Starting phenix.real_space_refine on Sun Feb 18 15:50:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/02_2024/7tao_25779_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/02_2024/7tao_25779.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/02_2024/7tao_25779_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/02_2024/7tao_25779_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/02_2024/7tao_25779_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/02_2024/7tao_25779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/02_2024/7tao_25779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/02_2024/7tao_25779_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tao_25779/02_2024/7tao_25779_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.231 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 14800 2.51 5 N 3542 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 121": "OD1" <-> "OD2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 3": "OE1" <-> "OE2" Residue "H GLU 3": "OE1" <-> "OE2" Residue "L TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B ASP 191": "OD1" <-> "OD2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 804": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22497 Number of models: 1 Model: "" Number of chains: 23 Chain: "D" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1144 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1472 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 2, 'TRANS': 195} Chain: "N" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 400 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 570 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "O" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 529 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2801 Classifications: {'peptide': 345} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 335} Chain: "A" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6089 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 728} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'WEV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'WEV': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'WEV': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'WEV': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'WEV': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'WEV': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'WEV': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'WEV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.51, per 1000 atoms: 0.51 Number of scatterers: 22497 At special positions: 0 Unit cell: (124.324, 119.496, 133.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 4020 8.00 N 3542 7.00 C 14800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 75 " distance=2.02 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: 9.50 Conformation dependent library (CDL) restraints added in 3.7 seconds 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5252 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 107 helices and 3 sheets defined 73.9% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'D' and resid 15 through 51 removed outlier: 3.786A pdb=" N GLY D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 56 Processing helix chain 'D' and resid 61 through 83 removed outlier: 3.910A pdb=" N LEU D 69 " --> pdb=" O MET D 65 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN D 83 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 127 removed outlier: 3.949A pdb=" N VAL D 122 " --> pdb=" O MET D 118 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 124 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG D 125 " --> pdb=" O ASP D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 163 removed outlier: 4.263A pdb=" N VAL D 135 " --> pdb=" O ARG D 132 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL D 146 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 147 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER D 163 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 38 Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 56 through 90 removed outlier: 3.545A pdb=" N SER C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 124 removed outlier: 3.502A pdb=" N THR C 97 " --> pdb=" O PRO C 94 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR C 98 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 101 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE C 102 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL C 109 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C 110 " --> pdb=" O CYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 176 removed outlier: 3.790A pdb=" N ALA C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 205 removed outlier: 3.515A pdb=" N PHE C 181 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 182 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LEU C 185 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 186 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C 205 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 Processing helix chain 'N' and resid 252 through 254 No H-bonds generated for 'chain 'N' and resid 252 through 254' Processing helix chain 'M' and resid 4 through 24 Processing helix chain 'M' and resid 30 through 55 removed outlier: 3.567A pdb=" N GLN M 55 " --> pdb=" O THR M 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 43 removed outlier: 