Starting phenix.real_space_refine on Sun Mar 17 23:44:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/03_2024/6ig0_9660_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/03_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_9660/03_2024/6ig0_9660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/03_2024/6ig0_9660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/03_2024/6ig0_9660_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ig0_9660/03_2024/6ig0_9660_updated.pdb" } 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.56, per 1000 atoms: 0.55 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: 8.13 Conformation dependent library (CDL) restraints added in 3.4 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... running ksdssp... Secondary structure from input PDB file: 82 helices and 21 sheets defined 32.9% alpha, 8.1% beta 20 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 8.64 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 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 18 through 24 removed outlier: 3.750A pdb=" N ARG A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 38 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 46 through 53 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 70 through 80 removed outlier: 3.588A pdb=" N ILE A 75 " --> pdb=" O TYR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 146 through 159 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 172 through 183 removed outlier: 3.628A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N SER A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N PHE A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 219 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 232 through 237 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 266 through 290 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 314 through 335 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 364 through 367 No H-bonds generated for 'chain 'A' and resid 364 through 367' Processing helix chain 'A' and resid 369 through 377 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.663A pdb=" N LEU A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 removed outlier: 3.708A pdb=" N TYR A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 542 through 558 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 560 through 563 No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 585 through 602 removed outlier: 3.791A pdb=" N LYS A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 638 removed outlier: 3.633A pdb=" N GLN A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 638 " --> pdb=" O GLU A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 657 No H-bonds generated for 'chain 'A' and resid 655 through 657' Processing helix chain 'A' and resid 666 through 675 removed outlier: 3.563A pdb=" N ASN A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 693 Processing helix chain 'A' and resid 697 through 713 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 719 through 729 removed outlier: 4.091A pdb=" N LEU A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 752 Processing helix chain 'D' and resid 9 through 19 Processing helix chain 'D' and resid 37 through 51 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) Processing helix chain 'D' and resid 53 through 56 No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 62 through 79 removed outlier: 4.190A pdb=" N ILE D 66 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 67 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN D 72 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE D 73 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN D 76 " --> pdb=" O PHE D 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 79 " --> pdb=" O GLN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.630A pdb=" N GLU D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 102 through 121 Processing helix chain 'C' and resid 9 through 19 Processing helix chain 'C' and resid 37 through 51 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) Processing helix chain 'C' and resid 53 through 56 No H-bonds generated for 'chain 'C' and resid 53 through 56' Processing helix chain 'C' and resid 62 through 79 removed outlier: 4.190A pdb=" N ILE C 66 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA C 67 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C 72 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N PHE C 73 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN C 76 " --> pdb=" O PHE C 73 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG C 79 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.629A pdb=" N GLU C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 102 through 121 Processing helix chain 'G' and resid 49 through 58 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 106 through 111 Processing helix chain 'G' and resid 162 through 179 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) removed outlier: 4.320A pdb=" N LEU G 179 " --> pdb=" O LYS G 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 60 Processing helix chain 'F' and resid 72 through 74 No H-bonds generated for 'chain 'F' and resid 72 through 74' Processing helix chain 'F' and resid 