Starting phenix.real_space_refine on Thu Mar 21 06:36:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uvn_20908/03_2024/6uvn_20908.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uvn_20908/03_2024/6uvn_20908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uvn_20908/03_2024/6uvn_20908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uvn_20908/03_2024/6uvn_20908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uvn_20908/03_2024/6uvn_20908.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uvn_20908/03_2024/6uvn_20908.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 60 5.49 5 S 145 5.16 5 C 18542 2.51 5 N 5102 2.21 5 O 5636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "B ARG 99": "NH1" <-> "NH2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B ARG 538": "NH1" <-> "NH2" Residue "G ARG 31": "NH1" <-> "NH2" Residue "G ARG 40": "NH1" <-> "NH2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G GLU 120": "OE1" <-> "OE2" Residue "G ARG 150": "NH1" <-> "NH2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G ARG 247": "NH1" <-> "NH2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "F ARG 31": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F GLU 66": "OE1" <-> "OE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 150": "NH1" <-> "NH2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F GLU 257": "OE1" <-> "OE2" Residue "F ARG 289": "NH1" <-> "NH2" Residue "F GLU 321": "OE1" <-> "OE2" Residue "E ARG 31": "NH1" <-> "NH2" Residue "E ARG 40": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "H ARG 31": "NH1" <-> "NH2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "H ARG 101": "NH1" <-> "NH2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 123": "OE1" <-> "OE2" Residue "H ARG 150": "NH1" <-> "NH2" Residue "H ARG 213": "NH1" <-> "NH2" Residue "H ARG 247": "NH1" <-> "NH2" Residue "H ARG 289": "NH1" <-> "NH2" Residue "D ARG 31": "NH1" <-> "NH2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D GLU 66": "OE1" <-> "OE2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D GLU 120": "OE1" <-> "OE2" Residue "D ARG 150": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "C ARG 31": "NH1" <-> "NH2" Residue "C ARG 40": "NH1" <-> "NH2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "I GLU 15": "OE1" <-> "OE2" Residue "I ARG 32": "NH1" <-> "NH2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 121": "NH1" <-> "NH2" Residue "I ARG 133": "NH1" <-> "NH2" Residue "I PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 170": "NH1" <-> "NH2" Residue "I GLU 379": "OE1" <-> "OE2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J GLU 88": "OE1" <-> "OE2" Residue "J ARG 121": "NH1" <-> "NH2" Residue "J ARG 133": "NH1" <-> "NH2" Residue "J ARG 170": "NH1" <-> "NH2" Residue "J GLU 260": "OE1" <-> "OE2" Residue "J GLU 291": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29487 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1619 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain: "B" Number of atoms: 3921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3921 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 23, 'TRANS': 474} Chain breaks: 3 Chain: "G" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "F" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "E" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "H" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "D" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2695 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain breaks: 1 Chain: "C" Number of atoms: 2495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2495 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 16, 'TRANS': 291} Chain breaks: 2 Chain: "I" Number of atoms: 3124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3124 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain breaks: 2 Chain: "J" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3171 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 20, 'TRANS': 368} Chain breaks: 2 Chain: "M" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1275 Classifications: {'DNA': 2, 'RNA': 59} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 14, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 25, 'rna3p': 35} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 405 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'TRANS': 80} Chain breaks: 3 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'UNK:plan-1': 81} Unresolved non-hydrogen planarities: 81 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22533 SG CYS I 128 147.814 149.918 69.762 1.00117.96 S ATOM 22724 SG CYS I 150 146.594 150.159 66.366 1.00114.46 S ATOM 25657 SG CYS J 128 108.738 151.170 24.259 1.00139.86 S ATOM 25848 SG CYS J 150 111.025 151.827 27.144 1.00131.60 S Time building chain proxies: 15.01, per 1000 atoms: 0.51 Number of scatterers: 29487 At special positions: 0 Unit cell: (164.85, 175.35, 182.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 145 16.00 P 60 15.00 O 5636 8.00 N 5102 7.00 C 18542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS I 163 " - pdb=" SG CYS I 181 " distance=2.39 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.40 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN I 401 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 128 " pdb="ZN ZN I 401 " - pdb=" SG CYS I 150 " pdb="ZN ZN I 401 " - pdb=" ND1 HIS I 153 " pdb=" ZN J 401 " pdb="ZN ZN J 401 " - pdb=" ND1 HIS J 153 " pdb="ZN ZN J 401 " - pdb=" SG CYS J 128 " pdb="ZN ZN J 401 " - pdb=" SG CYS J 150 " 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6756 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 47 sheets defined 38.0% alpha, 16.2% beta 6 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 10.16 Creating SS restraints... Processing helix chain 'A' and resid 16 through 35 Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.710A pdb=" N ASP A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 105 through 108 Processing helix chain 'A' and resid 111 through 129 removed outlier: 3.850A pdb=" N ARG A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 9 Processing helix chain 'B' and resid 10 through 15 removed outlier: 4.659A pdb=" N ASP B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 15' Processing helix chain 'B' and resid 18 through 24 Processing helix chain 'B' and resid 36 through 47 removed outlier: 3.702A pdb=" N LEU B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 67 removed outlier: 3.789A pdb=" N LYS B 65 " --> pdb=" O LYS B 61 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 77 Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.755A pdb=" N ARG B 82 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.703A pdb=" N PHE B 135 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.568A pdb=" N LEU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 153' Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.878A pdb=" N ALA B 178 " --> pdb=" O CYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 223 through 228 removed outlier: 3.520A pdb=" N ARG B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.683A pdb=" N THR B 498 " --> pdb=" O ASP B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.755A pdb=" N LYS B 517 " --> pdb=" O ASP B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 removed outlier: 3.562A pdb=" N ALA