Starting phenix.real_space_refine on Mon Jul 22 16:35:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/07_2024/6ig0_9660_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/07_2024/6ig0_9660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/07_2024/6ig0_9660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/07_2024/6ig0_9660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/07_2024/6ig0_9660_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/07_2024/6ig0_9660_neut.cif" } resolution = 3.37 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.015 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 72 5.49 5 Mg 2 5.21 5 S 37 5.16 5 C 12090 2.51 5 N 3296 2.21 5 O 3856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 121": "NH1" <-> "NH2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A ARG 423": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "G ASP 24": "OD1" <-> "OD2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "G ARG 143": "NH1" <-> "NH2" Residue "G TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 160": "OE1" <-> "OE2" Residue "E TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 6": "NH1" <-> "NH2" Residue "H ARG 83": "NH1" <-> "NH2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "H ARG 158": "NH1" <-> "NH2" Residue "H PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19354 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5812 Classifications: {'peptide': 737} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 8, 'TRANS': 728} Chain breaks: 2 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 975 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 975 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1697 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1626 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2334 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2748 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 17, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "N" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNA': 34} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 17} Chain: "J" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 715 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 20, 'rna3p_pyr': 9} Link IDs: {'rna2p': 3, 'rna3p': 29} Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 2, ' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2929 SG CYS A 401 57.965 30.672 66.675 1.00 74.37 S ATOM 2952 SG CYS A 404 55.630 31.804 64.016 1.00 70.96 S ATOM 3074 SG CYS A 419 58.898 30.714 62.945 1.00 75.02 S ATOM 3096 SG CYS A 422 58.767 34.241 63.931 1.00 70.14 S Time building chain proxies: 13.51, per 1000 atoms: 0.70 Number of scatterers: 19354 At special positions: 0 Unit cell: (92.56, 136.24, 174.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 37 16.00 P 72 15.00 Mg 2 11.99 O 3856 8.00 N 3296 7.00 C 12090 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.37 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 401 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 422 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 404 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 419 " Number of angles added : 6 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4262 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 23 sheets defined 38.2% alpha, 10.4% beta 20 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 6.45 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.610A pdb=" N TYR A 10 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 11 " --> pdb=" O ASP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 25 removed outlier: 3.595A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 39 removed outlier: 3.754A pdb=" N VAL A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY A 35 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.981A pdb=" N GLN A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 81 removed outlier: 3.521A pdb=" N THR A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 75 " --> pdb=" O TYR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.250A pdb=" N TYR A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.855A pdb=" N ASN A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 197 through 220 removed outlier: 3.540A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 265 through 291 removed outlier: 3.726A pdb=" N SER A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 336 removed outlier: 3.947A pdb=" N THR A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 368 through 378 Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.663A pdb=" N LEU A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 431 removed outlier: 3.614A pdb=" N GLY A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 462 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 522 through 528 Processing helix chain 'A' and resid 541 through 558 removed outlier: 3.664A pdb=" N SER A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 585 through 603 removed outlier: 3.791A pdb=" N LYS A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 637 removed outlier: 3.633A pdb=" N GLN A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 681 through 695 removed outlier: 3.589A pdb=" N ILE A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 removed outlier: 3.913A pdb=" N ALA A 701 " --> pdb=" O ARG A 697 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 710 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 712 " --> pdb=" O THR A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 730 removed outlier: 3.737A pdb=" N PHE A 722 " --> pdb=" O ASP A 718 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 753 Processing helix chain 'D' and resid 8 through 20 Processing helix chain 'D' and resid 36 through 52 removed outlier: 3.734A