3.566A pdb=" N PHE E 23 " --> pdb=" O ALA E 20 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR E 24 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL E 37 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N CYS E 43 " --> pdb=" O CYS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 77 removed outlier: 3.868A pdb=" N ILE E 63 " --> pdb=" O MET E 59 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 118 Processing helix chain 'E' and resid 123 through 153 removed outlier: 3.790A pdb=" N VAL E 127 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER E 152 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 32 Processing helix chain 'O' and resid 36 through 39 No H-bonds generated for 'chain 'O' and resid 36 through 39' Processing helix chain 'O' and resid 48 through 74 Processing helix chain 'F' and resid 7 through 42 Proline residue: F 10 - end of helix removed outlier: 3.858A pdb=" N ALA F 20 " --> pdb=" O CYS F 17 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE F 23 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR F 24 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER F 35 " --> pdb=" O THR F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 75 removed outlier: 3.694A pdb=" N PHE F 51 " --> pdb=" O ASP F 48 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE F 54 " --> pdb=" O PHE F 51 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL F 55 " --> pdb=" O LYS F 52 " (cutoff:3.500A) Proline residue: F 56 - end of helix removed outlier: 3.518A pdb=" N MET F 59 " --> pdb=" O PRO F 56 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N CYS F 75 " --> pdb=" O VAL F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 119 removed outlier: 3.711A pdb=" N ALA F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA F 114 " --> pdb=" O ILE F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 153 removed outlier: 3.642A pdb=" N PHE F 126 " --> pdb=" O PRO F 123 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL F 127 " --> pdb=" O ARG F 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 45 removed outlier: 3.725A pdb=" N GLY G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE G 21 " --> pdb=" O CYS G 17 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER G 35 " --> pdb=" O GLY G 31 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU G 45 " --> pdb=" O ALA G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 75 Proline residue: G 56 - end of helix removed outlier: 3.561A pdb=" N ILE G 63 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA G 64 " --> pdb=" O GLY G 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS G 75 " --> pdb=" O VAL G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 117 removed outlier: 3.787A pdb=" N ALA G 103 " --> pdb=" O LEU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 121 No H-bonds generated for 'chain 'G' and resid 119 through 121' Processing helix chain 'G' and resid 123 through 152 removed outlier: 3.548A pdb=" N GLU G 137 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL G 138 " --> pdb=" O PHE G 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 45 removed outlier: 3.749A pdb=" N GLY H 13 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE H 21 " --> pdb=" O CYS H 17 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER H 35 " --> pdb=" O GLY H 31 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY H 38 " --> pdb=" O LYS H 34 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 77 removed outlier: 3.637A pdb=" N ILE H 62 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE H 63 " --> pdb=" O MET H 59 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE H 65 " --> pdb=" O GLY H 61 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 121 removed outlier: 4.679A pdb=" N GLY H 92 " --> pdb=" O PHE H 88 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA H 103 " --> pdb=" O LEU H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 153 removed outlier: 3.701A pdb=" N LEU H 139 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG H 153 " --> pdb=" O LEU H 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 43 Proline residue: I 10 - end of helix removed outlier: 3.739A pdb=" N SER I 19 " --> pdb=" O GLY I 16 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA I 20 " --> pdb=" O CYS I 17 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR I 24 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS I 34 " --> pdb=" O GLY I 31 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL I 37 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS I 43 " --> pdb=" O CYS I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 52 through 77 removed outlier: 3.626A pdb=" N VAL I 55 " --> pdb=" O LYS I 52 " (cutoff:3.500A) Proline residue: I 56 - end of helix Processing helix chain 'I' and resid 84 through 121 removed outlier: 4.089A pdb=" N ALA I 114 " --> pdb=" O ILE I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 154 Processing helix chain 'J' and resid 7 through 42 Proline residue: J 10 - end of helix removed outlier: 3.636A pdb=" N ALA J 20 " --> pdb=" O CYS J 17 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE J 23 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR J 24 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER J 35 " --> pdb=" O THR J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 49 No H-bonds generated for 'chain 'J' and resid 47 through 49' Processing