B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 555 Processing helix chain 'B' and resid 582 through 586 removed outlier: 3.679A pdb=" N TYR B 586 " --> pdb=" O LEU B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 613 removed outlier: 3.716A pdb=" N ILE B 612 " --> pdb=" O ASP B 608 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 removed outlier: 4.026A pdb=" N ALA G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 48 through 52' Processing helix chain 'G' and resid 108 through 126 removed outlier: 3.508A pdb=" N LEU G 118 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU G 120 " --> pdb=" O VAL G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 141 removed outlier: 3.558A pdb=" N ILE G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 189 through 203 removed outlier: 3.591A pdb=" N MET G 196 " --> pdb=" O ALA G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 272 Processing helix chain 'G' and resid 308 through 314 Processing helix chain 'G' and resid 315 through 323 Processing helix chain 'G' and resid 330 through 347 Processing helix chain 'F' and resid 48 through 52 removed outlier: 4.030A pdb=" N ALA F 52 " --> pdb=" O ALA F 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 48 through 52' Processing helix chain 'F' and resid 64 through 70 removed outlier: 3.798A pdb=" N GLN F 70 " --> pdb=" O GLU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.538A pdb=" N LEU F 118 " --> pdb=" O THR F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 141 removed outlier: 3.534A pdb=" N ASN F 138 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE F 139 " --> pdb=" O TYR F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 186 Processing helix chain 'F' and resid 189 through 203 removed outlier: 3.671A pdb=" N MET F 196 " --> pdb=" O ALA F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 272 Processing helix chain 'F' and resid 308 through 314 Processing helix chain 'F' and resid 315 through 325 Processing helix chain 'F' and resid 330 through 347 Processing helix chain 'E' and resid 48 through 52 removed outlier: 4.027A pdb=" N ALA E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 52' Processing helix chain 'E' and resid 66 through 70 removed outlier: 3.522A pdb=" N ALA E 69 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 128 through 141 removed outlier: 3.565A pdb=" N ASN E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 186 Processing helix chain 'E' and resid 190 through 203 removed outlier: 4.090A pdb=" N MET E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 272 Processing helix chain 'E' and resid 308 through 314 Processing helix chain 'E' and resid 315 through 325 removed outlier: 3.649A pdb=" N ALA E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 347 Processing helix chain 'H' and resid 48 through 52 removed outlier: 4.222A pdb=" N ALA H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 48 through 52' Processing helix chain 'H' and resid 64 through 70 removed outlier: 3.805A pdb=" N GLN H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 126 Processing helix chain 'H' and resid 128 through 141 removed outlier: 3.523A pdb=" N THR H 133 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN H 138 " --> pdb=" O ARG H 134 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE H 139 " --> pdb=" O TYR H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 186 Processing helix chain 'H' and resid 189 through 201 Processing helix chain 'H' and resid 263 through 272 Processing helix chain 'H' and resid 308 through 314 Processing helix chain 'H' and resid 315 through 325 Processing helix chain 'H' and resid 330 through 347 Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.764A pdb=" N ALA D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 52' Processing helix chain 'D' and resid 108 through 126 removed outlier: 3.555A pdb=" N LEU D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 141 removed outlier: 3.539A pdb=" N ILE D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 186 removed outlier: 3.806A pdb=" N PHE D 184 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 185 " --> pdb=" O ARG D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 203 removed outlier: 3.753A pdb=" N MET D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 272 Processing helix chain 'D' and resid 308 through 314 Processing helix chain 'D' and resid 315 through 325 Processing helix chain 'D' and resid 330 through 347 Processing helix chain 'C' and resid 108 through 126 removed outlier: 3.834A pdb=" N THR C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 141 removed outlier: 3.884A pdb=" N ASN C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 187 removed outlier: 3.529A pdb=" N ASN C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 203 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 308 through 314 removed outlier: 3.853A pdb=" N ILE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 325 Processing helix chain 'C' and resid 330 through 347 Processing helix chain 'I' and resid 13 through 26 removed outlier: 3.995A pdb=" N LYS I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY I 26 " --> pdb=" O ALA I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 3.518A pdb=" N PHE I 33 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 52 removed outlier: 4.463A pdb=" N THR I 51 " --> pdb=" O ASN I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 59 removed outlier: 3.678A pdb=" N ILE I 59 " --> pdb=" O ILE I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 Processing helix chain 'I' and resid 128 through 136 Processing helix chain 'I' and resid 139 through 144 removed outlier: 3.626A pdb=" N TRP I 142 " --> pdb=" O SER I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 173 Processing helix chain 'I' and resid 194 through 205 removed outlier: 4.436A pdb=" N VAL I 200 " --> pdb=" O ALA I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 231 Processing helix chain 'I' and resid 236 through 244 removed outlier: 3.649A pdb=" N PHE I 240 " --> pdb=" O ASP I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 265 removed outlier: 3.743A pdb=" N HIS I 252 " --> pdb=" O PRO I 248 " (cutoff:3.500A) Processing helix chain 'I' and resid 279 through 287 removed outlier: 3.522A pdb=" N PHE I 283 " --> pdb=" O LEU I 279 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE I 284 " --> pdb=" O GLY I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 Processing helix chain 'I' and resid 324 through 332 removed outlier: 3.512A pdb=" N VAL I 330 " --> pdb=" O LEU I 326 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 345 Processing helix chain 'I' and resid 369 through 380 Processing helix chain 'I' and resid 387 through 392 removed outlier: 4.109A pdb=" N SER I 392 " --> pdb=" O SER I 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 26 removed outlier: 3.824A pdb=" N LYS J 24 " --> pdb=" O ARG J 20 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN J 25 " --> pdb=" O VAL J 21 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 44 removed outlier: 3.662A pdb=" N ILE J 44 " --> pdb=" O PHE J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 52 removed outlier: 4.331A pdb=" N THR J 51 " --> pdb=" O ASN J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 59 removed outlier: 3.529A pdb=" N ILE J 59 " --> pdb=" O ILE