pdb=" N LEU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 46 " --> pdb=" O ASN D 42 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 57 removed outlier: 3.851A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 80 removed outlier: 3.575A pdb=" N ALA D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL D 74 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU D 80 " --> pdb=" O GLN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 removed outlier: 3.630A pdb=" N GLU D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 97 removed outlier: 3.885A pdb=" N LYS D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 Processing helix chain 'C' and resid 8 through 20 Processing helix chain 'C' and resid 36 through 52 removed outlier: 3.733A pdb=" N LEU C 43 " --> pdb=" O LYS C 39 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 57 removed outlier: 3.851A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 80 removed outlier: 3.575A pdb=" N ALA C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.629A pdb=" N GLU C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.886A pdb=" N LYS C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 122 Processing helix chain 'G' and resid 49 through 59 removed outlier: 3.803A pdb=" N LYS G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 112 Processing helix chain 'G' and resid 161 through 178 removed outlier: 4.010A pdb=" N GLU G 165 " --> pdb=" O ASN G 161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS G 175 " --> pdb=" O ARG G 171 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU G 176 " --> pdb=" O ASP G 172 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU G 178 " --> pdb=" O LEU G 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.620A pdb=" N LEU F 52 " --> pdb=" O PRO F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 75 removed outlier: 4.023A pdb=" N ASP F 75 " --> pdb=" O PRO F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.702A pdb=" N LEU F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 112 removed outlier: 3.644A pdb=" N ASP F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 178 removed outlier: 3.793A pdb=" N PHE F 167 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU F 178 " --> pdb=" O LEU F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 removed outlier: 3.505A pdb=" N ARG F 188 " --> pdb=" O SER F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 217 removed outlier: 3.883A pdb=" N LEU F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 54 through 64 removed outlier: 3.670A pdb=" N LEU E 60 " --> pdb=" O MET E 56 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 63 " --> pdb=" O LEU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 84 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 162 through 171 removed outlier: 3.973A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 176 Processing helix chain 'E' and resid 209 through 217 removed outlier: 3.553A pdb=" N ASN E 213 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU E 214 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU E 215 " --> pdb=" O THR E 211 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR E 217 " --> pdb=" O ASN E 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 41 removed outlier: 3.889A pdb=" N ILE B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.637A pdb=" N PHE B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 100 removed outlier: 3.646A pdb=" N ARG B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 117 Processing helix chain 'B' and resid 163 through 171 Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.702A pdb=" N MET B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 52 Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.686A pdb=" N ILE H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'H' and resid 75 through 82 removed outlier: 3.592A pdb=" N LEU H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 144 removed outlier: 3.719A pdb=" N ALA H 135 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR H 143 " --> pdb=" O ILE H 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR H 144 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 148 Processing helix chain 'H' and resid 179 through 182 Processing helix chain 'H' and resid 236 through 245 removed outlier: 3.800A pdb=" N LEU H 242 " --> pdb=" O GLU H 238 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU H 244 " --> pdb=" O GLY H 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 259 removed outlier: 4.402A pdb=" N GLN H 251 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA H 259 " --> pdb=" O LYS H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 270 removed outlier: 3.827A pdb=" N LYS H 269 " --> pdb=" O PRO H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 303 removed outlier: 3.683A pdb=" N ARG H 302 " --> pdb=" O LEU H 299 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR H 303 " --> pdb=" O GLN H 300 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 311 Processing sheet with id=AA2, first strand: chain 'A' and resid 245 through 246 removed outlier: 3.652A pdb=" N ALA A 306 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 249 removed outlier: 3.635A pdb=" N TYR A 340 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 448 removed outlier: 6.635A pdb=" N ALA A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS A 436 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 490 through 491 removed outlier: 4.047A pdb=" N TYR A 490 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 569 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER A 584 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE A 571 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 582 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 612 