helix chain 'J' and resid 51 through 53 No H-bonds generated for 'chain 'J' and resid 51 through 53' Processing helix chain 'J' and resid 55 through 77 removed outlier: 3.850A pdb=" N ILE J 63 " --> pdb=" O MET J 59 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER J 77 " --> pdb=" O LEU J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 118 removed outlier: 3.687A pdb=" N ALA J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 152 removed outlier: 3.758A pdb=" N VAL J 138 " --> pdb=" O PHE J 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 42 removed outlier: 3.654A pdb=" N GLY K 13 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 49 No H-bonds generated for 'chain 'K' and resid 47 through 49' Processing helix chain 'K' and resid 55 through 75 removed outlier: 3.801A pdb=" N ILE K 63 " --> pdb=" O MET K 59 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE K 65 " --> pdb=" O GLY K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 119 removed outlier: 3.698A pdb=" N ALA K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 153 removed outlier: 3.587A pdb=" N VAL K 127 " --> pdb=" O ARG K 124 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL K 138 " --> pdb=" O PHE K 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 43 removed outlier: 3.721A pdb=" N GLY L 13 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE L 21 " --> pdb=" O CYS L 17 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 49 No H-bonds generated for 'chain 'L' and resid 47 through 49' Processing helix chain 'L' and resid 53 through 77 Proline residue: L 56 - end of helix Processing helix chain 'L' and resid 84 through 121 removed outlier: 3.708A pdb=" N SER L 120 " --> pdb=" O VAL L 116 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN L 121 " --> pdb=" O ARG L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 153 removed outlier: 3.888A pdb=" N VAL L 127 " --> pdb=" O ARG L 124 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL L 138 " --> pdb=" O PHE L 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 9 No H-bonds generated for 'chain 'B' and resid 6 through 9' Processing helix chain 'B' and resid 11 through 22 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 39 through 48 removed outlier: 3.574A pdb=" N SER B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 86 Processing helix chain 'B' and resid 90 through 116 removed outlier: 3.712A pdb=" N GLY B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR B 102 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 137 through 140 Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 174 through 198 Processing helix chain 'B' and resid 204 through 228 Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 262 through 271 removed outlier: 4.489A pdb=" N ASN B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 284 through 301 Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.525A pdb=" N LYS B 314 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 332 " --> pdb=" O CYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'A' and resid 23 through 36 removed outlier: 5.684A pdb=" N ARG A 27 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 36 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 Processing helix chain 'A' and resid 88 through 91 No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 104 through 145 Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 193 through 207 removed outlier: 4.680A pdb=" N ALA A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N THR A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 280 through 303 Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 343 through 360 removed outlier: 4.366A pdb=" N ALA A 347 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.769A pdb=" N TYR A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 423 removed outlier: 3.704A pdb=" N ILE A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 426 through 441 removed outlier: 3.670A pdb=" N LEU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 453 through 456 No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 462 through 479 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'A' and resid 526 through 562 removed outlier: 4.466A pdb=" N LEU A 529 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN A 533 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 543 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE A 546 " --> pdb=" O MET A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 572 through 582 Processing helix chain 'A' and resid 584 through 595 Processing helix chain 'A' and resid 598 through 601 No H-bonds generated for 'chain 'A' and resid 598 through 601' Processing helix chain 'A' and resid 608 through 617 removed outlier: 3.812A pdb=" N PHE A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 657 Proline residue: A 646 - end of helix removed outlier: 5.136A pdb=" N LYS A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Proline residue: A 653 - end of helix Processing helix chain 'A' and resid 707 through 754 removed outlier: 3.914A pdb=" N VAL A 727 " --> pdb=" O CYS A 723 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU A 734 " --> pdb=" O THR A 730 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TRP A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 4.235A pdb=" N GLY A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 756 through 760' Processing helix chain 'A' and resid 763 through 784 Processing helix chain 'A' and resid 789 through 802 removed outlier: 3.678A pdb=" N MET A 794 " --> pdb=" O GLY A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 809 No H-bonds generated for 'chain 'A' and resid 806 through 809' Processing sheet with id= A, first strand: chain 'A' and resid 334 through 342 removed outlier: 3.802A pdb=" N ILE A 341 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 16 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 189 through 192 Processing sheet with id= C, first strand: chain 'A' and resid 222 through 224 removed outlier: 3.521A pdb=" N GLU A 229 " --> pdb=" O ASP A 224 " (cutoff:3.500A) 1613 hydrogen bonds defined for protein. 