79 through 82 No H-bonds generated for 'chain 'F' and resid 79 through 82' Processing helix chain 'F' and resid 106 through 111 removed outlier: 3.644A pdb=" N ASP F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 177 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) Processing helix chain 'F' and resid 186 through 188 No H-bonds generated for 'chain 'F' and resid 186 through 188' Processing helix chain 'F' and resid 213 through 216 No H-bonds generated for 'chain 'F' and resid 213 through 216' Processing helix chain 'E' and resid 49 through 53 Processing helix chain 'E' and resid 55 through 63 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 80 through 83 No H-bonds generated for 'chain 'E' and resid 80 through 83' Processing helix chain 'E' and resid 108 through 112 Processing helix chain 'E' and resid 163 through 170 removed outlier: 3.973A pdb=" N VAL E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 210 through 216 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) Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 90 through 99 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 111 through 116 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 198 through 201 No H-bonds generated for 'chain 'B' and resid 198 through 201' Processing helix chain 'B' and resid 225 through 231 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) No H-bonds generated for 'chain 'B' and resid 225 through 231' Processing helix chain 'H' and resid 43 through 51 Processing helix chain 'H' and resid 56 through 63 Processing helix chain 'H' and resid 70 through 73 Processing helix chain 'H' and resid 76 through 81 Processing helix chain 'H' and resid 129 through 143 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) Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing helix chain 'H' and resid 180 through 183 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 237 through 258 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) removed outlier: 3.868A pdb=" N LEU H 246 " --> pdb=" O LEU H 242 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLY H 247 " --> pdb=" O ILE H 243 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS H 248 " --> pdb=" O GLU H 244 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLN H 251 " --> pdb=" O GLY H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 269 No H-bonds generated for 'chain 'H' and resid 267 through 269' Processing helix chain 'H' and resid 299 through 302 removed outlier: 3.683A pdb=" N ARG H 302 " --> pdb=" O LEU H 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 299 through 302' Processing helix chain 'H' and resid 339 through 341 No H-bonds generated for 'chain 'H' and resid 339 through 341' Processing sheet with id= A, first strand: chain 'A' and resid 241 through 245 Processing sheet with id= B, first strand: chain 'A' and resid 452 through 456 removed outlier: 3.980A pdb=" N HIS A 436 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N THR A 483 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 652 through 654 removed outlier: 7.496A pdb=" N ALA A 611 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 612 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 582 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE A 571 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER A 584 " --> pdb=" O LEU A 569 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 569 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'G' and resid 152 through 155 removed outlier: 6.023A pdb=" N LYS G 7 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR G 202 " --> pdb=" O LYS G 7 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 146 through 149 Processing sheet with id= F, first strand: chain 'G' and resid 118 through 122 Processing sheet with id= G, first strand: chain 'F' and resid 4 through 6 Processing sheet with id= H, first strand: chain 'F' and resid 146 through 149 Processing sheet with id= I, first strand: chain 'F' and resid 118 through 123 Processing sheet with id= J, first strand: chain 'E' and resid 199 through 202 removed outlier: 3.740A pdb=" N LEU E 151 " --> pdb=" O PHE E 8 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 11 through 14 Processing sheet with id= L, 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= M, first strand: chain 'B' and resid 6 through 9 Processing sheet with id= N, first strand: chain 'B' and resid 71 through 73 Processing sheet with id= O, first strand: chain 'B' and resid 128 through 131 Processing sheet with id= P, first strand: chain 'B' and resid 265 through 267 Processing sheet with id= Q, first strand: chain 'H' and resid 10 through 13 Processing sheet with id= R, first strand: chain 'H' and resid 37 through 41 Processing sheet with id= S, first strand: chain 'H' and resid 184 through 186 Processing sheet with id= T, 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) Processing sheet with id= U, first strand: chain 'H' and resid 276 through 279 453 hydrogen bonds defined for protein. 