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER A 643 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 152 through 155 removed outlier: 6.572A pdb=" N LYS G 5 " --> pdb=" O VAL G 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 102 through 103 removed outlier: 4.052A pdb=" N PHE G 102 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 118 through 122 Processing sheet with id=AA9, first strand: chain 'F' and resid 97 through 98 removed outlier: 3.679A pdb=" N LEU F 151 " --> pdb=" O PHE F 8 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE F 8 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS F 5 " --> pdb=" O VAL F 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 146 through 149 Processing sheet with id=AB2, first strand: chain 'F' and resid 118 through 123 Processing sheet with id=AB3, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.740A pdb=" N LEU E 151 " --> pdb=" O PHE E 8 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.740A pdb=" N LEU E 151 " --> pdb=" O PHE E 8 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS E 5 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL E 203 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN E 11 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASN E 197 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG E 13 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE E 195 " --> pdb=" O ARG E 13 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 120 through 123 removed outlier: 3.585A pdb=" N GLU E 123 " --> pdb=" O ARG E 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.612A pdb=" N VAL B 158 " --> pdb=" O TYR B 6 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AB8, first strand: chain 'B' and resid 127 through 131 removed outlier: 3.840A pdb=" N VAL B 127 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 149 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 265 through 267 Processing sheet with id=AC1, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AC2, first strand: chain 'H' and resid 227 through 230 Processing sheet with id=AC3, first strand: chain 'H' and resid 37 through 41 Processing sheet with id=AC4, first strand: chain 'H' and resid 184 through 186 Processing sheet with id=AC5, first strand: chain 'H' and resid 211 through 214 removed outlier: 4.204A pdb=" N LYS H 211 " --> pdb=" O SER H 206 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 6.30 Time building geometry restraints manager: 9.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3727 1.32 - 1.45: 5207 1.45 - 1.57: 10720 1.57 - 1.69: 140 1.69 - 1.81: 66 Bond restraints: 19860 Sorted by residual: bond pdb=" C4 ATP A 802 " pdb=" C5 ATP A 802 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.50e+01 bond pdb=" C4 ATP A 803 " pdb=" C5 ATP A 803 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.41e+01 bond pdb=" C5 ATP A 802 " pdb=" C6 ATP A 802 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.11e+01 bond pdb=" C5 ATP A 803 " pdb=" C6 ATP A 803 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.08e+01 bond pdb=" C8 ATP A 803 " pdb=" N7 ATP A 803 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.18e+01 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 96.20 - 104.40: 454 104.40 - 112.60: 9955 112.60 - 120.81: 10576 120.81 - 129.01: 6026 129.01 - 137.21: 122 Bond angle restraints: 27133 Sorted by residual: angle pdb=" PB ATP A 802 " pdb=" O3B ATP A 802 " pdb=" PG ATP A 802 " ideal model delta sigma weight residual 139.87 123.73 16.14 1.00e+00 1.00e+00 2.60e+02 angle pdb=" PA ATP A 802 " pdb=" O3A ATP A 802 " pdb=" PB ATP A 802 " ideal model delta sigma weight residual 136.83 121.65 15.18 1.00e+00 1.00e+00 2.31e+02 angle pdb=" PB ATP A 803 " pdb=" O3B ATP A 803 " pdb=" PG ATP A 803 " ideal model delta sigma weight residual 139.87 126.01 13.86 1.00e+00 1.00e+00 1.92e+02 angle pdb=" PA ATP A 803 " pdb=" O3A ATP A 803 " pdb=" PB ATP A 803 " ideal model delta sigma weight residual 136.83 123.96 12.87 1.00e+00 1.00e+00 1.66e+02 angle pdb=" N ARG H 219 " pdb=" CA ARG H 219 " pdb=" C ARG H 219 " ideal model delta sigma weight residual 111.39 126.13 -14.74 1.38e+00 5.25e-01 1.14e+02 ... (remaining 27128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.35: 11682 32.35 - 64.69: 291 64.69 - 97.04: 35 97.04 - 129.39: 0 129.39 - 161.73: 3 Dihedral angle restraints: 12011 sinusoidal: 5403 harmonic: 6608 Sorted by residual: dihedral pdb=" O4' C N 8 " pdb=" C1' C N 8 " pdb=" N1 C N 8 " pdb=" C2 C N 8 " ideal model delta sinusoidal sigma weight residual -128.00 33.73 -161.73 1 1.70e+01 3.46e-03 6.48e+01 dihedral pdb=" O4' C N 14 " pdb=" C1' C N 14 " pdb=" N1 C N 14 " pdb=" C2 C N 14 " ideal model delta sinusoidal sigma weight residual -128.00 8.67 -136.67 1 1.70e+01 3.46e-03 5.74e+01 dihedral pdb=" CA ASN A 639 " pdb=" C ASN A 639 " pdb=" N GLU A 640 " pdb=" CA GLU A 640 " ideal model delta harmonic sigma weight residual 180.00 142.78 37.22 0 5.00e+00 4.00e-02 5.54e+01 ... (remaining 12008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 2922 0.132 - 0.264: 123 0.264 - 0.396: 13 0.396 - 0.528: 3 0.528 - 0.659: 1 Chirality restraints: 3062 Sorted by residual: chirality pdb=" CA TYR H 218 " pdb=" N TYR H 218 " pdb=" C TYR H 218 " pdb=" CB TYR H 218 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" CA PRO H 160 " pdb=" N PRO H 160 " pdb=" C PRO H 160 " pdb=" CB PRO H 160 " both_signs ideal model delta sigma weight residual False 2.72 2.21 0.50 2.00e-01 2.50e+01 6.35e+00 chirality pdb=" CA TYR B 78 " pdb=" N TYR B 78 " pdb=" C TYR B 78 " pdb=" CB TYR B 78 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.75e+00 ... (remaining 3059 not shown) Planarity restraints: 3243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN H 154 " -0.020 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C