3321 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.55 Time building geometry restraints manager: 10.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3491 1.32 - 1.45: 6118 1.45 - 1.57: 13117 1.57 - 1.70: 24 1.70 - 1.83: 204 Bond restraints: 22954 Sorted by residual: bond pdb=" C15 WEV K 901 " pdb=" C16 WEV K 901 " ideal model delta sigma weight residual 1.687 1.350 0.337 2.00e-02 2.50e+03 2.84e+02 bond pdb=" C15 WEV D 202 " pdb=" C16 WEV D 202 " ideal model delta sigma weight residual 1.687 1.351 0.336 2.00e-02 2.50e+03 2.82e+02 bond pdb=" C15 WEV F 201 " pdb=" C16 WEV F 201 " ideal model delta sigma weight residual 1.687 1.352 0.335 2.00e-02 2.50e+03 2.81e+02 bond pdb=" C15 WEV H 201 " pdb=" C16 WEV H 201 " ideal model delta sigma weight residual 1.687 1.352 0.335 2.00e-02 2.50e+03 2.80e+02 bond pdb=" C15 WEV I 201 " pdb=" C16 WEV I 201 " ideal model delta sigma weight residual 1.687 1.353 0.334 2.00e-02 2.50e+03 2.79e+02 ... (remaining 22949 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.28: 417 106.28 - 113.21: 12811 113.21 - 120.14: 8164 120.14 - 127.08: 9643 127.08 - 134.01: 170 Bond angle restraints: 31205 Sorted by residual: angle pdb=" C14 WEV E 201 " pdb=" C15 WEV E 201 " pdb=" C21 WEV E 201 " ideal model delta sigma weight residual 68.66 123.15 -54.49 3.00e+00 1.11e-01 3.30e+02 angle pdb=" C14 WEV J 201 " pdb=" C15 WEV J 201 " pdb=" C21 WEV J 201 " ideal model delta sigma weight residual 68.66 122.71 -54.05 3.00e+00 1.11e-01 3.25e+02 angle pdb=" C03 WEV F 201 " pdb=" C04 WEV F 201 " pdb=" C44 WEV F 201 " ideal model delta sigma weight residual 68.54 121.33 -52.79 3.00e+00 1.11e-01 3.10e+02 angle pdb=" C14 WEV F 201 " pdb=" C15 WEV F 201 " pdb=" C21 WEV F 201 " ideal model delta sigma weight residual 68.66 121.40 -52.74 3.00e+00 1.11e-01 3.09e+02 angle pdb=" C03 WEV H 201 " pdb=" C04 WEV H 201 " pdb=" C44 WEV H 201 " ideal model delta sigma weight residual 68.54 121.25 -52.71 3.00e+00 1.11e-01 3.09e+02 ... (remaining 31200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 12957 35.53 - 71.06: 253 71.06 - 106.59: 46 106.59 - 142.12: 13 142.12 - 177.65: 21 Dihedral angle restraints: 13290 sinusoidal: 5016 harmonic: 8274 Sorted by residual: dihedral pdb=" C04 WEV G 201 " pdb=" C05 WEV G 201 " pdb=" C06 WEV G 201 " pdb=" C07 WEV G 201 " ideal model delta sinusoidal sigma weight residual -2.23 175.42 -177.65 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C04 WEV F 201 " pdb=" C05 WEV F 201 " pdb=" C06 WEV F 201 " pdb=" C07 WEV F 201 " ideal model delta sinusoidal sigma weight residual -2.23 -178.07 175.84 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C04 WEV H 201 " pdb=" C05 WEV H 201 " pdb=" C06 WEV H 201 " pdb=" C07 WEV H 201 " ideal model delta sinusoidal sigma weight residual -2.23 -177.00 174.77 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 13287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 3746 1.007 - 2.013: 0 2.013 - 3.020: 0 3.020 - 4.026: 0 4.026 - 5.033: 9 Chirality restraints: 3755 Sorted by residual: chirality pdb=" C26 WEV I 201 " pdb=" C24 WEV I 201 " pdb=" C27 WEV I 201 " pdb=" O41 WEV I 201 " both_signs ideal model delta sigma weight residual False -2.52 2.52 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C26 WEV D 202 " pdb=" C24 WEV D 202 " pdb=" C27 WEV D 202 " pdb=" O41 WEV D 202 " both_signs ideal model delta sigma weight residual False -2.52 2.51 -5.03 2.00e-01 2.50e+01 6.32e+02 chirality pdb=" C26 WEV D 201 " pdb=" C24 WEV D 201 " pdb=" C27 WEV D 201 " pdb=" O41 WEV D 201 " both_signs ideal model delta sigma weight residual False -2.52 2.50 -5.02 2.00e-01 2.50e+01 6.29e+02 ... (remaining 3752 not shown) Planarity restraints: 3841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 618 " 0.042 5.00e-02 4.00e+02 6.37e-02 6.49e+00 pdb=" N PRO A 619 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 619 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 619 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 77 " -0.012 2.00e-02 2.50e+03 1.15e-02 3.28e+00 pdb=" CG TRP C 77 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP C 77 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 77 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 77 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 77 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 77 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 77 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 77 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 77 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN N 259 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO N 260 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO N 260 