J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 82 Processing helix chain 'J' and resid 89 through 93 Processing helix chain 'J' and resid 128 through 136 Processing helix chain 'J' and resid 139 through 144 removed outlier: 3.535A pdb=" N TRP J 142 " --> pdb=" O SER J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 173 Processing helix chain 'J' and resid 194 through 205 removed outlier: 3.516A pdb=" N THR J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA J 205 " --> pdb=" O SER J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 231 removed outlier: 4.067A pdb=" N TRP J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY J 222 " --> pdb=" O SER J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 244 removed outlier: 3.575A pdb=" N PHE J 240 " --> pdb=" O ASP J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 265 removed outlier: 3.752A pdb=" N PHE J 251 " --> pdb=" O TRP J 247 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N HIS J 252 " --> pdb=" O PRO J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 287 removed outlier: 3.679A pdb=" N PHE J 283 " --> pdb=" O LEU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 309 Processing helix chain 'J' and resid 324 through 332 removed outlier: 4.438A pdb=" N VAL J 330 " --> pdb=" O LEU J 326 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 345 Processing helix chain 'J' and resid 369 through 378 removed outlier: 3.636A pdb=" N LEU J 375 " --> pdb=" O ASP J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 390 Processing helix chain 'N' and resid 276 through 282 Processing helix chain 'N' and resid 284 through 300 removed outlier: 3.573A pdb=" N UNK N 288 " --> pdb=" O UNK N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 305 through 321 Processing helix chain 'N' and resid 334 through 346 Processing helix chain 'N' and resid 356 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 43 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 150 through 155 Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 146 removed outlier: 3.655A pdb=" N THR A 144 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 41 " --> pdb=" O THR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 5.683A pdb=" N GLU B 592 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR B 570 " --> pdb=" O GLU B 592 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE B 594 " --> pdb=" O VAL B 568 " (cutoff:3.500A) removed outlier: 15.380A pdb=" N SER B 566 " --> pdb=" O PRO B 627 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 568 " --> pdb=" O VAL B 625 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL B 625 " --> pdb=" O VAL B 568 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 139 through 142 Processing sheet with id=AA9, first strand: chain 'B' and resid 201 through 205 removed outlier: 4.185A pdb=" N LYS B 587 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 510 through 511 Processing sheet with id=AB2, first strand: chain 'B' and resid 510 through 511 removed outlier: 4.664A pdb=" N ASN B 392 " --> pdb=" O PHE B 479 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N PHE B 479 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER B 480 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL B 442 " --> pdb=" O SER B 480 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE B 482 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE B 440 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN B 484 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE B 438 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 398 through 399 Processing sheet with id=AB4, first strand: chain 'G' and resid 105 through 106 Processing sheet with id=AB5, first strand: chain 'G' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 21 through 26 current: chain 'G' and resid 154 through 161 Processing sheet with id=AB6, first strand: chain 'G' and resid 32 through 33 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 87 through 97 current: chain 'G' and resid 251 through 254 Processing sheet with id=AB7, first strand: chain 'G' and resid 38 through 44 Processing sheet with id=AB8, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'F' and resid 105 through 106 Processing sheet with id=AC1, first strand: chain 'F' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 21 through 26 current: chain 'F' and resid 154 through 161 Processing sheet with id=AC2, first strand: chain 'F' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 87 through 97 current: chain 'F' and resid 251 through 254 Processing sheet with id=AC3, first strand: chain 'F' and resid 38 through 44 Processing sheet with id=AC4, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'E' and resid 105 through 106 Processing sheet with id=AC6, first strand: chain 'E' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 21 through 26 current: chain 'E' and resid 154 through 161 Processing sheet with id=AC7, first strand: chain 'E' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 87 through 97 current: chain 'E' and resid 251 through 254 Processing sheet with id=AC8, first strand: chain 'E' and resid 38 through 44 Processing sheet with id=AC9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'H' and resid 105 through 106 removed outlier: 3.595A pdb=" N LYS H 105 " --> pdb=" O ALA H 11 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 32 through 34 Processing sheet with id=AD3, first strand: chain 'H' and resid 32 through 34 removed outlier: 4.181A pdb=" N PHE H 23 " --> pdb=" O PRO H 260 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N VAL H 25 " --> pdb=" O ARG H 258 " (cutoff:3.500A) removed outlier: 13.589A pdb=" N ARG H 258 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 37 through 44 Processing sheet with id=AD5, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.543A pdb=" N GLN H 58 " --> pdb=" O ASP H 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 228 through 229 removed outlier: 4.563A pdb=" N VAL H 248 " --> pdb=" O VAL H 229 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 273 through 275 Processing sheet with id=AD8, first strand: chain 'D' and resid 105 through 106 Processing sheet with id=AD9, first strand: chain 'D' and resid 17 through 18 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 21 through 26 current: chain 'D' and resid 154 through 161 Processing sheet with id=AE1, first strand: chain 'D' and resid 32 through 34 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 87 through 97 current: chain 'D' and resid 251 through 254 Processing sheet with id=AE2, first strand: chain 'D' and resid 38 through 44 Processing sheet with id=AE3, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AE4, first strand: chain 'D' and resid 273 through 275 Processing sheet with id=AE5, first strand: chain 'C' and resid 105 through 106 Processing sheet with id=AE6, first strand: chain 'C' and resid 32 through 34 Processing sheet with id=AE7, first strand: chain 'C' and resid 32 through 34 removed outlier: 4.115A pdb=" N PHE C 23 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 10.779A pdb=" N VAL C 25 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 14.055A pdb=" N ARG C 258 " --> pdb=" O VAL C 25 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 273 through 275 Processing sheet with id=AE9, first strand: chain 'I' and resid 95 through 101 removed outlier: 6.422A pdb=" N THR I 97 " --> pdb=" O VAL I 109 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL I 109 " --> pdb=" O THR I 97 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N MET I 99 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA I 107 " --> pdb=" O MET I 99 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR I 105 " --> pdb=" O TYR I 101 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 95 through 101 removed outlier: 6.845A pdb=" N THR J 97 " --> pdb=" O VAL J 109 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL J 109 " --> pdb=" O THR J 97 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N MET J 99 " --> pdb=" O ALA J 107 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA J 107 " --> pdb=" O MET J 99 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR J 105 " --> pdb=" O TYR J 101 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 322 through 323 1083 hydrogen bonds defined for protein. 