ASN H 154 " 0.072 2.00e-02 2.50e+03 pdb=" O ASN H 154 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP H 155 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 163 " 0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C ASN H 163 " -0.068 2.00e-02 2.50e+03 pdb=" O ASN H 163 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS H 164 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 732 " -0.031 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP A 732 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP A 732 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 732 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 732 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 732 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 732 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 732 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 732 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 732 " -0.010 2.00e-02 2.50e+03 ... (remaining 3240 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.86: 6 1.86 - 2.62: 333 2.62 - 3.38: 25599 3.38 - 4.14: 48867 4.14 - 4.90: 88496 Nonbonded interactions: 163301 Sorted by model distance: nonbonded pdb=" NH1 ARG E 81 " pdb=" OE1 GLN E 162 " model vdw 1.102 2.520 nonbonded pdb=" CZ ARG E 81 " pdb=" OE1 GLN E 162 " model vdw 1.434 3.270 nonbonded pdb=" NH1 ARG E 81 " pdb=" CD GLN E 162 " model vdw 1.711 3.350 nonbonded pdb=" CD2 LEU A 749 " pdb=" CD1 ILE E 29 " model vdw 1.748 3.880 nonbonded pdb=" O SER B 264 " pdb=" CE1 PHE B 266 " model vdw 1.804 3.340 ... (remaining 163296 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 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 2 through 159 or (resid 160 and (name N or name CA or name \ C or name O or name CB )) or resid 161 through 217)) selection = (chain 'F' and (resid 2 through 66 or resid 76 through 156 or (resid 157 through \ 158 and (name N or name CA or name C or name O or name CB )) or resid 159 or (r \ esid 160 and (name N or name CA or name C or name O or name CB )) or resid 161 t \ hrough 217)) selection = (chain 'G' and (resid 2 through 66 or resid 76 through 217)) } 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: 0.860 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: 0.150 Extract box with map and model: 0.590 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 63.260 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 0.099 19860 Z= 0.562 Angle : 1.183 20.818 27133 Z= 0.686 Chirality : 0.068 0.659 3062 Planarity : 0.006 0.070 3243 Dihedral : 14.281 161.733 7749 Min Nonbonded Distance : 1.102 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.44 % Favored : 89.43 % Rotamer: Outliers : 1.40 % Allowed : 7.16 % Favored : 91.44 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -5.65 (0.12), residues: 2232 helix: -4.34 (0.08), residues: 787 sheet: -3.24 (0.23), residues: 372 loop : -3.40 (0.14), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.006 TRP A 732 HIS 0.011 0.002 HIS A 695 PHE 0.043 0.004 PHE F 98 TYR 0.031 0.003 TYR A 149 ARG 0.016 0.001 ARG F 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 616 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 TYR cc_start: 0.7350 (m-80) cc_final: 0.6901 (m-80) REVERT: A 205 THR cc_start: 0.8582 (m) cc_final: 0.8334 (p) REVERT: A 384 TYR cc_start: 0.7803 (t80) cc_final: 0.7102 (t80) REVERT: A 415 ASP cc_start: 0.6442 (p0) cc_final: 0.5815 (t0) REVERT: A 490 TYR cc_start: 0.7375 (t80) cc_final: 0.7060 (t80) REVERT: A 521 ASP cc_start: 0.8128 (m-30) cc_final: 0.7773 (m-30) REVERT: D 14 GLU cc_start: 0.7780 (tt0) cc_final: 0.7450 (tt0) REVERT: D 34 PHE cc_start: 0.8298 (m-10) cc_final: 0.8043 (m-80) REVERT: D 63 LEU cc_start: 0.7572 (pt) cc_final: 0.6975 (tt) REVERT: D 85 ASP cc_start: 0.6754 (t70) cc_final: 0.5413 (t0) REVERT: D 89 LYS cc_start: 0.8022 (mptm) cc_final: 0.7763 (mptp) REVERT: D 91 GLN cc_start: 0.7418 (pm20) cc_final: 0.6851 (pm20) REVERT: G 137 GLN cc_start: 0.7877 (mt0) cc_final: 0.7635 (mt0) REVERT: F 62 LYS cc_start: 0.8628 (mttt) cc_final: 0.8423 (mmtt) REVERT: F 74 ASP cc_start: 0.8182 (t70) cc_final: 0.7936 (t70) REVERT: F 137 GLN cc_start: 0.8182 (mt0) cc_final: 0.7684 (mt0) REVERT: E 9 SER cc_start: 0.8450 (m) cc_final: 0.8246 (t) REVERT: E 39 ASP cc_start: 0.8310 (t0) cc_final: 0.8092 (t0) REVERT: E 88 ASP cc_start: 0.7543 (t0) cc_final: 0.7268 (t0) REVERT: E 144 ASN cc_start: 0.7770 (p0) cc_final: 0.7534 (m110) REVERT: E 167 PHE cc_start: 0.7379 (m-10) cc_final: 0.6651 (m-80) REVERT: B 229 MET cc_start: 0.8543 (mmt) cc_final: 0.8297 (mmm) REVERT: B 276 ASP cc_start: 0.7980 (t0) cc_final: 0.6507 (t0) REVERT: B 278 ARG cc_start: 0.8014 (ptp-170) cc_final: 0.7122 (ptp-170) REVERT: H 22 ASN cc_start: 0.8292 (t0) cc_final: 0.7877 (t0) REVERT: H 86 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.5031 (mp0) REVERT: H 89 PHE cc_start: 0.6518 (m-80) cc_final: 0.5500 (m-80) outliers start: 26 outliers final: 11 residues processed: 637 average time/residue: 0.3909 time to fit residues: 349.4046 Evaluate side-chains 324 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 312 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain B residue 270 PHE Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 166 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 3.9990 chunk 172 optimal weight: 0.0170 chunk 95 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 178 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 207 optimal weight: 0.2980 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 ASN A 312 ASN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS A 504 ASN A 598 ASN A 639 ASN A 661 ASN A 675 ASN A 735 ASN G 85 ASN G 134 ASN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 197 ASN F 33 ASN F 43 ASN F 144 ASN F 213 ASN E 134 ASN ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS B 144 GLN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN B 208 HIS B 284 HIS B 288 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 ASN H 338 ASN H 339 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19860 Z= 0.181 Angle : 0.698 12.935 27133 Z= 0.365 Chirality : 0.044 0.321 3062 Planarity : 0.005 0.069 3243 Dihedral : 15.226 164.212 3557 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.42 % Favored : 91.53 % Rotamer: Outliers : 3.82 % Allowed : 13.08 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.45 (0.14), residues: 2232 helix: -2.78 (0.13), residues: 821 sheet: -2.82 (0.26), residues: 324 loop : -3.11 (0.15), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 732 HIS 0.005 0.001 HIS A 695 PHE 0.031 0.002 PHE A 591 TYR 0.030 0.002 TYR C 59 ARG 0.008 0.001 ARG G 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 399 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 LEU cc_start: 0.8602 (tp) cc_final: 0.8265 (tp) REVERT: A 300 TYR cc_start: 0.7219 (t80) cc_final: 0.6824 (t80) REVERT: A 373 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8210 (ttt) REVERT: A 384 TYR cc_start: 0.7681 (t80) cc_final: 0.7344 (t80) REVERT: A 415 ASP cc_start: 0.6589 (p0) cc_final: 0.5691 (t0) REVERT: A 490 TYR cc_start: 0.7020 (t80) cc_final: 0.6792 (t80) REVERT: A 521 ASP cc_start: 0.7795 (m-30) cc_final: 0.7421 (m-30) REVERT: A 552 MET cc_start: 0.8637 (mmp) cc_final: 0.8374 (mmp) REVERT: D 34 PHE cc_start: 0.8361 (m-10) cc_final: 0.8078 (m-80) REVERT: D 63 LEU cc_start: 0.7458 (pt) cc_final: 0.6779 (tt) REVERT: D 89 LYS cc_start: 0.7896 (mptm) cc_final: 0.7622 (mttm) REVERT: C 87 ILE cc_start: 0.8509 (pt) cc_final: 0.8246 (pt) REVERT: G 86 SER cc_start: 0.8274 (p) cc_final: 0.7973 (t) REVERT: F 74 ASP cc_start: 0.8167 (t70) cc_final: 0.7829 (t70) REVERT: E 9 SER cc_start: 0.8204 (m) cc_final: 0.7885 (t) REVERT: E 167 PHE cc_start: 0.7411 (m-10) cc_final: 0.6828 (m-80) REVERT: B 47 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7973 (t0) REVERT: H 22 ASN cc_start: 0.8336 (t0) cc_final: 0.8016 (t0) REVERT: H 161 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7362 (ptpp) outliers start: 71 outliers final: 28 residues processed: 444 average time/residue: 0.3523 time to fit residues: 228.8031 Evaluate side-chains 336 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 305 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 78 TYR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 172 optimal weight: 0.1980 chunk 140 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 207 optimal weight: 0.0770 chunk 224 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 166 optimal weight: 0.0670 overall best weight: 1.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 ASN A 661 ASN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN B 288 ASN H 69 ASN H 72 ASN H 151 ASN ** H 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19860 Z= 0.185 Angle : 0.642 12.909 27133 Z= 0.334 Chirality : 0.042 0.285 3062 Planarity : 0.004 0.040 3243 Dihedral : 14.985 165.672 3543 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.09 % Favored : 90.86 % Rotamer: Outliers : 3.93 % Allowed : 15.88 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.15), residues: 2232 helix: -1.68 (0.16), residues: 815 sheet: -2.49 (0.27), residues: 321 loop : -2.88 (0.16), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 732 HIS 0.006 0.001 HIS A 695 PHE 0.030 0.001 PHE A 348 TYR 0.021 0.002 TYR C 68 ARG 0.005 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 342 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6709 (mm) REVERT: A 300 TYR cc_start: 0.7241 (t80) cc_final: 0.6901 (t80) REVERT: A 373 MET cc_start: 0.8449 (ttt) cc_final: 0.8156 (ttt) REVERT: A 384 TYR cc_start: 0.7792 (t80) cc_final: 0.7421 (t80) REVERT: A 395 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7896 (mtpt) REVERT: A 415 ASP cc_start: 0.6587 (p0) cc_final: 0.5756 (t0) REVERT: A 460 LYS cc_start: 0.8431 (mptm) cc_final: 0.8007 (tppt) REVERT: A 490 TYR cc_start: 0.7115 (t80) cc_final: 0.6808 (t80) REVERT: A 521 ASP cc_start: 0.7848 (m-30) cc_final: 0.7417 (m-30) REVERT: A 552 MET cc_start: 0.8674 (mmp) cc_final: 0.8402 (mmp) REVERT: A 573 TYR cc_start: 0.6674 (t80) cc_final: 0.6243 (t80) REVERT: D 55 LYS cc_start: 0.8433 (mptt) cc_final: 0.8129 (mptt) REVERT: D 63 LEU cc_start: 0.7316 (pt) cc_final: 0.6741 (tt) REVERT: D 91 GLN cc_start: 0.7484 (mp10) cc_final: 0.7243 (mp10) REVERT: C 87 ILE cc_start: 0.8485 (pt) cc_final: 0.8233 (pt) REVERT: C 110 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7674 (mtt90) REVERT: G 67 LYS cc_start: 0.8531 (mmtt) cc_final: 0.8205 (mtpp) REVERT: G 103 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8513 (tp) REVERT: G 181 TYR cc_start: 0.8114 (p90) cc_final: 0.7770 (p90) REVERT: F 74 ASP cc_start: 0.8171 (t70) cc_final: 0.7747 (t70) REVERT: F 143 ARG cc_start: 0.7885 (ttt90) cc_final: 0.7659 (ttt90) REVERT: E 9 SER cc_start: 0.8204 (m) cc_final: 0.7880 (t) REVERT: E 123 GLU cc_start: 0.7102 (tt0) cc_final: 0.6898 (mt-10) REVERT: B 47 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7988 (t0) REVERT: H 22 ASN cc_start: 0.8276 (t0) cc_final: 0.7870 (t0) outliers start: 73 outliers final: 42 residues processed: 393 average time/residue: 0.3391 time to fit residues: 197.6021 Evaluate side-chains 341 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 295 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 284 SER Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 220 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN D 42 ASN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 ASN H 72 ASN H 80 ASN ** H 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19860 Z= 0.351 Angle : 0.710 12.937 27133 Z= 