Starting phenix.real_space_refine on Thu Jun 19 05:51:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tao_25779/06_2025/7tao_25779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tao_25779/06_2025/7tao_25779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tao_25779/06_2025/7tao_25779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tao_25779/06_2025/7tao_25779.map" model { file = "/net/cci-nas-00/data/ceres_data/7tao_25779/06_2025/7tao_25779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tao_25779/06_2025/7tao_25779.cif" } 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. Time to flip 26 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 15.27, per 1000 atoms: 0.68 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.48 Conformation dependent library (CDL) restraints added in 3.3 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... Secondary structure from input PDB file: 112 helices and 6 sheets defined 79.1% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'D' and resid 14 through 52 removed outlier: 3.847A pdb=" N PHE D 18 " --> pdb=" O TYR D 14 " (cutoff:3.500A) 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 57 removed outlier: 3.843A pdb=" N MET D 57 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 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 91 through 128 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 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 164 removed outlier: 4.220A pdb=" N LEU D 147 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY D 148 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU D 164 " --> pdb=" O THR D 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 39 Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 55 through 91 removed outlier: 3.637A pdb=" N TRP C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 123 removed outlier: 4.240A pdb=" N LYS C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ILE C 102 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER C 103 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 177 removed outlier: 3.790A pdb=" N ALA C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 206 removed outlier: 4.639A pdb=" N VAL C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ILE C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 194 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 220 through 247 Processing helix chain 'N' and resid 251 through 255 removed outlier: 3.715A pdb=" N GLU N 255 " --> pdb=" O GLY N 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 25 removed outlier: 4.001A pdb=" N VAL M 7 " --> pdb=" O SER M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 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 44 removed outlier: 4.215A pdb=" N GLY E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL E 44 " --> pdb=" O CYS E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 51 removed outlier: 4.027A pdb=" N LEU E 50 " --> pdb=" O PRO E 47 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE E 51 " --> pdb=" O ASP E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 47 through 51' Processing helix chain 'E' and resid 54 through 78 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 83 through 119 Processing helix chain 'E' and resid 124 through 153 removed outlier: 4.438A pdb=" N GLY E 128 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU E 139 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG E 153 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 33 Processing helix chain 'O' and resid 35 through 40 Processing helix chain 'O' and resid 47 through 75 removed outlier: 3.708A pdb=" N VAL O 51 " --> pdb=" O ASP O 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 43 removed outlier: 4.319A pdb=" N PHE F 12 " --> pdb=" O TYR F 8 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE F 21 " --> pdb=" O CYS F 17 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 Processing helix chain 'F' and resid 54 through 76 removed outlier: 3.758A pdb=" N ILE F 63 " --> pdb=" O MET F 59 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 120 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) removed outlier: 3.672A pdb=" N SER F 120 " --> pdb=" O VAL F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 152 removed outlier: 4.493A pdb=" N GLY F 128 " --> pdb=" O ARG F 124 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU F 139 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 46 removed outlier: 4.129A pdb=" N PHE G 12 " --> pdb=" O TYR G 8 " (cutoff:3.500A) 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 54 through 78 removed outlier: 3.771A pdb=" N ILE G 63 " --> pdb=" O MET G 59 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE G 65 " --> pdb=" O GLY G 61 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 118 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 122 Processing helix chain 'G' and resid 123 through 153 removed outlier: 4.159A pdb=" N VAL G 127 " --> pdb=" O PRO G 123 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU G 139 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 46 removed outlier: 4.178A pdb=" N PHE H 12 " --> pdb=" O TYR H 8 " (cutoff:3.500A) 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 54 through 61 Processing helix chain 'H' and resid 62 through 76 Processing helix chain 'H' and resid 