 0.001 PHE c 80 TYR 0.020 0.001 TYR o 127 ARG 0.006 0.000 ARG j 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4806.34 seconds wall clock time: 87 minutes 25.38 seconds (5245.38 seconds total)