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO N 260 " 0.022 5.00e-02 4.00e+02 ... (remaining 3838 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 250 2.67 - 3.23: 23040 3.23 - 3.78: 37896 3.78 - 4.34: 51315 4.34 - 4.90: 84422 Nonbonded interactions: 196923 Sorted by model distance: nonbonded pdb=" OH TYR A 31 " pdb=" OE1 GLU A 316 " model vdw 2.109 2.440 nonbonded pdb=" ND2 ASN A 480 " pdb=" O LEU A 518 " model vdw 2.145 2.520 nonbonded pdb=" OH TYR H 142 " pdb=" O19 WEV H 201 " model vdw 2.175 2.440 nonbonded pdb=" OH TYR J 142 " pdb=" O19 WEV J 201 " model vdw 2.177 2.440 nonbonded pdb=" ND2 ASN B 106 " pdb=" O HIS B 128 " model vdw 2.186 2.520 ... (remaining 196918 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 'E' and resid 1 through 159) selection = (chain 'F' and resid 1 through 159) selection = (chain 'G' and resid 1 through 159) selection = (chain 'H' and resid 1 through 159) selection = (chain 'I' and resid 1 through 159) selection = (chain 'J' and resid 1 through 159) selection = (chain 'K' and resid 1 through 159) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.010 Extract box with map and model: 4.980 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 59.420 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 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 : 0.011 0.337 22954 Z= 0.712 Angle : 2.558 54.490 31205 Z= 0.879 Chirality : 0.247 5.033 3755 Planarity : 0.004 0.064 3841 Dihedral : 18.057 177.650 8035 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.16), residues: 2881 helix: 1.89 (0.11), residues: 2140 sheet: -0.80 (1.01), residues: 29 loop : -0.34 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 77 HIS 0.003 0.001 HIS A 547 PHE 0.020 0.001 PHE I 88 TYR 0.017 0.001 TYR A 141 ARG 0.005 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 2.375 Fit side-chains REVERT: M 24 MET cc_start: 0.6138 (ppp) cc_final: 0.5809 (ppp) REVERT: B 293 MET cc_start: 0.6727 (mmp) cc_final: 0.6432 (mmp) REVERT: A 720 ILE cc_start: 0.7991 (mm) cc_final: 0.7725 (mm) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.3493 time to fit residues: 155.6486 Evaluate side-chains 246 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 237 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 220 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 255 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 ASN M 29 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN G 121 GLN I 80 GLN B 209 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22954 Z= 0.239 Angle : 1.071 28.554 31205 Z= 0.423 Chirality : 0.048 0.535 3755 Planarity : 0.006 0.040 3841 Dihedral : 17.485 179.540 3290 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.81 % Allowed : 5.59 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.15), residues: 2881 helix: 1.29 (0.11), residues: 2112 sheet: -0.81 (0.99), residues: 29 loop : -0.31 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 77 HIS 0.004 0.001 HIS A 801 PHE 0.038 0.001 PHE I 88 TYR 0.015 0.001 TYR A 328 ARG 0.004 0.000 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 275 time to evaluate : 2.553 Fit side-chains REVERT: G 129 MET cc_start: 0.7687 (ttp) cc_final: 0.7456 (ttp) REVERT: A 149 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6913 (m-30) REVERT: A 234 ASN cc_start: 0.7374 (m-40) cc_final: 0.7010 (m-40) REVERT: A 720 ILE cc_start: 0.7968 (mm) cc_final: 0.7630 (mm) REVERT: A 794 MET cc_start: 0.7402 (ttp) cc_final: 0.6915 (ttp) outliers start: 19 outliers final: 13 residues processed: 285 average time/residue: 0.3597 time to fit residues: 159.3022 Evaluate side-chains 275 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 261 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 823 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 141 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 255 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 253 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 205 optimal weight: 4.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 29 ASN K 53 ASN B 209 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22954 Z= 0.227 Angle : 1.000 28.154 31205 Z= 0.394 Chirality : 0.042 0.440 3755 Planarity : 0.005 0.038 3841 Dihedral : 17.318 177.865 3290 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.32 % Allowed : 7.77 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 2881 helix: 0.88 (0.11), residues: 2136 sheet: -0.85 (0.98), residues: 29 loop : -0.27 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 77 HIS 0.004 0.001 HIS A 801 PHE 0.027 0.001 PHE C 80 TYR 0.014 0.001 TYR C 57 ARG 0.004 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 275 time to evaluate : 2.372 Fit side-chains REVERT: E 21 ILE cc_start: 0.8432 (mm) cc_final: 0.8183 (mm) REVERT: K 131 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8357 (mp) REVERT: L 8 TYR cc_start: 0.8806 (p90) cc_final: 0.8519 (p90) REVERT: A 149 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.6931 (m-30) REVERT: A 234 ASN cc_start: 0.7275 (m-40) cc_final: 0.6924 (m-40) REVERT: A 349 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6962 (tp) REVERT: A 720 ILE cc_start: 0.8003 (mm) cc_final: 0.7731 (mm) REVERT: A 794 MET cc_start: 0.7440 (ttp) cc_final: 0.6987 (ttp) outliers start: 31 outliers final: 20 residues processed: 292 average time/residue: 0.3433 time to fit residues: 156.6354 Evaluate side-chains 280 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 