2985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 11.30 Time building geometry restraints manager: 12.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7220 1.33 - 1.45: 6879 1.45 - 1.57: 15926 1.57 - 1.69: 120 1.69 - 1.81: 206 Bond restraints: 30351 Sorted by residual: bond pdb=" CA ASP J 371 " pdb=" C ASP J 371 " ideal model delta sigma weight residual 1.523 1.468 0.054 1.41e-02 5.03e+03 1.49e+01 bond pdb=" N TYR C 278 " pdb=" CA TYR C 278 " ideal model delta sigma weight residual 1.456 1.487 -0.031 9.40e-03 1.13e+04 1.05e+01 bond pdb=" N VAL I 259 " pdb=" CA VAL I 259 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.14e+00 bond pdb=" C HIS C 217 " pdb=" N LEU C 218 " ideal model delta sigma weight residual 1.327 1.285 0.042 1.39e-02 5.18e+03 8.96e+00 bond pdb=" N VAL H 55 " pdb=" CA VAL H 55 " ideal model delta sigma weight residual 1.457 1.492 -0.036 1.19e-02 7.06e+03 8.93e+00 ... (remaining 30346 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.38: 838 105.38 - 112.58: 16231 112.58 - 119.77: 9871 119.77 - 126.97: 13961 126.97 - 134.17: 582 Bond angle restraints: 41483 Sorted by residual: angle pdb=" N PRO B 391 " pdb=" CA PRO B 391 " pdb=" C PRO B 391 " ideal model delta sigma weight residual 113.47 122.01 -8.54 1.43e+00 4.89e-01 3.56e+01 angle pdb=" N LYS C 143 " pdb=" CA LYS C 143 " pdb=" C LYS C 143 " ideal model delta sigma weight residual 114.56 107.74 6.82 1.27e+00 6.20e-01 2.89e+01 angle pdb=" N THR B 413 " pdb=" CA THR B 413 " pdb=" C THR B 413 " ideal model delta sigma weight residual 111.71 105.56 6.15 1.15e+00 7.56e-01 2.86e+01 angle pdb=" N PRO I 290 " pdb=" CA PRO I 290 " pdb=" C PRO I 290 " ideal model delta sigma weight residual 112.47 102.01 10.46 2.06e+00 2.36e-01 2.58e+01 angle pdb=" N PRO J 290 " pdb=" CA PRO J 290 " pdb=" CB PRO J 290 " ideal model delta sigma weight residual 103.25 98.19 5.06 1.05e+00 9.07e-01 2.33e+01 ... (remaining 41478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.38: 17304 28.38 - 56.75: 706 56.75 - 85.13: 123 85.13 - 113.50: 9 113.50 - 141.88: 1 Dihedral angle restraints: 18143 sinusoidal: 7754 harmonic: 10389 Sorted by residual: dihedral pdb=" O4' U M 43 " pdb=" C1' U M 43 " pdb=" N1 U M 43 " pdb=" C2 U M 43 " ideal model delta sinusoidal sigma weight residual 200.00 58.12 141.88 1 1.50e+01 4.44e-03 7.62e+01 dihedral pdb=" O4' U M 42 " pdb=" C1' U M 42 " pdb=" N1 U M 42 " pdb=" C2 U M 42 " ideal model delta sinusoidal sigma weight residual -160.00 -64.32 -95.68 1 1.50e+01 4.44e-03 4.69e+01 dihedral pdb=" CA ASP D 296 " pdb=" C ASP D 296 " pdb=" N VAL D 297 " pdb=" CA VAL D 297 " ideal model delta harmonic sigma weight residual -180.00 -150.80 -29.20 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 18140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3681 0.062 - 0.123: 836 0.123 - 0.184: 78 0.184 - 0.246: 7 0.246 - 0.307: 6 Chirality restraints: 4608 Sorted by residual: chirality pdb=" CA LEU I 289 " pdb=" N LEU I 289 " pdb=" C LEU I 289 " pdb=" CB LEU I 289 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA PRO J 290 " pdb=" N PRO J 290 " pdb=" C PRO J 290 " pdb=" CB PRO J 290 " both_signs ideal model delta sigma weight residual False 2.72 3.00 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA ILE B 393 " pdb=" N ILE B 393 " pdb=" C ILE B 393 " pdb=" CB ILE B 393 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 4605 not shown) Planarity restraints: 5088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 50 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C SER H 50 " -0.060 2.00e-02 2.50e+03 pdb=" O SER H 50 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU H 51 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U M 33 " 0.041 2.00e-02 2.50e+03 2.02e-02 9.18e+00 pdb=" N1 U M 33 " -0.040 2.00e-02 2.50e+03 pdb=" C2 U M 33 " -0.008 2.00e-02 2.50e+03 pdb=" O2 U M 33 " -0.005 2.00e-02 2.50e+03 pdb=" N3 U M 33 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U M 33 " 0.008 2.00e-02 2.50e+03 pdb=" O4 U M 33 " 0.013 2.00e-02 2.50e+03 pdb=" C5 U M 33 " -0.005 2.00e-02 2.50e+03 pdb=" C6 U M 33 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS I 161 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C CYS I 161 " -0.047 2.00e-02 2.50e+03 pdb=" O CYS I 161 " 0.018 2.00e-02 2.50e+03 pdb=" N SER I 162 " 0.015 2.00e-02 2.50e+03 ... (remaining 5085 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1003 2.67 - 3.23: 30776 3.23 - 3.79: 49537 3.79 - 4.34: 68318 4.34 - 4.90: 109726 Nonbonded interactions: 259360 Sorted by model distance: nonbonded pdb=" O VAL H 55 " pdb=" OG SER H 56 " model vdw 2.114 2.440 nonbonded pdb=" OH TYR G 53 " pdb=" OD2 ASP F 308 " model vdw 2.196 2.440 nonbonded pdb=" OH TYR F 53 " pdb=" OD2 ASP E 308 " model vdw 2.200 2.440 nonbonded pdb=" NH1 ARG E 289 " pdb=" OD1 ASN E 343 " model vdw 2.202 2.520 nonbonded pdb=" O TRP D 277 " pdb=" NH2 ARG D 301 " model vdw 2.204 2.520 ... (remaining 259355 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' and (resid 4 through 43 or resid 73 through 353)) selection = (chain 'E' and (resid 4 through 43 or resid 73 through 353)) selection = (chain 'F' and (resid 4 through 43 or resid 73 through 353)) selection = (chain 'G' and (resid 4 through 43 or resid 73 through 353)) selection = (chain 'H' and (resid 4 through 43 or resid 73 through 353)) } ncs_group { reference = (chain 'I' and (resid 1 through 162 or resid 164 through 394 or resid 401)) selection = (chain 'J' and (resid 1 through 354 or resid 362 through 394 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 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: 5.380 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 87.790 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.010 0.079 30351 Z= 0.619 Angle : 0.843 10.458 41483 Z= 0.485 Chirality : 0.050 0.307 4608 Planarity : 0.005 0.051 5088 Dihedral : 15.465 141.875 11384 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.09 % Favored : 91.77 % Rotamer: Outliers : 0.52 % Allowed : 7.49 % Favored : 91.