0.370 Chirality : 0.046 0.288 3062 Planarity : 0.004 0.048 3243 Dihedral : 15.073 163.701 3536 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.44 % Favored : 89.52 % Rotamer: Outliers : 5.01 % Allowed : 17.06 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.16), residues: 2232 helix: -1.16 (0.17), residues: 806 sheet: -2.43 (0.27), residues: 321 loop : -2.77 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 732 HIS 0.008 0.001 HIS A 55 PHE 0.024 0.002 PHE A 655 TYR 0.022 0.002 TYR A 275 ARG 0.005 0.001 ARG F 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 304 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6856 (mm) REVERT: A 276 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8724 (mp) REVERT: A 300 TYR cc_start: 0.7256 (t80) cc_final: 0.6978 (t80) REVERT: A 373 MET cc_start: 0.8500 (ttt) cc_final: 0.8038 (ttt) REVERT: A 384 TYR cc_start: 0.7891 (t80) cc_final: 0.6949 (t80) REVERT: A 415 ASP cc_start: 0.6707 (p0) cc_final: 0.5685 (t0) REVERT: A 521 ASP cc_start: 0.7882 (m-30) cc_final: 0.7469 (m-30) REVERT: A 573 TYR cc_start: 0.6679 (t80) cc_final: 0.6130 (t80) REVERT: A 604 ASN cc_start: 0.7913 (t0) cc_final: 0.7507 (t0) REVERT: C 87 ILE cc_start: 0.8794 (pt) cc_final: 0.8577 (pt) REVERT: C 110 ARG cc_start: 0.8360 (mtm-85) cc_final: 0.8041 (mtm-85) REVERT: G 67 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8317 (mtpp) REVERT: F 74 ASP cc_start: 0.8261 (t70) cc_final: 0.7755 (t0) REVERT: F 143 ARG cc_start: 0.8030 (ttt90) cc_final: 0.7752 (ttt90) REVERT: E 9 SER cc_start: 0.8301 (m) cc_final: 0.7876 (p) REVERT: E 24 ASP cc_start: 0.7052 (OUTLIER) cc_final: 0.6511 (p0) REVERT: H 22 ASN cc_start: 0.8410 (t0) cc_final: 0.8106 (t0) REVERT: H 280 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7534 (mp) outliers start: 93 outliers final: 63 residues processed: 370 average time/residue: 0.3391 time to fit residues: 186.9798 Evaluate side-chains 338 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 271 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 181 TYR Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 280 LEU Chi-restraints excluded: chain H residue 284 SER Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 164 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN D 76 GLN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19860 Z= 0.337 Angle : 0.705 12.903 27133 Z= 0.365 Chirality : 0.045 0.292 3062 Planarity : 0.004 0.038 3243 Dihedral : 15.104 161.665 3536 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.53 % Favored : 89.43 % Rotamer: Outliers : 5.44 % Allowed : 18.62 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.17), residues: 2232 helix: -0.91 (0.17), residues: 813 sheet: -2.34 (0.26), residues: 332 loop : -2.76 (0.17), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 732 HIS 0.008 0.001 HIS A 55 PHE 0.022 0.002 PHE A 655 TYR 0.020 0.002 TYR D 59 ARG 0.005 0.001 ARG C 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 294 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7002 (mm) REVERT: A 276 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8736 (mp) REVERT: A 300 TYR cc_start: 0.7360 (t80) cc_final: 0.7088 (t80) REVERT: A 373 MET cc_start: 0.8534 (ttt) cc_final: 0.7997 (ttt) REVERT: A 415 ASP cc_start: 0.6904 (p0) cc_final: 0.5869 (t0) REVERT: A 521 ASP cc_start: 0.7985 (m-30) cc_final: 0.7576 (m-30) REVERT: A 573 TYR cc_start: 0.6757 (t80) cc_final: 0.6231 (t80) REVERT: A 604 ASN cc_start: 0.7968 (t0) cc_final: 0.7482 (t0) REVERT: C 68 TYR cc_start: 0.8414 (t80) cc_final: 0.8211 (t80) REVERT: C 110 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.8044 (mtm-85) REVERT: G 67 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8314 (mtpp) REVERT: F 74 ASP cc_start: 0.8255 (t70) cc_final: 0.7772 (t0) REVERT: E 9 SER cc_start: 0.8249 (m) cc_final: 0.7845 (p) REVERT: E 24 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6232 (p0) REVERT: E 130 THR cc_start: 0.8392 (m) cc_final: 0.8157 (p) REVERT: H 22 ASN cc_start: 0.8389 (t0) cc_final: 0.8031 (t0) REVERT: H 50 MET cc_start: 0.7083 (ttp) cc_final: 0.6875 (ttp) outliers start: 101 outliers final: 70 residues processed: 370 average time/residue: 0.3327 time to fit residues: 184.3470 Evaluate side-chains 345 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 272 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 25 ARG Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 25 LYS Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 416 GLN A 504 ASN A 639 ASN D 42 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19860 Z= 0.201 Angle : 0.645 12.265 27133 Z= 0.332 Chirality : 0.042 0.287 3062 Planarity : 0.003 0.038 3243 Dihedral : 14.992 165.338 3536 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.41 % Favored : 90.55 % Rotamer: Outliers : 4.47 % Allowed : 19.59 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.70 (0.17), residues: 2232 helix: -0.55 (0.18), residues: 808 sheet: -2.27 (0.27), residues: 337 loop : -2.63 (0.17), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 732 HIS 0.008 0.001 HIS A 55 PHE 0.030 0.001 PHE A 348 TYR 0.024 0.002 TYR A 275 ARG 0.004 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 305 time to evaluate : 2.