257 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain K residue 131 LEU Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 823 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 252 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 chunk 132 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 271 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 243 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22954 Z= 0.192 Angle : 0.980 28.001 31205 Z= 0.384 Chirality : 0.041 0.413 3755 Planarity : 0.005 0.037 3841 Dihedral : 16.844 178.258 3290 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.58 % Allowed : 9.22 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 2881 helix: 0.84 (0.11), residues: 2138 sheet: -0.95 (0.98), residues: 29 loop : -0.28 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 243 HIS 0.004 0.001 HIS A 79 PHE 0.025 0.001 PHE C 80 TYR 0.011 0.001 TYR A 328 ARG 0.004 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 271 time to evaluate : 2.209 Fit side-chains REVERT: E 21 ILE cc_start: 0.8466 (mm) cc_final: 0.8245 (mm) REVERT: L 8 TYR cc_start: 0.8821 (p90) cc_final: 0.8488 (p90) REVERT: B 136 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7662 (tp) REVERT: B 149 TYR cc_start: 0.6453 (t80) cc_final: 0.6179 (t80) REVERT: A 149 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.6977 (m-30) REVERT: A 200 GLU cc_start: 0.7309 (tt0) cc_final: 0.6753 (tm-30) REVERT: A 349 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6876 (tp) REVERT: A 537 MET cc_start: 0.7645 (mtm) cc_final: 0.7340 (mtm) REVERT: A 543 MET cc_start: 0.7974 (mmm) cc_final: 0.7683 (mmm) REVERT: A 712 MET cc_start: 0.8247 (tpt) cc_final: 0.8032 (tpp) REVERT: A 720 ILE cc_start: 0.7924 (mm) cc_final: 0.7627 (mm) REVERT: A 794 MET cc_start: 0.7410 (ttp) cc_final: 0.6959 (ttp) outliers start: 37 outliers final: 24 residues processed: 294 average time/residue: 0.3443 time to fit residues: 158.3352 Evaluate side-chains 285 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 258 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 129 MET Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 823 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 226 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 202 optimal weight: 0.5980 chunk 112 optimal weight: 0.4980 chunk 231 optimal weight: 2.9990 chunk 187 optimal weight: 0.0050 chunk 0 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 243 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22954 Z= 0.178 Angle : 0.964 27.803 31205 Z= 0.378 Chirality : 0.041 0.400 3755 Planarity : 0.005 0.036 3841 Dihedral : 16.617 179.599 3290 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.71 % Allowed : 10.08 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 2881 helix: 0.87 (0.11), residues: 2137 sheet: -0.95 (1.00), residues: 29 loop : -0.27 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 243 HIS 0.003 0.000 HIS A 79 PHE 0.024 0.001 PHE C 80 TYR 0.015 0.001 TYR A 69 ARG 0.003 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 265 time to evaluate : 2.332 Fit side-chains REVERT: M 24 MET cc_start: 0.6225 (ppp) cc_final: 0.5641 (ppp) REVERT: B 136 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7668 (tp) REVERT: B 149 TYR cc_start: 0.6475 (t80) cc_final: 0.6182 (t80) REVERT: A 149 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7137 (m-30) REVERT: A 200 GLU cc_start: 0.7267 (tt0) cc_final: 0.6758 (tm-30) REVERT: A 349 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6912 (tp) REVERT: A 537 MET cc_start: 0.7640 (mtm) cc_final: 0.7216 (ttm) REVERT: A 720 ILE cc_start: 0.7999 (mm) cc_final: 0.7723 (mm) REVERT: A 794 MET cc_start: 0.7383 (ttp) cc_final: 0.6956 (ttp) outliers start: 40 outliers final: 30 residues processed: 291 average time/residue: 0.3326 time to fit residues: 152.7765 Evaluate side-chains 290 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 257 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 823 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 91 optimal weight: 0.6980 chunk 244 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 271 optimal weight: 0.5980 chunk 225 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 142 optimal weight: 0.0050 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22954 Z= 0.174 Angle : 0.961 27.548 31205 Z= 0.376 Chirality : 0.041 0.402 3755 Planarity : 0.005 0.036 3841 Dihedral : 16.388 179.051 3290 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.75 % Allowed : 11.27 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 2881 helix: 0.89 (0.11), residues: 2138 sheet: -1.21 (0.99), residues: 29 loop : -0.25 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 243 HIS 0.004 0.001 HIS A 79 PHE 0.023 0.001 PHE C 80 TYR 0.018 0.001 TYR A 69 ARG 0.004 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 273 time to evaluate : 2.334 Fit side-chains REVERT: M 24 MET cc_start: 0.6226 (ppp) cc_final: 0.5671 (ppp) REVERT: F 59 MET cc_start: 0.8090 (mtt) cc_final: 0.7713 (mmm) REVERT: B 136 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7671 (tp) REVERT: B 149 TYR cc_start: 0.6525 (t80) cc_final: 0.6207 (t80) REVERT: A 149 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7142 (m-30) REVERT: A 200 GLU cc_start: 0.7221 (tt0) cc_final: 0.6854 (tm-30) REVERT: A 213 PHE cc_start: 0.8593 (t80) cc_final: 0.8207 (t80) REVERT: A 349 