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.12), residues: 3413 helix: -2.45 (0.12), residues: 1141 sheet: -2.01 (0.21), residues: 555 loop : -2.85 (0.13), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 277 HIS 0.005 0.001 HIS B 158 PHE 0.028 0.002 PHE E 92 TYR 0.017 0.002 TYR J 390 ARG 0.010 0.001 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8148 (p) cc_final: 0.7889 (t) REVERT: B 21 ARG cc_start: 0.8228 (mmt-90) cc_final: 0.7876 (mmm-85) REVERT: B 221 MET cc_start: 0.7917 (ttt) cc_final: 0.7604 (ttt) REVERT: B 456 PHE cc_start: 0.7647 (t80) cc_final: 0.7335 (t80) REVERT: G 137 MET cc_start: 0.7314 (mtp) cc_final: 0.6918 (mtp) REVERT: G 349 MET cc_start: 0.7835 (mpp) cc_final: 0.7142 (mtm) REVERT: F 128 TRP cc_start: 0.7990 (m100) cc_final: 0.7766 (m100) REVERT: F 337 MET cc_start: 0.7397 (tpt) cc_final: 0.7185 (mmm) REVERT: F 349 MET cc_start: 0.7405 (mtm) cc_final: 0.7126 (mtp) REVERT: E 22 CYS cc_start: 0.7260 (m) cc_final: 0.6939 (m) REVERT: E 223 MET cc_start: 0.7302 (ttp) cc_final: 0.7034 (ttp) REVERT: H 116 VAL cc_start: 0.8464 (t) cc_final: 0.8178 (m) REVERT: H 223 MET cc_start: 0.7510 (ttp) cc_final: 0.7228 (ttm) REVERT: H 289 ARG cc_start: 0.7875 (mpt90) cc_final: 0.7191 (mmt-90) REVERT: C 75 GLN cc_start: 0.8461 (tt0) cc_final: 0.7888 (tm-30) REVERT: C 223 MET cc_start: 0.8192 (ttp) cc_final: 0.7889 (ttt) REVERT: C 331 GLN cc_start: 0.8203 (tp-100) cc_final: 0.7743 (tp-100) REVERT: J 15 GLU cc_start: 0.8216 (mp0) cc_final: 0.7804 (mp0) REVERT: J 287 ILE cc_start: 0.9085 (tp) cc_final: 0.8810 (tp) outliers start: 16 outliers final: 9 residues processed: 234 average time/residue: 0.4666 time to fit residues: 168.4692 Evaluate side-chains 157 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 148 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain I residue 181 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 8.9990 chunk 267 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 276 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 320 optimal weight: 9.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 ASN B 120 HIS B 171 GLN ** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN B 420 HIS B 446 HIS ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 621 ASN B 626 GLN G 38 ASN G 221 ASN G 250 GLN G 318 HIS G 331 GLN G 335 ASN G 338 HIS G 352 HIS ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN F 245 ASN F 250 GLN F 335 ASN F 338 HIS E 75 GLN E 182 GLN E 335 ASN E 352 HIS H 74 HIS H 80 HIS H 182 GLN H 331 GLN H 335 ASN H 338 HIS H 343 ASN D 182 GLN D 335 ASN D 338 HIS D 352 HIS ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN ** C 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 HIS I 60 ASN I 66 ASN I 225 HIS I 262 ASN I 381 GLN J 46 HIS J 47 ASN J 153 HIS J 225 HIS J 381 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30351 Z= 0.201 Angle : 0.597 12.547 41483 Z= 0.308 Chirality : 0.042 0.208 4608 Planarity : 0.004 0.072 5088 Dihedral : 13.670 140.866 4763 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.42 % Favored : 94.52 % Rotamer: Outliers : 1.79 % Allowed : 11.53 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.13), residues: 3413 helix: -1.09 (0.14), residues: 1165 sheet: -1.20 (0.23), residues: 493 loop : -2.37 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 162 HIS 0.004 0.001 HIS B 588 PHE 0.014 0.001 PHE F 265 TYR 0.016 0.001 TYR B 119 ARG 0.007 0.000 ARG J 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 183 time to evaluate : 3.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 ARG cc_start: 0.8140 (mmt-90) cc_final: 0.7903 (mmm-85) REVERT: B 221 MET cc_start: 0.7832 (ttt) cc_final: 0.7594 (ttp) REVERT: G 137 MET cc_start: 0.7156 (mtp) cc_final: 0.6777 (mtp) REVERT: G 353 LYS cc_start: 0.6454 (mppt) cc_final: 0.6009 (mmtt) REVERT: F 337 MET cc_start: 0.7298 (tpt) cc_final: 0.7096 (mmm) REVERT: E 22 CYS cc_start: 0.7224 (m) cc_final: 0.6919 (m) REVERT: E 223 MET cc_start: 0.7255 (ttp) cc_final: 0.6936 (ttp) REVERT: E 341 MET cc_start: 0.8307 (mmt) cc_final: 0.8099 (mmp) REVERT: H 223 MET cc_start: 0.7487 (ttp) cc_final: 0.7215 (ttm) REVERT: C 223 MET cc_start: 0.8179 (ttp) cc_final: 0.7899 (ttt) REVERT: I 123 HIS cc_start: 0.8093 (p90) cc_final: 0.7833 (p90) REVERT: J 15 GLU cc_start: 0.8217 (mp0) cc_final: 0.7854 (mp0) outliers start: 55 outliers final: 30 residues processed: 232 average time/residue: 0.3903 time to fit residues: 149.1670 Evaluate side-chains 187 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 392 ASN Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 277 TRP Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 279 LEU Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 332 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 178 optimal weight: 7.9990 chunk 99 optimal weight: 0.1980 chunk 266 optimal weight: 1.9990 chunk 218 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 321 optimal weight: 8.9990 chunk 346 optimal weight: 50.0000 chunk 286 optimal weight: 3.9990 chunk 318 optimal weight: 30.0000 chunk 109 optimal weight: 0.9990 chunk 257 optimal weight: 5.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 ASN B 171 GLN B 224 HIS B 392 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 ASN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN E 331 GLN ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 ASN D 217 HIS ** D 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN C 335 ASN I 60 ASN J 80 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30351 Z= 0.311 Angle : 0.615 11.925 41483 Z= 0.313 Chirality : 0.043 0.227 4608 Planarity : 0.004 0.061 5088 Dihedral : 13.514 138.240 4758 Min Nonbonded Distance : 1.568 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.51 % Allowed : 13.23 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.14), residues: 3413 helix: -0.51 (0.15), residues: 1160 sheet: -1.07 (0.23), residues: 524 loop : -2.13 (0.14), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 155 HIS 0.025 0.001 HIS J 153 PHE 0.019 0.002 PHE H 92 TYR 0.023 0.002 TYR B 123 ARG 0.005 0.000 ARG J 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 172 time to evaluate : 3.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 ARG cc_start: 0.8012 (mmt-90) cc_final: 0.7739 (mmm-85) REVERT: B 221 MET cc_start: 0.7872 (ttt) cc_final: 0.7519 (ttp) REVERT: B 477 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8426 (p) REVERT: G 137 MET cc_start: 0.7209 (mtp) cc_final: 0.6815 (mtp) REVERT: G 337 MET cc_start: 0.6580 (tpt) cc_final: 0.6196 (tpp) REVERT: G 353 LYS cc_start: 0.6478 (mppt) cc_final: 0.6065 (mmtt) REVERT: F 337 MET cc_start: 0.7408 (tpt) cc_final: 0.7174 (mmm) REVERT: E 5 LYS cc_start: 0.8131 (pptt) cc_final: 0.7815 (tptp) REVERT: E 22 CYS cc_start: 0.7211 (m) cc_final: 0.7001 (m) REVERT: E 223 MET cc_start: 0.7253 (ttp) cc_final: 0.6938 (ttp) REVERT: E 308 ASP cc_start: 0.6565 (OUTLIER) cc_final: 0.6197 (p0) REVERT: I 123 HIS cc_start: 0.8144 (p90) cc_final: 0.7870 (p90) REVERT: I 323 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7781 (mpp) REVERT: J 95 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.7781 (p0) outliers start: 77 outliers final: 52 residues processed: 235 average time/residue: 0.3780 time to fit residues: 148.3668 Evaluate side-chains 211 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 155 time to evaluate : 3.