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6926 (mm) REVERT: A 276 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8735 (mp) REVERT: A 373 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7984 (ttt) REVERT: A 415 ASP cc_start: 0.6806 (p0) cc_final: 0.5822 (t0) REVERT: A 521 ASP cc_start: 0.7973 (m-30) cc_final: 0.7588 (m-30) REVERT: A 573 TYR cc_start: 0.6666 (t80) cc_final: 0.6133 (t80) REVERT: A 604 ASN cc_start: 0.7931 (t0) cc_final: 0.7438 (t0) REVERT: D 4 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8421 (pp) REVERT: C 21 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: C 85 ASP cc_start: 0.8360 (p0) cc_final: 0.7911 (p0) REVERT: C 110 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.7754 (mtm110) REVERT: G 67 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8284 (mtpp) REVERT: F 74 ASP cc_start: 0.8240 (t70) cc_final: 0.7776 (t0) REVERT: E 9 SER cc_start: 0.8208 (m) cc_final: 0.7813 (p) REVERT: E 24 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6268 (p0) REVERT: E 130 THR cc_start: 0.8403 (m) cc_final: 0.8187 (p) REVERT: B 47 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.8042 (t0) REVERT: H 22 ASN cc_start: 0.8361 (t0) cc_final: 0.8139 (t0) outliers start: 83 outliers final: 54 residues processed: 367 average time/residue: 0.3374 time to fit residues: 185.7598 Evaluate side-chains 336 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 275 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 639 ASN A 661 ASN D 42 ASN F 11 GLN E 19 HIS ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19860 Z= 0.266 Angle : 0.676 15.063 27133 Z= 0.346 Chirality : 0.044 0.288 3062 Planarity : 0.004 0.034 3243 Dihedral : 14.971 166.303 3536 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.35 % Favored : 89.61 % Rotamer: Outliers : 4.20 % Allowed : 20.45 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.60 (0.17), residues: 2232 helix: -0.42 (0.18), residues: 810 sheet: -2.19 (0.27), residues: 336 loop : -2.62 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 732 HIS 0.007 0.001 HIS A 55 PHE 0.026 0.002 PHE B 64 TYR 0.023 0.002 TYR A 275 ARG 0.005 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 277 time to evaluate : 2.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7321 (t60) cc_final: 0.6692 (t60) REVERT: A 130 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6979 (mm) REVERT: A 276 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8723 (mp) REVERT: A 373 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.7988 (ttt) REVERT: A 521 ASP cc_start: 0.7995 (m-30) cc_final: 0.7552 (m-30) REVERT: A 552 MET cc_start: 0.8631 (mmp) cc_final: 0.8395 (mmp) REVERT: A 573 TYR cc_start: 0.6653 (t80) cc_final: 0.6142 (t80) REVERT: A 604 ASN cc_start: 0.7964 (t0) cc_final: 0.7490 (t0) REVERT: D 4 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8417 (pp) REVERT: C 21 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6902 (pm20) REVERT: C 103 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7510 (tm-30) REVERT: C 110 ARG cc_start: 0.8353 (mtm-85) cc_final: 0.8061 (mtm-85) REVERT: G 67 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8289 (mtpp) REVERT: F 74 ASP cc_start: 0.8275 (t70) cc_final: 0.7799 (t0) REVERT: E 9 SER cc_start: 0.8209 (m) cc_final: 0.7805 (p) REVERT: E 24 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6205 (p0) REVERT: E 130 THR cc_start: 0.8410 (m) cc_final: 0.8200 (p) REVERT: B 47 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.8041 (t0) REVERT: B 91 LYS cc_start: 0.8289 (mmtm) cc_final: 0.7973 (mptt) REVERT: H 241 ARG cc_start: 0.7947 (mmp80) cc_final: 0.7741 (mmp80) outliers start: 78 outliers final: 60 residues processed: 329 average time/residue: 0.3404 time to fit residues: 166.3960 Evaluate side-chains 328 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 261 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.3980 chunk 87 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 20 optimal weight: 30.0000 chunk 172 optimal weight: 5.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 ASN A 699 ASN D 42 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19860 Z= 0.258 Angle : 0.669 15.270 27133 Z= 0.343 Chirality : 0.044 0.288 3062 Planarity : 0.004 0.034 3243 Dihedral : 14.956 166.497 3534 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.90 % Favored : 90.05 % Rotamer: Outliers : 4.57 % Allowed : 19.97 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.55 (0.17), residues: 2232 helix: -0.30 (0.18), residues: 823 sheet: -2.16 (0.27), residues: 346 loop : -2.70 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 732 HIS 0.007 0.001 HIS A 55 PHE 0.019 0.001 PHE B 64 TYR 0.029 0.002 TYR A 490 ARG 0.005 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 278 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7052 (mm) REVERT: A 276 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8742 (mp) REVERT: A 373 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7989 (ttt) REVERT: A 521 ASP cc_start: 0.7970 (m-30) cc_final: 0.7571 (m-30) REVERT: A 552 MET cc_start: 0.8653 (mmp) cc_final: 0.8422 (mmp) REVERT: A 573 TYR cc_start: 0.6666 (t80) cc_final: 0.6173 (t80) REVERT: A 604 ASN cc_start: 0.8010 (t0) cc_final: 0.7541 (t0) REVERT: D 4 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8418 (pp) REVERT: C 21 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6966 (pm20) REVERT: C 85 ASP cc_start: 0.8266 (p0) cc_final: 0.7558 (p0) REVERT: C 103 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7466 (tm-30) REVERT: C 110 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.8068 (mtm-85) REVERT: G 67 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8284 (mtpp) REVERT: F 74 ASP cc_start: 0.8294 (t70) cc_final: 0.7825 (t0) REVERT: E 24 ASP cc_start: 0.6944 (OUTLIER) cc_final: 0.6343 (p0) REVERT: B 47 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.8010 (t0) REVERT: B 91 LYS cc_start: 0.8271 (mmtm) cc_final: 0.7934 (mptt) REVERT: B 286 VAL cc_start: 0.8344 (t) cc_final: 0.8143 (t) outliers start: 85 outliers final: 67 residues processed: 336 average time/residue: 0.3315 time to fit residues: 167.9580 Evaluate side-chains 333 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 259 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 196 GLU Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 192 optimal weight: 7.9990 chunk 204 optimal