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6866 (tp) REVERT: A 537 MET cc_start: 0.7631 (mtm) cc_final: 0.7336 (mtm) REVERT: A 712 MET cc_start: 0.7509 (tpp) cc_final: 0.7231 (tpt) REVERT: A 720 ILE cc_start: 0.7912 (mm) cc_final: 0.7620 (mm) REVERT: A 794 MET cc_start: 0.7315 (ttp) cc_final: 0.6849 (ttp) outliers start: 41 outliers final: 29 residues processed: 300 average time/residue: 0.3346 time to fit residues: 158.9937 Evaluate side-chains 291 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 259 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 823 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 262 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 153 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 270 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 ASN M 29 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22954 Z= 0.246 Angle : 0.976 27.920 31205 Z= 0.386 Chirality : 0.042 0.422 3755 Planarity : 0.005 0.039 3841 Dihedral : 16.313 179.144 3290 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.84 % Allowed : 11.91 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.15), residues: 2881 helix: 0.77 (0.11), residues: 2139 sheet: -1.40 (1.00), residues: 29 loop : -0.35 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 77 HIS 0.005 0.001 HIS A 801 PHE 0.028 0.001 PHE C 80 TYR 0.014 0.001 TYR L 8 ARG 0.008 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 265 time to evaluate : 2.223 Fit side-chains REVERT: M 24 MET cc_start: 0.6339 (ppp) cc_final: 0.5865 (ppp) REVERT: F 59 MET cc_start: 0.8194 (mtt) cc_final: 0.7833 (mmm) REVERT: I 80 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: L 8 TYR cc_start: 0.9041 (p90) cc_final: 0.8591 (p90) REVERT: B 149 TYR cc_start: 0.6667 (t80) cc_final: 0.6364 (t80) REVERT: A 149 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7150 (m-30) REVERT: A 213 PHE cc_start: 0.8660 (t80) cc_final: 0.8400 (t80) REVERT: A 234 ASN cc_start: 0.7232 (m-40) cc_final: 0.6903 (m-40) REVERT: A 349 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6893 (tp) REVERT: A 537 MET cc_start: 0.7641 (mtm) cc_final: 0.7352 (mtm) REVERT: A 611 MET cc_start: 0.7667 (ttp) cc_final: 0.7315 (ttt) REVERT: A 720 ILE cc_start: 0.7931 (mm) cc_final: 0.7667 (mm) REVERT: A 794 MET cc_start: 0.7470 (ttp) cc_final: 0.6976 (ttp) outliers start: 43 outliers final: 31 residues processed: 294 average time/residue: 0.3506 time to fit residues: 159.6307 Evaluate side-chains 293 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 259 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 823 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 167 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 161 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 172 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22954 Z= 0.217 Angle : 0.967 27.832 31205 Z= 0.381 Chirality : 0.041 0.419 3755 Planarity : 0.005 0.036 3841 Dihedral : 16.281 178.888 3290 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.71 % Allowed : 12.60 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 2881 helix: 0.80 (0.11), residues: 2133 sheet: -1.45 (1.01), residues: 29 loop : -0.40 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.004 0.001 HIS A 801 PHE 0.025 0.001 PHE C 80 TYR 0.014 0.001 TYR A 69 ARG 0.008 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 262 time to evaluate : 2.325 Fit side-chains REVERT: M 24 MET cc_start: 0.6339 (ppp) cc_final: 0.5888 (ppp) REVERT: F 59 MET cc_start: 0.8142 (mtt) cc_final: 0.7839 (mmm) REVERT: I 80 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8458 (tt0) REVERT: J 75 CYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7166 (m) REVERT: L 8 TYR cc_start: 0.9055 (p90) cc_final: 0.8610 (p90) REVERT: B 149 TYR cc_start: 0.6601 (t80) cc_final: 0.6205 (t80) REVERT: A 149 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7149 (m-30) REVERT: A 213 PHE cc_start: 0.8633 (t80) cc_final: 0.8398 (t80) REVERT: A 234 ASN cc_start: 0.7176 (m-40) cc_final: 0.6824 (m-40) REVERT: A 349 LEU cc_start: 0.7104 (OUTLIER) cc_final: 0.6887 (tp) REVERT: A 537 MET cc_start: 0.7665 (mtm) cc_final: 0.7233 (ttm) REVERT: A 611 MET cc_start: 0.7620 (ttp) cc_final: 0.7267 (ttt) REVERT: A 720 ILE cc_start: 0.7871 (mm) cc_final: 0.7608 (mm) REVERT: A 794 MET cc_start: 0.7430 (ttp) cc_final: 0.6961 (ttp) outliers start: 40 outliers final: 33 residues processed: 288 average time/residue: 0.3421 time to fit residues: 153.9010 Evaluate side-chains 291 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 254 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 75 CYS Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 823 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 246 optimal weight: 1.9990 chunk 259 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 198 optimal weight: 30.0000 chunk 77 optimal weight: 0.9980 chunk 228 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 251 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS A 743 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22954 Z= 0.318 Angle : 0.996 27.976 31205 Z= 0.399 Chirality : 0.043 0.435 3755 Planarity : 0.005 0.037 3841 Dihedral : 16.276 173.612 3290 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.67 % Allowed : 12.98 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 2881 helix: 0.64 (0.11), residues: 2108 sheet: -1.75 (0.92), residues: 35 loop : -0.45 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 