1236 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: 5.92 Time building geometry restraints manager: 8.70 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: 343 2.62 - 3.38: 25712 3.38 - 4.14: 49123 4.14 - 4.90: 88617 Nonbonded interactions: 163801 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 163796 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.910 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 59.800 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.270 ------------------------------------------------------------------------------- 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= 0.567 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 : 2.200 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: 0.3978 time to fit residues: 354.7094 Evaluate side-chains 324 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 312 time to evaluate : 2.110 ------------------------------------------------------------------------------- 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: 2.9990 chunk 172 optimal weight: 0.0170 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 178 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 207 optimal weight: 0.2980 overall best weight: 0.6422 ------------------------------------------------------------------------------- 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 661 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS B 288 ASN H 154 ASN H 338 ASN H 339 HIS ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19860 Z= 0.179 Angle : 0.684 13.311 27133 Z= 0.356 Chirality : 0.043 0.304 3062 Planarity : 0.004 0.065 3243 Dihedral : 15.206 163.794 3557 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.33 % Favored : 91.58 % Rotamer: Outliers : 3.77 % Allowed : 13.35 % Favored : 82.88 % 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: -4.61 (0.14), residues: 2232 helix: -2.97 (0.13), residues: 805 sheet: -2.97 (0.26), residues: 315 loop : -3.15 (0.15), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 732 HIS 0.006 0.001 HIS A 695 PHE 0.029 0.002 PHE A 591 TYR 0.028 0.002 TYR C 59 ARG 0.006 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 464 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 394 time to evaluate : 1.927 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: symmetry clash REVERT: A 198 LEU cc_start: 0.8616 (tp) cc_final: 0.8279 (tp) REVERT: A 235 PHE cc_start: 0.7227 (t80) cc_final: 0.6939 (t80) REVERT: A 373 MET cc_start: 0.8392 (ttt) cc_final: 0.8141 (ttt) REVERT: A 384 TYR cc_start: 0.7723 (t80) cc_final: 0.7419 (t80) REVERT: A 415 ASP cc_start: 0.6523 (p0) cc_final: 0.5596 (t0) REVERT: A 490 TYR cc_start: 0.7071 (t80) cc_final: 0.6805 (t80) REVERT: A 521 ASP cc_start: 0.7842 (m-30) cc_final: 0.7476 (m-30) REVERT: A 552 MET cc_start: 0.8641 (mmp) cc_final: 0.8340 (mmp) REVERT: A 686 TYR cc_start: 0.7848 (t80) cc_final: 0.7577 (t80) REVERT: D 34 PHE cc_start: 0.8309 (m-10) cc_final: 0.8047 (m-80) REVERT: D 63 LEU cc_start: 0.7508 (pt) cc_final: 0.6861 (tt) REVERT: D 89 LYS cc_start: 0.7912 (mptm) cc_final: 0.7657 (mttm) REVERT: C 87 ILE cc_start: 0.8620 (pt) cc_final: 0.8379 (pt) REVERT: G 86 SER cc_start: 0.8283 (p) cc_final: 0.7964 (t) REVERT: G 103 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8768 (tp) REVERT: G 122 PHE cc_start: 0.7576 (m-80) cc_final: 0.7323 (m-80) REVERT: G 181 TYR cc_start: 0.8089 (p90) cc_final: 0.7744 (p90) REVERT: F 74 ASP cc_start: 0.8176 (t70) cc_final: 0.7822 (t70) REVERT: E 9 SER cc_start: 0.7963 (m) cc_final: 0.7696 (t) REVERT: E 167 PHE cc_start: 0.7209 (m-10) cc_final: 0.6679 (m-80) REVERT: H 22 ASN cc_start: 0.8322 (t0) cc_final: 0.8002 (t0) REVERT: H 50 MET cc_start: 0.7333 (ttp) cc_final: 0.7086 (ttp) REVERT: H 83 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7033 (mmm160) REVERT: H 161 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7361 (ptpp) outliers start: 70 outliers final: 32 residues processed: 438 average time/residue: 0.3654 time to fit residues: 236.2979 Evaluate side-chains 338 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 303 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 332 LEU 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 72 GLN Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 180 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 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 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 83 ARG Chi-restraints excluded: chain H residue 86 GLU Chi-restraints excluded: chain H residue 131 SER 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 204 ASP Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 172 optimal weight: 0.0010 chunk 140 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 224 optimal weight: 10.0000 chunk 184 optimal weight: 0.6980 chunk 205 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 166 optimal weight: 0.2980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN A 661 ASN A 675 ASN G 159 ASN F 197 ASN E 197 ASN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN H 151 ASN ** H 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 339 HIS ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19860 Z= 0.150 Angle : 0.618 12.920 27133 Z= 0.317 Chirality : 0.041 0.283 3062 Planarity : 0.003 0.037 3243 Dihedral : 14.901 165.172 3547 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.42 % Favored : 91.53 % Rotamer: Outliers : 3.66 % Allowed : 16.47 % Favored : 79.87 % 