83 through 122 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 125 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 8 through 44 removed outlier: 4.181A pdb=" N PHE I 12 " --> pdb=" O TYR I 8 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY I 13 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE I 21 " --> pdb=" O CYS I 17 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY I 38 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL I 44 " --> pdb=" O CYS I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 50 removed outlier: 3.790A pdb=" N LEU I 50 " --> pdb=" O PRO I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 53 No H-bonds generated for 'chain 'I' and resid 51 through 53' Processing helix chain 'I' and resid 54 through 77 removed outlier: 3.576A pdb=" N SER I 77 " --> pdb=" O LEU I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 122 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 155 removed outlier: 4.191A pdb=" N GLY I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU I 139 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR I 155 " --> pdb=" O ASN I 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 43 removed outlier: 4.081A pdb=" N PHE J 12 " --> pdb=" O TYR J 8 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY J 13 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE J 21 " --> pdb=" O CYS J 17 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 53 removed outlier: 3.641A pdb=" N LEU J 49 " --> pdb=" O ARG J 46 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE J 51 " --> pdb=" O ASP J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 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 83 through 119 removed outlier: 3.687A pdb=" N ALA J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 153 removed outlier: 4.207A pdb=" N GLY J 128 " --> pdb=" O ARG J 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU J 139 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 43 removed outlier: 3.974A pdb=" N PHE K 12 " --> pdb=" O TYR K 8 " (cutoff:3.500A) 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 46 through 50 removed outlier: 3.801A pdb=" N LEU K 50 " --> pdb=" O PRO K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 76 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 83 through 120 removed outlier: 3.698A pdb=" N ALA K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 123 No H-bonds generated for 'chain 'K' and resid 121 through 123' Processing helix chain 'K' and resid 124 through 152 removed outlier: 4.000A pdb=" N GLY K 128 " --> pdb=" O ARG K 124 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE K 135 " --> pdb=" O LEU K 131 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA K 136 " --> pdb=" O ILE K 132 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 44 removed outlier: 3.907A pdb=" N PHE L 12 " --> pdb=" O TYR L 8 " (cutoff:3.500A) 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) removed outlier: 3.903A pdb=" N VAL L 44 " --> pdb=" O CYS L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 50 Processing helix chain 'L' and resid 54 through 78 removed outlier: 3.937A pdb=" N ILE L 63 " --> pdb=" O MET L 59 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA L 64 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR L 76 " --> pdb=" O VAL L 72 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER L 77 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 120 removed outlier: 3.708A pdb=" N SER L 120 " --> pdb=" O VAL L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 152 removed outlier: 4.411A pdb=" N GLY L 128 " --> pdb=" O ARG L 124 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU L 139 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY L 140 " --> pdb=" O ALA L 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 removed outlier: 4.564A pdb=" N ASP B 9 " --> pdb=" O TYR B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 23 Processing helix chain 'B' and resid 26 through 35 Processing helix chain 'B' and resid 38 through 49 removed outlier: 3.574A pdb=" N SER B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 49 " --> pdb=" O GLN B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 86 Processing helix chain 'B' and resid 89 through 117 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 119 through 127 Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.869A pdb=" N ASP B 167 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 168 " --> pdb=" O CYS B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 164 through 168' Processing helix chain 'B' and resid 173 through 199 Processing helix chain 'B' and resid 203 through 229 removed outlier: 3.863A pdb=" N GLN B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'B' and resid 250 through 259 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 275 through 281 removed outlier: 3.767A pdb=" N LEU B 279 " --> pdb=" O TYR B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 300 Processing helix chain 'B' and resid 306 through 333 removed outlier: 4.076A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 338 removed outlier: 4.292A pdb=" N ARG B 337 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 338' Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 55 through 79 Processing helix chain 'A' and resid 87 through 92 removed