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 277 TRP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 343 ASN Chi-restraints excluded: chain H residue 349 MET Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 331 MET Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 317 optimal weight: 8.9990 chunk 241 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 322 optimal weight: 4.9990 chunk 341 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 305 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN B 392 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 HIS H 343 ASN D 70 GLN C 138 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30351 Z= 0.283 Angle : 0.591 11.362 41483 Z= 0.301 Chirality : 0.042 0.237 4608 Planarity : 0.004 0.062 5088 Dihedral : 13.456 137.783 4756 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.77 % Allowed : 14.99 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.14), residues: 3413 helix: -0.22 (0.15), residues: 1167 sheet: -0.98 (0.23), residues: 541 loop : -2.01 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 155 HIS 0.010 0.001 HIS J 153 PHE 0.015 0.001 PHE H 92 TYR 0.020 0.002 TYR B 123 ARG 0.006 0.000 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 166 time to evaluate : 3.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ARG cc_start: 0.7966 (mmt-90) cc_final: 0.7675 (mmm-85) REVERT: B 221 MET cc_start: 0.7865 (ttt) cc_final: 0.7511 (ttp) REVERT: B 477 VAL cc_start: 0.8697 (OUTLIER) cc_final: 0.8445 (p) REVERT: G 137 MET cc_start: 0.7222 (mtp) cc_final: 0.6810 (mtp) REVERT: G 337 MET cc_start: 0.6579 (tpt) cc_final: 0.6135 (tpp) REVERT: G 353 LYS cc_start: 0.6510 (mppt) cc_final: 0.6165 (mmtt) REVERT: F 337 MET cc_start: 0.7381 (tpt) cc_final: 0.7122 (mmm) REVERT: E 5 LYS cc_start: 0.8210 (pptt) cc_final: 0.7925 (tptp) REVERT: E 22 CYS cc_start: 0.7194 (m) cc_final: 0.6982 (m) REVERT: E 223 MET cc_start: 0.7254 (ttp) cc_final: 0.6943 (ttp) REVERT: E 341 MET cc_start: 0.8298 (mmt) cc_final: 0.8083 (mmm) REVERT: H 320 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7965 (mt) REVERT: C 337 MET cc_start: 0.8026 (tpp) cc_final: 0.7634 (tpp) REVERT: I 123 HIS cc_start: 0.8134 (p90) cc_final: 0.7890 (p90) REVERT: I 323 MET cc_start: 0.8306 (ptp) cc_final: 0.7773 (mpp) REVERT: J 18 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8893 (m-80) REVERT: J 95 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.7686 (p0) outliers start: 85 outliers final: 62 residues processed: 238 average time/residue: 0.3721 time to fit residues: 149.8749 Evaluate side-chains 221 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 155 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 392 ASN Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 331 MET Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 284 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 254 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 291 optimal weight: 0.9990 chunk 235 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 306 optimal weight: 8.9990 chunk 86 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS B 493 GLN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN D 80 HIS I 262 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30351 Z= 0.173 Angle : 0.543 11.697 41483 Z= 0.276 Chirality : 0.040 0.254 4608 Planarity : 0.004 0.060 5088 Dihedral : 13.380 136.547 4756 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.97 % Allowed : 15.71 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3413 helix: 0.04 (0.16), residues: 1183 sheet: -0.80 (0.23), residues: 542 loop : -1.81 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 162 HIS 0.009 0.001 HIS J 153 PHE 0.013 0.001 PHE F 265 TYR 0.015 0.001 TYR J 390 ARG 0.004 0.000 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 177 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.8389 (tmmt) cc_final: 0.8159 (tmmt) REVERT: B 21 ARG cc_start: 0.7900 (mmt-90) cc_final: 0.7646 (mmm-85) REVERT: B 221 MET cc_start: 0.7822 (ttt) cc_final: 0.7588 (ttm) REVERT: G 137 MET cc_start: 0.7205 (mtp) cc_final: 0.6795 (mtp) REVERT: G 337 MET cc_start: 0.6559 (tpt) cc_final: 0.6169 (tpp) REVERT: G 353 LYS cc_start: 0.6526 (mppt) cc_final: 0.6222 (mmtt) REVERT: F 337 MET cc_start: 0.7306 (tpt) cc_final: 0.7078 (mmm) REVERT: E 5 LYS cc_start: 0.8231 (pptt) cc_final: 0.7932 (tptp) REVERT: E 46 MET cc_start: 0.7946 (mmt) cc_final: 0.7632 (mmm) REVERT: E 116 VAL cc_start: 0.8536 (p) cc_final: 0.8308 (m) REVERT: E 223 MET cc_start: 0.7254 (ttp) cc_final: 0.6953 (ttp) REVERT: E 276 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7255 (p0) REVERT: E 341 MET cc_start: 0.8376 (mmt) cc_final: 0.7964 (mmp) REVERT: H 61 LYS cc_start: 0.6648 (mmmt) cc_final: 0.5951 (mmtt) REVERT: H 320 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7961 (mt) REVERT: H 341 MET cc_start: 0.7317 (mmp) cc_final: 0.6848 (mmm) REVERT: C 30 ASP cc_start: 0.7794 (t0) cc_final: 0.7533 (t0) REVERT: C 337 MET cc_start: 0.7926 (tpp) cc_final: 0.7684 (tpp) REVERT: I 123 HIS cc_start: 0.8011 (p90) cc_final: 0.7784 (p90) REVERT: I 384 GLU cc_start: 0.8173 (pm20) cc_final: 0.7913 (pm20) REVERT: J 18 PHE cc_start: 0.9287 (OUTLIER) cc_final: 0.8855 (m-80) outliers start: 91 outliers final: 56 residues processed: 257 average time/residue: 0.3787 time to fit residues: 163.5009 Evaluate side-chains 214 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 155 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain G residue 296 ASP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 332 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 114 optimal weight: 0.2980 chunk 307 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 341 optimal weight: 8.9990 chunk 283 optimal weight: 0.1980 chunk 158 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS B 392 ASN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 ASN D 75 GLN I 262 ASN J 345 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30351 Z= 0.217 Angle : 0.559 13.800 41483 Z= 0.281 Chirality : 0.041 0.217 4608 Planarity : 0.004 0.063 5088 Dihedral : 13.348 135.926 4756 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.26 % Allowed : 16.06 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3413 helix: 0.17 (0.16), residues: 1183 sheet: -0.76 (0.22), residues: 553 loop : -1.77 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 155 HIS 0.009 0.001 HIS J 153 PHE 0.012 0.001 PHE F 265 TYR 0.021 0.001 TYR I 49 ARG 0.010 0.000 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 165 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 ARG cc_start: 0.7898 (mmt-90) cc_final: 0.7643 (mmm-85) REVERT: B 86 ASN cc_start: 0.7125 (OUTLIER) cc_final: 0.6680 (p0) REVERT: B 177 MET cc_start: 0.7472 (mmm) cc_final: 0.6378 (mmm) REVERT: B 221 MET cc_start: 0.7843 (ttt) cc_final: 0.7596 (ttm) REVERT: G 137 MET cc_start: 0.7220 (mtp) cc_final: 0.6808 (mtp) REVERT: G 353 LYS cc_start: 0.6582 (mppt) cc_final: 0.6286 (mmtt) REVERT: F 337 MET cc_start: 0.7337 (tpt) cc_final: 0.7096 (mmm) REVERT: E 5 LYS cc_start: 0.8282 (pptt) cc_final: 0.7963 (tptp) REVERT: E 116 VAL cc_start: 0.8587 (p) cc_final: 0.8351 (m) REVERT: E 223 MET cc_start: 0.7251 (ttp) cc_final: 0.6938 (ttp) REVERT: E 276 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7270 (p0) REVERT: E 341 MET cc_start: 0.8402 (mmt) cc_final: 0.7989 (mmp) REVERT: H 61 LYS cc_start: 0.6632 (mmmt) cc_final: 0.5939 (mmtt) REVERT: H 320 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7976 (mt) REVERT: C 30 ASP cc_start: 0.7790 (t0) cc_final: 0.7528 (t0) REVERT: C 337 MET cc_start: 0.7919 (tpp) cc_final: 0.7700 (tpp) REVERT: I 384 GLU cc_start: 0.8151 (pm20) cc_final: 0.7845 (pm20) REVERT: J 18 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8943 (m-80) REVERT: J 95 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.7696 (p0) outliers start: 100 outliers final: 74 residues processed: 253 average time/residue: 0.3960 time to fit residues: 170.2141 Evaluate side-chains 233 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 154 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 392 ASN Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain G residue 296 ASP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 343 ASN Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 329 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 249 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 287 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 340 optimal weight: 7.9990 chunk 212 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS H 187 ASN H 343 ASN I 262 ASN J 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30351 Z= 0.182 Angle : 0.544 12.768 41483 Z= 0.273 Chirality : 0.040 0.333 4608 Planarity : 0.004 0.070 5088 Dihedral : 13.317 136.238 4756 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.00 % Allowed : 16.55 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3413 helix: 0.30 (0.16), residues: 1180 sheet: -0.70 (0.23), residues: 547 loop : -1.68 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 155 HIS 0.007 0.001 HIS J 153 PHE 0.012 0.001 PHE F 265 TYR 0.024 0.001 TYR A 83 ARG 0.008 0.000 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 169 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 21 ARG cc_start: 0.7908 (mmt-90) cc_final: 0.7664 (mmm-85) REVERT: B 86 ASN cc_start: 0.7128 (OUTLIER) cc_final: 0.6674 (p0) REVERT: B 221 MET cc_start: 0.7800 (ttt) cc_final: 0.7543 (ttm) REVERT: G 137 MET cc_start: 0.7199 (mtp) cc_final: 0.6803 (mtp) REVERT: G 337 MET cc_start: 0.6531 (tpt) cc_final: 0.6193 (tpp) REVERT: G 353 LYS cc_start: 0.6571 (mppt) cc_final: 0.6333 (mppt) REVERT: F 337 MET cc_start: 0.7295 (tpt) cc_final: 0.7062 (mmm) REVERT: E 5 LYS cc_start: 0.8269 (pptt) cc_final: 0.7903 (tptp) REVERT: E 46 MET cc_start: 0.7959 (mmt) cc_final: 0.7639 (mmm) REVERT: E 116 VAL cc_start: 0.8575 (p) cc_final: 0.8322 (m) REVERT: E 223 MET cc_start: 0.7244 (ttp) cc_final: 0.6940 (ttp) REVERT: E 276 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7246 (p0) REVERT: E 341 MET cc_start: 0.8410 (mmt) cc_final: 0.7962 (mmp) REVERT: H 61 LYS cc_start: 0.6652 (mmmt) cc_final: 0.5931 (mmtt) REVERT: H 320 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7971 (mt) REVERT: H 341 MET cc_start: 0.7245 (mmp) cc_final: 0.6782 (mmm) REVERT: C 30 ASP cc_start: 0.7751 (t0) cc_final: 0.7485 (t0) REVERT: C 123 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6990 (tm-30) REVERT: C 337 MET cc_start: 0.7917 (tpp) cc_final: 0.7674 (tpp) REVERT: I 384 GLU cc_start: 0.8119 (pm20) cc_final: 0.7828 (pm20) REVERT: J 18 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8949 (m-80) REVERT: J 95 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.7738 (p0) outliers start: 92 outliers final: 73 residues processed: 249 average time/residue: 0.3782 time to fit residues: 158.5304 Evaluate side-chains 235 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 157 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 20 ASP Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain G residue 296 ASP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 343 ASN Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 181 CYS Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 210 optimal weight: 0.0000 chunk 135 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 216 optimal weight: 0.0270 chunk 231 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 267 optimal weight: 0.0670 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 343 ASN D 189 ASN C 221 ASN ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 153 HIS ** J 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30351 Z= 0.163 Angle : 0.532 12.473 41483 Z= 0.268 Chirality : 0.040 0.348 4608 Planarity : 0.004 0.067 5088 Dihedral : 13.289 136.821 4756 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.61 % Allowed : 17.46 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3413 helix: 0.39 (0.16), residues: 1181 sheet: -0.52 (0.23), residues: 537 loop : -1.61 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 155 HIS 0.007 0.001 HIS J 153 PHE 0.012 0.001 PHE F 265 TYR 0.024 0.001 TYR A 83 ARG 0.006 0.000 ARG D 213 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 167 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8076 (tpp) cc_final: 0.7806 (tpp) REVERT: B 21 ARG cc_start: 0.7881 (mmt-90) cc_final: 0.7642 (mmm-85) REVERT: B 86 ASN cc_start: 0.7119 (OUTLIER) cc_final: 0.6670 (p0) REVERT: B 221 MET cc_start: 0.7806 (ttt) cc_final: 0.7547 (ttm) REVERT: G 137 MET cc_start: 0.7185 (mtp) cc_final: 0.6810 (mtp) REVERT: G 337 MET cc_start: 0.6522 (tpt) cc_final: 0.6200 (tpp) REVERT: F 30 ASP cc_start: 0.7310 (m-30) cc_final: 0.6886 (m-30) REVERT: F 337 MET cc_start: 0.7184 (tpt) cc_final: 0.6968 (mmm) REVERT: E 116 VAL cc_start: 0.8571 (p) cc_final: 0.8320 (m) REVERT: E 223 MET cc_start: 0.7253 (ttp) cc_final: 0.6932 (ttp) REVERT: E 341 MET cc_start: 0.8415 (mmt) cc_final: 0.7942 (mmp) REVERT: H 61 LYS cc_start: 0.6676 (mmmt) cc_final: 0.6031 (mmtt) REVERT: H 341 MET cc_start: 0.7278 (mmp) cc_final: 0.6846 (mmm) REVERT: C 30 ASP cc_start: 0.7705 (t0) cc_final: 0.7438 (t0) REVERT: C 123 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6971 (tm-30) REVERT: C 289 ARG cc_start: 0.7903 (mpt180) cc_final: 0.7665 (mpt180) REVERT: C 337 MET cc_start: 0.7905 (tpp) cc_final: 0.7600 (tpp) REVERT: I 384 GLU cc_start: 0.8119 (pm20) cc_final: 0.7802 (pm20) REVERT: J 18 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8863 (m-80) REVERT: J 95 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.7744 (p0) outliers start: 80 outliers final: 63 residues processed: 237 average time/residue: 0.3671 time to fit residues: 146.8082 Evaluate side-chains 227 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 161 time to evaluate : 3.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 20 ASP Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 196 MET Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 296 ASP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 290 PHE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 332 LEU Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 309 optimal weight: 0.0030 chunk 325 optimal weight: 5.9990 chunk 297 optimal weight: 6.9990 chunk 317 optimal weight: 7.9990 chunk 190 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 286 optimal weight: 8.9990 chunk 299 optimal weight: 4.9990 chunk 315 optimal weight: 10.0000 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS B 392 ASN G 80 HIS G 250 GLN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN E 221 ASN I 46 HIS I 60 ASN J 207 HIS J 345 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 30351 Z= 0.445 Angle : 0.649 12.417 41483 Z= 0.327 Chirality : 0.045 0.408 4608 Planarity : 0.005 0.065 5088 Dihedral : 13.330 138.709 4753 Min Nonbonded Distance : 1.449 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.23 % Allowed : 17.01 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3413 helix: 0.15 (0.16), residues: 1191 sheet: -0.77 (0.23), residues: 553 loop : -1.69 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 155 HIS 0.033 0.001 HIS I 153 PHE 0.024 0.002 PHE H 92 TYR 0.026 0.002 TYR B 123 ARG 0.007 0.001 ARG C 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 160 time to evaluate : 4.