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: -3.72 (0.15), residues: 2232 helix: -1.84 (0.16), residues: 802 sheet: -2.59 (0.27), residues: 312 loop : -2.92 (0.15), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 732 HIS 0.005 0.001 HIS A 695 PHE 0.031 0.001 PHE A 348 TYR 0.016 0.001 TYR A 275 ARG 0.005 0.000 ARG B 94 *********************** 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 432 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 364 time to evaluate : 2.202 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: A 130 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6552 (mt) REVERT: A 373 MET cc_start: 0.8414 (ttt) cc_final: 0.8071 (ttt) REVERT: A 384 TYR cc_start: 0.7794 (t80) cc_final: 0.7302 (t80) REVERT: A 415 ASP cc_start: 0.6537 (p0) cc_final: 0.5592 (t0) REVERT: A 490 TYR cc_start: 0.7014 (t80) cc_final: 0.6626 (t80) REVERT: A 521 ASP cc_start: 0.7785 (m-30) cc_final: 0.7419 (m-30) REVERT: A 552 MET cc_start: 0.8612 (mmp) cc_final: 0.8349 (mmp) REVERT: A 573 TYR cc_start: 0.6496 (t80) cc_final: 0.6107 (t80) REVERT: D 34 PHE cc_start: 0.8376 (m-10) cc_final: 0.8047 (m-80) REVERT: D 55 LYS cc_start: 0.8343 (mptt) cc_final: 0.8076 (mptt) REVERT: D 63 LEU cc_start: 0.7500 (pt) cc_final: 0.6863 (tt) REVERT: G 103 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8706 (tp) REVERT: F 74 ASP cc_start: 0.8114 (t70) cc_final: 0.7684 (t70) REVERT: F 143 ARG cc_start: 0.7923 (ttt90) cc_final: 0.7704 (ttt90) REVERT: E 9 SER cc_start: 0.7769 (m) cc_final: 0.7495 (t) REVERT: E 167 PHE cc_start: 0.7305 (m-10) cc_final: 0.6734 (m-80) REVERT: E 206 ASN cc_start: 0.6807 (p0) cc_final: 0.6515 (p0) REVERT: B 47 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7887 (t0) REVERT: B 182 ARG cc_start: 0.8488 (ptt90) cc_final: 0.8211 (ptt-90) REVERT: H 22 ASN cc_start: 0.8228 (t0) cc_final: 0.7858 (t0) REVERT: H 336 VAL cc_start: 0.8576 (m) cc_final: 0.8294 (t) outliers start: 68 outliers final: 32 residues processed: 408 average time/residue: 0.3411 time to fit residues: 205.0714 Evaluate side-chains 337 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 302 time to evaluate : 2.045 ------------------------------------------------------------------------------- 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 130 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 60 ASP Chi-restraints excluded: chain D residue 72 GLN 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 64 ASP Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 212 LEU 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 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 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 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: 0.0020 chunk 155 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 139 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 197 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 overall best weight: 3.9794 ------------------------------------------------------------------------------- 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 639 ASN D 42 ASN H 80 ASN H 82 ASN ** H 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 19860 Z= 0.323 Angle : 0.684 12.754 27133 Z= 0.354 Chirality : 0.044 0.283 3062 Planarity : 0.004 0.049 3243 Dihedral : 14.900 163.456 3531 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.54 % Favored : 90.41 % Rotamer: Outliers : 4.74 % Allowed : 17.12 % Favored : 78.15 % 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: -3.25 (0.16), residues: 2232 helix: -1.25 (0.17), residues: 799 sheet: -2.50 (0.28), residues: 314 loop : -2.76 (0.16), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 732 HIS 0.013 0.001 HIS A 55 PHE 0.023 0.002 PHE A 655 TYR 0.036 0.002 TYR C 59 ARG 0.005 0.001 ARG F 81 *********************** 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 390 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 302 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7219 (t60) cc_final: 0.6863 (t60) REVERT: A 130 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6791 (mm) REVERT: A 275 TYR cc_start: 0.8364 (t80) cc_final: 0.8112 (t80) REVERT: A 276 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8794 (mp) REVERT: A 373 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8043 (ttt) REVERT: A 384 TYR cc_start: 0.7894 (t80) cc_final: 0.7539 (t80) REVERT: A 490 TYR cc_start: 0.7337 (t80) cc_final: 0.6994 (t80) REVERT: A 521 ASP cc_start: 0.7975 (m-30) cc_final: 0.7428 (m-30) REVERT: A 573 TYR cc_start: 0.6636 (t80) cc_final: 0.6038 (t80) REVERT: A 686 TYR cc_start: 0.7819 (t80) cc_final: 0.7590 (t80) REVERT: D 3 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6814 (tt) REVERT: D 34 PHE cc_start: 0.8541 (m-10) cc_final: 0.8337 (m-80) REVERT: D 55 LYS cc_start: 0.8454 (mptt) cc_final: 0.8175 (mptt) REVERT: D 63 LEU cc_start: 0.7726 (pt) cc_final: 0.7074 (tt) REVERT: G 67 LYS cc_start: 0.8609 (mmtt) cc_final: 0.8289 (mtpp) REVERT: G 138 ILE cc_start: 0.9086 (pt) cc_final: 0.8686 (pt) REVERT: E 9 SER cc_start: 0.8163 (m) cc_final: 0.7938 (t) REVERT: E 24 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6559 (p0) REVERT: E 206 ASN cc_start: 0.6861 (p0) cc_final: 0.6554 (p0) REVERT: B 47 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7953 (t0) REVERT: H 22 ASN cc_start: 0.8368 (t0) cc_final: 0.8104 (t0) REVERT: H 280 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7375 (mp) outliers start: 88 outliers final: 56 residues processed: 360 average time/residue: 0.3321 time to fit residues: 178.0626 Evaluate side-chains 336 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 273 time to evaluate : 2.208 ------------------------------------------------------------------------------- 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 52 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 373 MET 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 485 VAL Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 GLN 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 64 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 68 VAL Chi-restraints excluded: chain F residue 180 ASP 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 163 VAL Chi-restraints excluded: chain E residue 180 ASP 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 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 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 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: 9.9990 chunk 125 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 164 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 368 GLN D 42 ASN E 33 ASN E 213 ASN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 19860 Z= 0.419 Angle : 0.746 13.525 27133 Z= 0.385 Chirality : 0.047 0.295 3062 Planarity : 0.004 0.049 3243 Dihedral : 15.126 158.778 3531 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.11 % Favored : 88.84 % Rotamer: Outliers : 5.60 % Allowed : 18.03 % Favored : 76.37 % 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: -1.13 (0.17), residues: 795 sheet: -2.48 (0.27), residues: 332 loop : -2.76 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 732 HIS 0.013 0.001 HIS A 55 PHE 0.027 0.002 PHE A 655 TYR 0.025 0.002 TYR C 59 ARG 0.007 0.001 ARG B 94 *********************** 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 404 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 300 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8471 (tp) cc_final: 0.8227 (tt) REVERT: A 130 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6966 (mm) REVERT: A 276 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8732 (mp) REVERT: A 373 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7990 (ttt) REVERT: A 384 TYR cc_start: 0.8067 (t80) cc_final: 0.7297 (t80) REVERT: A 395 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7969 (mtpt) REVERT: A 490 TYR cc_start: 0.7443 (t80) cc_final: 0.7159 (t80) REVERT: A 521 ASP cc_start: 0.8052 (m-30) cc_final: 0.7623 (m-30) REVERT: A 604 ASN cc_start: 0.7842 (t0) cc_final: 0.7440 (t0) REVERT: A 686 TYR cc_start: 0.8077 (t80) cc_final: 0.7831 (t80) REVERT: D 34 PHE cc_start: 0.8630 (m-10) cc_final: 0.8327 (m-80) REVERT: C 110 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.7823 (mtm110) REVERT: G 67 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8396 (mtpp) REVERT: E 9 SER cc_start: 0.8248 (m) cc_final: 0.7813 (p) REVERT: E 24 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6145 (p0) REVERT: E 130 THR cc_start: 0.8399 (m) cc_final: 0.8128 (p) REVERT: E 206 ASN cc_start: 0.7028 (p0) cc_final: 0.6697 (p0) outliers start: 104 outliers final: 70 residues processed: 377 average time/residue: 0.3363 time to fit residues: 189.6266 Evaluate side-chains 351 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 276 time to evaluate : 2.264 ------------------------------------------------------------------------------- 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 202 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 373 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 395 LYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 485 VAL 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 622 ILE Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 72 GLN 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 C residue 102 ARG Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 145 SER 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 F residue 212 LEU Chi-restraints excluded: chain E residue 12 ILE 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 163 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 28 SER 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 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 165 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 84 ILE 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 Chi-restraints excluded: chain H residue 339 HIS 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: 0.6980 chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 220 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 368 GLN A 504 ASN A 639 ASN A 661 ASN D 42 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN B 161 ASN H 80 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19860 Z= 0.159 Angle : 0.625 14.589 27133 Z= 0.318 Chirality : 0.041 0.284 3062 Planarity : 0.003 0.038 3243 Dihedral : 14.890 162.645 3531 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.97 % Favored : 91.98 % Rotamer: Outliers : 3.71 % Allowed : 20.56 % Favored : 