weight: 0.0670 chunk 123 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19860 Z= 0.201 Angle : 0.645 15.126 27133 Z= 0.330 Chirality : 0.042 0.286 3062 Planarity : 0.003 0.035 3243 Dihedral : 14.889 168.613 3534 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.72 % Favored : 90.23 % Rotamer: Outliers : 4.36 % Allowed : 20.61 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.39 (0.17), residues: 2232 helix: -0.10 (0.19), residues: 809 sheet: -2.12 (0.27), residues: 346 loop : -2.62 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 732 HIS 0.008 0.001 HIS A 55 PHE 0.015 0.001 PHE B 64 TYR 0.030 0.002 TYR A 490 ARG 0.004 0.000 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 277 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7025 (mm) REVERT: A 276 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8730 (mp) REVERT: A 365 GLN cc_start: 0.8237 (mp-120) cc_final: 0.7907 (mp10) REVERT: A 373 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7964 (ttt) REVERT: A 521 ASP cc_start: 0.7986 (m-30) cc_final: 0.7583 (m-30) REVERT: A 552 MET cc_start: 0.8647 (mmp) cc_final: 0.8394 (mmp) REVERT: A 573 TYR cc_start: 0.6635 (t80) cc_final: 0.6145 (t80) REVERT: A 604 ASN cc_start: 0.7988 (t0) cc_final: 0.7461 (t0) REVERT: D 4 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8400 (pp) REVERT: C 21 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6987 (pm20) REVERT: C 85 ASP cc_start: 0.8112 (p0) cc_final: 0.7559 (p0) REVERT: C 103 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7370 (tm-30) REVERT: C 110 ARG cc_start: 0.8349 (mtm-85) cc_final: 0.7847 (mtm110) REVERT: G 67 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8295 (mtpp) REVERT: G 137 GLN cc_start: 0.7813 (mt0) cc_final: 0.7453 (mm-40) REVERT: F 74 ASP cc_start: 0.8277 (t70) cc_final: 0.7822 (t0) REVERT: E 24 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.6302 (p0) REVERT: B 47 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.8030 (t0) outliers start: 81 outliers final: 65 residues processed: 334 average time/residue: 0.3303 time to fit residues: 165.5484 Evaluate side-chains 330 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 258 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 ASN D 42 ASN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19860 Z= 0.180 Angle : 0.639 14.845 27133 Z= 0.326 Chirality : 0.042 0.282 3062 Planarity : 0.003 0.035 3243 Dihedral : 14.805 169.948 3534 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.36 % Favored : 90.59 % Rotamer: Outliers : 3.88 % Allowed : 21.64 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.24 (0.17), residues: 2232 helix: 0.05 (0.19), residues: 811 sheet: -2.03 (0.27), residues: 346 loop : -2.57 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 38 HIS 0.008 0.001 HIS A 55 PHE 0.024 0.001 PHE B 64 TYR 0.022 0.002 TYR D 68 ARG 0.004 0.000 ARG F 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 279 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6997 (mm) REVERT: A 157 LYS cc_start: 0.7587 (mmtt) cc_final: 0.7219 (mmtt) REVERT: A 276 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8707 (mp) REVERT: A 365 GLN cc_start: 0.8157 (mp-120) cc_final: 0.7867 (mp10) REVERT: A 373 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7954 (ttt) REVERT: A 521 ASP cc_start: 0.7900 (m-30) cc_final: 0.7454 (m-30) REVERT: A 573 TYR cc_start: 0.6633 (t80) cc_final: 0.6149 (t80) REVERT: A 604 ASN cc_start: 0.7979 (t0) cc_final: 0.7435 (t0) REVERT: C 21 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: C 80 GLU cc_start: 0.6915 (tp30) cc_final: 0.6661 (tp30) REVERT: C 85 ASP cc_start: 0.8118 (p0) cc_final: 0.7586 (p0) REVERT: C 103 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7359 (tm-30) REVERT: C 110 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7798 (mtm110) REVERT: G 67 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8253 (mtpp) REVERT: F 74 ASP cc_start: 0.8319 (t70) cc_final: 0.7919 (t70) REVERT: E 9 SER cc_start: 0.8146 (m) cc_final: 0.7741 (p) REVERT: E 24 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6628 (p0) REVERT: B 6 TYR cc_start: 0.7380 (m-10) cc_final: 0.6709 (m-10) REVERT: H 241 ARG cc_start: 0.8076 (mmp80) cc_final: 0.7842 (mmp80) outliers start: 72 outliers final: 57 residues processed: 326 average time/residue: 0.3117 time to fit residues: 153.9393 Evaluate side-chains 321 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 259 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 21 GLU Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain H residue 24 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 166 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** G 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 HIS B 273 GLN H 69 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.128909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.108578 restraints weight = 35815.593| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.11 r_work: 0.3294 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19860 Z= 0.171 Angle : 0.640 14.534 27133 Z= 0.325 Chirality : 0.042 0.282 3062 Planarity : 0.003 0.034 3243 Dihedral : 14.732 171.440 3534 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.27 % Favored : 90.68 % Rotamer: Outliers : 3.50 % Allowed : 22.23 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.16 (0.18), residues: 2232 helix: 0.14 (0.19), residues: 814 sheet: -1.95 (0.27), residues: 354 loop : -2.56 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 38 HIS 0.008 0.001 HIS A 55 PHE 0.019 0.001 PHE A 548 TYR 0.021 0.001 TYR F 181 ARG 0.004 0.000 ARG F 81 =============================================================================== Job complete usr+sys time: 4428.68 seconds wall clock time: 80 minutes 1.51 seconds (4801.51 seconds total)