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8204 (tpp) cc_final: 0.7783 (tpp) REVERT: B 21 ARG cc_start: 0.7914 (mmt-90) cc_final: 0.7648 (mmm-85) REVERT: B 86 ASN cc_start: 0.7193 (OUTLIER) cc_final: 0.6786 (p0) REVERT: B 221 MET cc_start: 0.7869 (ttt) cc_final: 0.7585 (ttm) REVERT: B 487 PHE cc_start: 0.7788 (t80) cc_final: 0.7503 (t80) REVERT: G 137 MET cc_start: 0.7185 (mtp) cc_final: 0.6801 (mtp) REVERT: F 337 MET cc_start: 0.7329 (tpt) cc_final: 0.7071 (mmm) REVERT: E 5 LYS cc_start: 0.8263 (pptt) cc_final: 0.7892 (tptp) REVERT: E 120 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7551 (mm-30) REVERT: E 223 MET cc_start: 0.7311 (ttp) cc_final: 0.6989 (ttp) REVERT: E 276 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7285 (p0) REVERT: H 61 LYS cc_start: 0.6815 (mmmt) cc_final: 0.6147 (mmtt) REVERT: H 320 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7998 (mt) REVERT: H 337 MET cc_start: 0.7415 (tpp) cc_final: 0.7071 (ttp) REVERT: C 30 ASP cc_start: 0.7817 (t0) cc_final: 0.7559 (t0) REVERT: C 280 GLU cc_start: 0.6545 (pp20) cc_final: 0.6265 (pp20) REVERT: C 337 MET cc_start: 0.8060 (tpp) cc_final: 0.7720 (tpp) REVERT: I 384 GLU cc_start: 0.8164 (pm20) cc_final: 0.7788 (pm20) REVERT: J 18 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.9047 (m-80) REVERT: J 95 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.7836 (p0) outliers start: 99 outliers final: 77 residues processed: 245 average time/residue: 0.3694 time to fit residues: 154.5758 Evaluate side-chains 238 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 155 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 392 ASN Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 20 ASP Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 277 TRP Chi-restraints excluded: chain G residue 296 ASP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 154 CYS Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 123 HIS Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 208 optimal weight: 0.9990 chunk 335 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 233 optimal weight: 0.4980 chunk 351 optimal weight: 50.0000 chunk 323 optimal weight: 0.9980 chunk 280 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 216 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS J 345 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30351 Z= 0.175 Angle : 0.554 12.154 41483 Z= 0.279 Chirality : 0.041 0.376 4608 Planarity : 0.004 0.068 5088 Dihedral : 13.316 139.772 4753 Min Nonbonded Distance : 1.515 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.31 % Allowed : 18.21 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 3413 helix: 0.36 (0.16), residues: 1182 sheet: -0.64 (0.23), residues: 542 loop : -1.58 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 162 HIS 0.027 0.001 HIS I 153 PHE 0.013 0.001 PHE F 265 TYR 0.026 0.001 TYR A 83 ARG 0.012 0.000 ARG D 213 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6826 Ramachandran restraints generated. 3413 Oldfield, 0 Emsley, 3413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 160 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8067 (tpp) cc_final: 0.7687 (tpp) REVERT: B 21 ARG cc_start: 0.7855 (mmt-90) cc_final: 0.7588 (mmm-85) REVERT: B 86 ASN cc_start: 0.7142 (OUTLIER) cc_final: 0.6693 (p0) REVERT: B 221 MET cc_start: 0.7784 (ttt) cc_final: 0.7523 (ttm) REVERT: G 137 MET cc_start: 0.7193 (mtp) cc_final: 0.6817 (mtp) REVERT: G 337 MET cc_start: 0.6527 (tpt) cc_final: 0.6158 (tpp) REVERT: F 337 MET cc_start: 0.7276 (tpt) cc_final: 0.7060 (mmm) REVERT: E 46 MET cc_start: 0.7920 (mmt) cc_final: 0.7604 (mmm) REVERT: E 116 VAL cc_start: 0.8602 (p) cc_final: 0.8347 (m) REVERT: E 223 MET cc_start: 0.7257 (ttp) cc_final: 0.6954 (ttp) REVERT: E 276 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7221 (p0) REVERT: H 61 LYS cc_start: 0.6783 (mmmt) cc_final: 0.6161 (mmtt) REVERT: H 337 MET cc_start: 0.7318 (tpp) cc_final: 0.6927 (ttp) REVERT: H 341 MET cc_start: 0.7287 (mmp) cc_final: 0.6729 (mmm) REVERT: C 30 ASP cc_start: 0.7709 (t0) cc_final: 0.7443 (t0) REVERT: C 123 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7091 (tm-30) REVERT: C 337 MET cc_start: 0.7880 (tpp) cc_final: 0.7493 (tpp) REVERT: I 384 GLU cc_start: 0.8145 (pm20) cc_final: 0.7822 (pm20) REVERT: J 18 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.9039 (m-80) REVERT: J 95 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.7770 (p0) outliers start: 71 outliers final: 61 residues processed: 224 average time/residue: 0.3828 time to fit residues: 145.9565 Evaluate side-chains 220 residues out of total 3069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 155 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain G residue 20 ASP Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 273 THR Chi-restraints excluded: chain G residue 296 ASP Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 245 ASN Chi-restraints excluded: chain E residue 276 ASP Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain C residue 106 CYS Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 277 TRP Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 95 ASN Chi-restraints excluded: chain I residue 114 VAL Chi-restraints excluded: chain I residue 115 PHE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 157 LEU Chi-restraints excluded: chain I residue 332 LEU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 372 ILE Chi-restraints excluded: chain J residue 18 PHE Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 95 ASN Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain J residue 153 HIS Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 268 VAL Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 343 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 222 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 258 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 280 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 288 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 51 optimal weight: 30.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 HIS ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.075365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.059870 restraints weight = 95164.115| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.73 r_work: 0.3171 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 30351 Z= 0.325 Angle : 0.598 11.595 41483 Z= 0.302 Chirality : 0.043 0.412 4608 Planarity : 0.004 0.065 5088 Dihedral : 13.288 139.476 4753 Min Nonbonded Distance : 1.534 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.54 % Allowed : 17.95 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3413 helix: 0.26 (0.16), residues: 1192 sheet: -0.74 (0.23), residues: 553 loop : -1.59 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 72 HIS 0.023 0.001 HIS I 153 PHE 0.019 0.002 PHE H 92 TYR 0.022 0.002 TYR B 123 ARG 0.004 0.000 ARG C 150 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5505.75 seconds wall clock time: 101 minutes 47.89 seconds (6107.89 seconds total)