75.73 % 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: -2.78 (0.17), residues: 2232 helix: -0.71 (0.18), residues: 814 sheet: -2.33 (0.27), residues: 339 loop : -2.60 (0.17), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 732 HIS 0.011 0.001 HIS A 55 PHE 0.023 0.001 PHE A 348 TYR 0.025 0.002 TYR A 275 ARG 0.011 0.000 ARG A 657 *********************** 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 391 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 322 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6828 (mm) REVERT: A 276 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8672 (mp) REVERT: A 373 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8223 (ttt) REVERT: A 490 TYR cc_start: 0.7276 (t80) cc_final: 0.6967 (t80) REVERT: A 521 ASP cc_start: 0.7969 (m-30) cc_final: 0.7453 (m-30) REVERT: A 573 TYR cc_start: 0.6517 (t80) cc_final: 0.6075 (t80) REVERT: A 604 ASN cc_start: 0.7702 (t0) cc_final: 0.7231 (t0) REVERT: D 34 PHE cc_start: 0.8554 (m-10) cc_final: 0.8250 (m-80) REVERT: C 110 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7673 (mtm110) REVERT: G 67 LYS cc_start: 0.8552 (mmtt) cc_final: 0.8255 (mtpp) REVERT: G 181 TYR cc_start: 0.8338 (p90) cc_final: 0.8000 (p90) REVERT: E 24 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6308 (p0) REVERT: E 206 ASN cc_start: 0.7033 (p0) cc_final: 0.6513 (p0) REVERT: B 47 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7989 (t0) REVERT: H 22 ASN cc_start: 0.8290 (t0) cc_final: 0.7964 (t0) outliers start: 69 outliers final: 37 residues processed: 369 average time/residue: 0.3320 time to fit residues: 182.6235 Evaluate side-chains 332 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 290 time to evaluate : 2.251 ------------------------------------------------------------------------------- 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 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 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 622 ILE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain F residue 58 THR 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 107 ASP Chi-restraints excluded: chain E residue 163 VAL 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 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 165 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 75 LEU 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: 7.9990 chunk 24 optimal weight: 0.0980 chunk 125 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 219 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 263 ASN A 368 GLN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19860 Z= 0.205 Angle : 0.635 14.357 27133 Z= 0.323 Chirality : 0.042 0.280 3062 Planarity : 0.003 0.059 3243 Dihedral : 14.796 165.799 3531 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.59 % Favored : 90.37 % Rotamer: Outliers : 3.55 % Allowed : 21.31 % Favored : 75.13 % 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: -2.58 (0.17), residues: 2232 helix: -0.44 (0.18), residues: 805 sheet: -2.24 (0.27), residues: 356 loop : -2.55 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 732 HIS 0.012 0.001 HIS A 55 PHE 0.025 0.001 PHE B 64 TYR 0.022 0.002 TYR A 275 ARG 0.008 0.000 ARG G 95 *********************** 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 370 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 304 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6902 (mm) REVERT: A 276 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8659 (mp) REVERT: A 373 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8063 (ttt) REVERT: A 490 TYR cc_start: 0.7330 (t80) cc_final: 0.7014 (t80) REVERT: A 521 ASP cc_start: 0.7992 (m-30) cc_final: 0.7472 (m-30) REVERT: A 604 ASN cc_start: 0.7731 (t0) cc_final: 0.7213 (t0) REVERT: D 34 PHE cc_start: 0.8603 (m-10) cc_final: 0.8252 (m-80) REVERT: D 113 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7031 (mt-10) REVERT: C 68 TYR cc_start: 0.8303 (t80) cc_final: 0.8082 (t80) REVERT: C 103 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7556 (tm-30) REVERT: C 110 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7705 (mtm110) REVERT: G 67 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8307 (mtpp) REVERT: G 181 TYR cc_start: 0.8436 (p90) cc_final: 0.8038 (p90) REVERT: F 74 ASP cc_start: 0.8236 (t70) cc_final: 0.7810 (t0) REVERT: E 24 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6332 (p0) REVERT: E 130 THR cc_start: 0.8382 (m) cc_final: 0.8141 (p) REVERT: E 206 ASN cc_start: 0.6900 (p0) cc_final: 0.6556 (p0) REVERT: B 47 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8025 (t0) REVERT: H 241 ARG cc_start: 0.8013 (mmp80) cc_final: 0.7813 (mmp80) REVERT: H 280 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7289 (mp) outliers start: 66 outliers final: 48 residues processed: 345 average time/residue: 0.3486 time to fit residues: 179.7395 Evaluate side-chains 339 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 285 time to evaluate : 2.052 ------------------------------------------------------------------------------- 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 160 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 298 MET 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 