77 HIS 0.006 0.001 HIS A 801 PHE 0.031 0.002 PHE C 80 TYR 0.016 0.001 TYR A 69 ARG 0.007 0.000 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 269 time to evaluate : 2.316 Fit side-chains revert: symmetry clash REVERT: M 24 MET cc_start: 0.6366 (ppp) cc_final: 0.5905 (ppp) REVERT: F 59 MET cc_start: 0.8224 (mtt) cc_final: 0.7903 (mmm) REVERT: H 135 PHE cc_start: 0.8758 (m-80) cc_final: 0.8268 (m-80) REVERT: I 80 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: J 75 CYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7116 (m) REVERT: L 8 TYR cc_start: 0.9069 (p90) cc_final: 0.8636 (p90) REVERT: B 149 TYR cc_start: 0.6843 (t80) cc_final: 0.6438 (t80) REVERT: A 14 MET cc_start: 0.8052 (mtt) cc_final: 0.7840 (mmt) REVERT: A 149 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7108 (m-30) REVERT: A 234 ASN cc_start: 0.7230 (m-40) cc_final: 0.6875 (m-40) REVERT: A 254 GLU cc_start: 0.8240 (tp30) cc_final: 0.7844 (tp30) REVERT: A 349 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6871 (tp) REVERT: A 537 MET cc_start: 0.7681 (mtm) cc_final: 0.7234 (ttm) REVERT: A 611 MET cc_start: 0.7708 (ttp) cc_final: 0.7333 (ttt) REVERT: A 788 MET cc_start: 0.6810 (tpt) cc_final: 0.6564 (tpt) REVERT: A 794 MET cc_start: 0.7487 (ttp) cc_final: 0.6966 (ttp) outliers start: 39 outliers final: 32 residues processed: 294 average time/residue: 0.3461 time to fit residues: 158.2807 Evaluate side-chains 299 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 263 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain I residue 80 GLN Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 75 CYS Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 755 ILE Chi-restraints excluded: chain A residue 823 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 165 optimal weight: 0.7980 chunk 266 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 185 optimal weight: 0.2980 chunk 279 optimal weight: 0.3980 chunk 257 optimal weight: 0.6980 chunk 222 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN B 209 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22954 Z= 0.188 Angle : 0.965 27.782 31205 Z= 0.381 Chirality : 0.041 0.424 3755 Planarity : 0.005 0.037 3841 Dihedral : 16.257 174.261 3290 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.37 % Allowed : 13.58 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 2881 helix: 0.77 (0.11), residues: 2127 sheet: -1.40 (1.05), residues: 29 loop : -0.38 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 48 HIS 0.004 0.001 HIS A 79 PHE 0.023 0.001 PHE C 80 TYR 0.012 0.001 TYR L 8 ARG 0.007 0.000 ARG A 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5762 Ramachandran restraints generated. 2881 Oldfield, 0 Emsley, 2881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 274 time to evaluate : 2.595 Fit side-chains REVERT: M 24 MET cc_start: 0.6334 (ppp) cc_final: 0.5896 (ppp) REVERT: F 59 MET cc_start: 0.8031 (mtt) cc_final: 0.7757 (mmm) REVERT: J 75 CYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7289 (m) REVERT: L 8 TYR cc_start: 0.9068 (p90) cc_final: 0.8602 (p90) REVERT: B 149 TYR cc_start: 0.6728 (t80) cc_final: 0.6344 (t80) REVERT: A 149 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7149 (m-30) REVERT: A 234 ASN cc_start: 0.7167 (m-40) cc_final: 0.6822 (m-40) REVERT: A 254 GLU cc_start: 0.8213 (tp30) cc_final: 0.7903 (tp30) REVERT: A 349 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6888 (tp) REVERT: A 537 MET cc_start: 0.7666 (mtm) cc_final: 0.7272 (ttm) REVERT: A 611 MET cc_start: 0.7624 (ttp) cc_final: 0.7288 (ttt) REVERT: A 788 MET cc_start: 0.6412 (tpt) cc_final: 0.6188 (tpt) REVERT: A 794 MET cc_start: 0.7425 (ttp) cc_final: 0.6963 (ttp) outliers start: 32 outliers final: 24 residues processed: 294 average time/residue: 0.3617 time to fit residues: 164.5519 Evaluate side-chains 293 residues out of total 2355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 266 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 75 CYS Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 498 ASP Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 823 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 177 optimal weight: 0.8980 chunk 237 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 chunk 32 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 223 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 229 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 83 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 ASN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.168138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.122061 restraints weight = 21349.514| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.33 r_work: 0.3146 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22954 Z= 0.197 Angle : 0.966 27.783 31205 Z= 0.382 Chirality : 0.041 0.427 3755 Planarity : 0.005 0.036 3841 Dihedral : 16.213 174.522 3290 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.58 % Allowed : 13.71 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 2881 helix: 0.71 (0.11), residues: 2177 sheet: -1.57 (0.94), residues: 35 loop : -0.43 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 494 HIS 0.004 0.001 HIS A 79 PHE 0.024 0.001 PHE C 80 TYR 0.015 0.001 TYR A 84 ARG 0.009 0.000 ARG A 120 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4514.78 seconds wall clock time: 83 minutes 6.00 seconds (4986.00 seconds total)