746 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 58 THR 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 79 LEU 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 180 ASP Chi-restraints excluded: chain B residue 8 MET Chi-restraints excluded: chain B residue 41 LEU 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 165 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain H residue 75 LEU 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 323 LEU Chi-restraints excluded: chain H residue 339 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 172 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 19860 Z= 0.158 Angle : 0.615 14.096 27133 Z= 0.311 Chirality : 0.041 0.284 3062 Planarity : 0.003 0.051 3243 Dihedral : 14.670 168.311 3531 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.06 % Favored : 91.89 % Rotamer: Outliers : 3.39 % Allowed : 21.69 % Favored : 74.92 % 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: -2.38 (0.17), residues: 2232 helix: -0.23 (0.19), residues: 803 sheet: -2.18 (0.27), residues: 350 loop : -2.45 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 732 HIS 0.012 0.001 HIS A 55 PHE 0.014 0.001 PHE G 122 TYR 0.021 0.001 TYR A 275 ARG 0.005 0.000 ARG H 67 *********************** 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 384 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 321 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8655 (mp) REVERT: A 373 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8195 (ttt) REVERT: A 490 TYR cc_start: 0.7145 (t80) cc_final: 0.6841 (t80) REVERT: A 521 ASP cc_start: 0.7913 (m-30) cc_final: 0.7434 (m-30) REVERT: A 573 TYR cc_start: 0.6284 (t80) cc_final: 0.5873 (t80) REVERT: A 604 ASN cc_start: 0.7668 (t0) cc_final: 0.7078 (t0) REVERT: D 34 PHE cc_start: 0.8591 (m-10) cc_final: 0.8204 (m-80) REVERT: D 55 LYS cc_start: 0.8372 (mptt) cc_final: 0.8079 (mptt) REVERT: D 113 GLU cc_start: 0.7308 (mt-10) cc_final: 0.7076 (mt-10) REVERT: C 103 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7391 (tm-30) REVERT: C 110 ARG cc_start: 0.8244 (mtm-85) cc_final: 0.7798 (mtm110) REVERT: G 67 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8234 (mtpp) REVERT: G 181 TYR cc_start: 0.8236 (p90) cc_final: 0.7837 (p90) REVERT: F 74 ASP cc_start: 0.8211 (t70) cc_final: 0.7814 (t0) REVERT: F 143 ARG cc_start: 0.8355 (tpt-90) cc_final: 0.7810 (ttt90) REVERT: E 130 THR cc_start: 0.8386 (m) cc_final: 0.8169 (p) REVERT: B 47 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7977 (t0) REVERT: H 241 ARG cc_start: 0.8053 (mmp80) cc_final: 0.7820 (mmp80) outliers start: 63 outliers final: 42 residues processed: 359 average time/residue: 0.3266 time to fit residues: 175.1663 Evaluate side-chains 335 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 290 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 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 298 MET 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 607 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 163 VAL 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 41 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 165 LEU 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 75 LEU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP 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: 8.9990 chunk 210 optimal weight: 2.9990 chunk 192 optimal weight: 0.5980 chunk 204 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 185 optimal weight: 0.2980 chunk 193 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 368 GLN F 144 ASN E 19 HIS ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 19860 Z= 0.188 Angle : 0.626 13.875 27133 Z= 0.315 Chirality : 0.041 0.280 3062 Planarity : 0.003 0.047 3243 Dihedral : 14.632 169.679 3531 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.92 % Favored : 91.04 % Rotamer: Outliers : 2.85 % Allowed : 22.44 % Favored : 74.70 % 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: -2.28 (0.18), residues: 2232 helix: -0.10 (0.19), residues: 806 sheet: -2.16 (0.26), residues: 361 loop : -2.42 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 38 HIS 0.012 0.001 HIS A 55 PHE 0.013 0.001 PHE G 122 TYR 0.021 0.001 TYR A 275 ARG 0.005 0.000 ARG H 301 *********************** 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 350 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 297 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6845 (mm) REVERT: A 276 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8648 (mp) REVERT: A 373 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8053 (ttt) REVERT: A 490 TYR cc_start: 0.7277 (t80) cc_final: 0.6963 (t80) REVERT: A 521 ASP cc_start: 0.7928 (m-30) cc_final: 0.7463 (m-30) REVERT: A 573 TYR cc_start: 0.6275 (t80) cc_final: 0.5804 (t80) REVERT: A 604 ASN cc_start: 0.7704 (t0) cc_final: 0.7165 (t0) REVERT: D 3 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6589 (tt) REVERT: D 34 PHE cc_start: 0.8620 (m-10) cc_final: 0.8210 (m-80) REVERT: C 103 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7535 (tm-30) REVERT: C 110 ARG cc_start: 0.8279 (mtm-85) cc_final: 0.7817 (mtm110) REVERT: G 67 LYS cc_start: 0.8464 (mmtt) cc_final: 0.8239 (mtpp) REVERT: F 74 ASP cc_start: 0.8261 (t70) cc_final: 0.7865 (t0) REVERT: E 39 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7844 (m-30) REVERT: B 47 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.8013 (t0) REVERT: H 241 ARG cc_start: 0.8102 (mmp80) cc_final: 0.7876 (mmp80) outliers start: 53 outliers final: 41 residues processed: 332 average time/residue: 0.3271 time to fit residues: 163.0501 Evaluate side-chains 328 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 281 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 216 LEU Chi-restraints excluded: chain A residue 276 LEU 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 607 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 163 VAL 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 41 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR 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 75 LEU 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: 10.0000 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 150 optimal weight: 0.0970 chunk 227 optimal weight: 10.0000 chunk 209 optimal weight: 7.9990 chunk 180 optimal weight: 0.0370 chunk 18 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 overall best weight: 2.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN H 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 19860 Z= 0.228 Angle : 0.646 14.067 27133 Z= 0.326 Chirality : 0.042 0.290 3062 Planarity : 0.003 0.052 3243 Dihedral : 14.666 170.094 3531 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.27 % Favored : 90.68 % Rotamer: Outliers : 2.58 % Allowed : 22.66 % Favored : 74.76 % 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: -2.23 (0.18), residues: 2232 helix: -0.02 (0.19), residues: 804 sheet: -2.18 (0.26), residues: 366 loop : -2.40 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 38 HIS 0.011 0.001 HIS A 55 PHE 0.024 0.001 PHE B 64 TYR 0.021 0.002 TYR A 275 ARG 0.007 0.000 ARG F 143 ********************** 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 333 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 285 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6921 (mm) REVERT: A 276 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8634 (mp) REVERT: A 373 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8053 (ttt) REVERT: A 490 TYR cc_start: 0.7321 (t80) cc_final: 0.6982 (t80) REVERT: A 521 ASP cc_start: 0.7934 (m-30) cc_final: 0.7470 (m-30) REVERT: A 573 TYR cc_start: 0.6249 (t80) cc_final: 0.5757 (t80) REVERT: A 604 ASN cc_start: 0.7780 (t0) cc_final: 0.7241 (t0) REVERT: D 3 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6615 (tt) REVERT: D 34 PHE cc_start: 0.8623 (m-10) cc_final: 0.8217 (m-80) REVERT: C 103 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7527 (tm-30) REVERT: C 110 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7734 (mtm110) REVERT: G 67 LYS cc_start: 0.8494 (mmtt) cc_final: 0.8269 (mtpp) REVERT: F 74 ASP cc_start: 0.8268 (t70) cc_final: 0.7856 (t0) REVERT: E 39 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: B 47 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.8036 (t0) outliers start: 48 outliers final: 41 residues processed: 317 average time/residue: 0.3377 time to fit residues: 159.5490 Evaluate side-chains 329 residues out of total 1954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 282 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 216 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 298 MET 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 607 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 41 ILE Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 163 VAL 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 41 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 132 THR 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 75 LEU Chi-restraints excluded: chain H residue 161 LYS Chi-restraints excluded: chain H residue 169 TRP 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: 0.9980 chunk 55 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 181 optimal weight: 8.9990 chunk 75 optimal weight: 30.0000 chunk 186 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** E 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN H 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.124422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.103902 restraints weight = 35931.393| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.05 r_work: 0.3227 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 19860 Z= 0.297 Angle : 0.687 14.379 27133 Z= 0.348 Chirality : 0.044 0.292 3062 Planarity : 0.004 0.059 3243 Dihedral : 14.768 167.911 3531 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.35 % Favored : 89.61 % Rotamer: Outliers : 3.07 % Allowed : 22.39 % Favored : 74.54 % 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: -2.32 (0.17), residues: 2232 helix: -0.08 (0.19), residues: 803 sheet: -2.18 (0.26), residues: 356 loop : -2.49 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 732 HIS 0.012 0.001 HIS A 55 PHE 0.025 0.002 PHE B 64 TYR 0.021 0.002 TYR A 275 ARG 0.007 0.001 ARG F 143 =============================================================================== Job complete usr+sys time: 4574.21 seconds wall clock time: 83 minutes 5.81 seconds (4985.81 seconds total)