outlier: 4.279A pdb=" N TYR A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 146 Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 193 through 208 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 242 through 256 removed outlier: 3.606A pdb=" N LEU A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 279 through 304 Processing helix chain 'A' and resid 305 through 324 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.769A pdb=" N TYR A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 398 " --> pdb=" O CYS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 424 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 425 through 442 removed outlier: 3.670A pdb=" N LEU A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 449 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 461 through 480 Processing helix chain 'A' and resid 519 through 523 Processing helix chain 'A' and resid 527 through 563 removed outlier: 3.904A pdb=" N SER A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 554 " --> pdb=" O TYR A 550 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 555 " --> pdb=" O SER A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 571 Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.650A pdb=" N GLY A 575 " --> pdb=" O ASN A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 595 Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 607 through 618 removed outlier: 3.812A pdb=" N PHE A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 658 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 733 removed outlier: 3.914A pdb=" N VAL A 727 " --> pdb=" O CYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 761 removed outlier: 4.030A pdb=" N GLN A 756 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE A 757 " --> pdb=" O MET A 753 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA A 758 " --> pdb=" O THR A 754 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 761 " --> pdb=" O ILE A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 785 Processing helix chain 'A' and resid 788 through 803 removed outlier: 3.678A pdb=" N MET A 794 " --> pdb=" O GLY A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 810 removed outlier: 4.031A pdb=" N PHE A 809 " --> pdb=" O SER A 805 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 63 through 64 Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 3.632A pdb=" N ILE A 336 " --> pdb=" O ASN A 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 40 through 41 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=AA4, first strand: chain 'A' and resid 214 through 215 Processing sheet with id=AA5, 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) Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 495 1728 hydrogen bonds defined for protein. 5082 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: 8.64 Time building geometry restraints manager: 9.20 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=" C05 WEV E 201 " pdb=" C06 WEV E 201 " ideal model delta sigma weight residual 1.449 1.565 -0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C05 WEV D 201 " pdb=" C06 WEV D 201 " ideal model delta sigma weight residual 1.449 1.564 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C05 WEV H 201 " pdb=" C06 WEV H 201 " ideal model delta sigma weight residual 1.449 1.563 -0.114 2.00e-02 2.50e+03 3.23e+01 bond pdb=" C05 WEV K 901 " pdb=" C06 WEV K 901 " ideal model delta sigma weight residual 1.449 1.562 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" C05 WEV F 201 " pdb=" C06 WEV F 201 " ideal model delta sigma weight residual 1.449 1.562 -0.113 2.00e-02 2.50e+03 3.19e+01 ... (remaining 22949 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 30772 2.55 - 5.10: 333 5.10 - 7.64: 71 7.64 - 10.19: 17 10.19 - 12.74: 12 Bond angle restraints: 31205 Sorted by residual: angle pdb=" C ILE H 54 " pdb=" N VAL H 55 " pdb=" CA VAL H 55 " ideal model delta sigma weight residual 120.24 123.09 -2.85 6.30e-01 2.52e+00 2.05e+01 angle pdb=" C09 WEV E 201 " pdb=" O10 WEV E 201 " pdb=" C11 WEV E 201 " ideal model delta sigma weight residual 126.28 113.54 12.74 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C09 WEV K 901 " pdb=" O10 WEV K 901 " pdb=" C11 WEV K 901 " ideal model delta sigma weight residual 126.28 113.63 12.65 3.00e+00 1.11e-01 1.78e+01 angle pdb=" C09 WEV G 201 " pdb=" O10 WEV G 201 " pdb=" C11 WEV G 201 " ideal model delta sigma weight residual 126.28 114.57 11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C02 WEV G 201 " pdb=" C03 WEV G 201 " pdb=" C04 WEV G 201 " ideal model delta sigma weight residual 120.47 108.83 11.64 3.00e+00 1.11e-01 1.51e+01 ... (remaining 31200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 13290 35.39 - 70.78: 362 70.78 - 106.17: 59 106.17 - 141.56: 5 141.56 - 176.94: 15 Dihedral angle restraints: 13731 sinusoidal: 5457 harmonic: 8274 Sorted by residual: dihedral pdb=" C14 WEV J 201 " pdb=" C11 WEV J 201 " pdb=" C13 WEV J 201 " pdb=" O10 WEV J 201 " ideal model delta sinusoidal sigma weight residual 138.77 -44.29 -176.94 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C02 WEV G 201 " pdb=" C03 WEV G 201 " pdb=" C04 WEV G 201 " pdb=" C05 WEV G 201 " ideal model delta sinusoidal sigma weight residual 221.53 47.52 174.01 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C29 WEV K 901 " pdb=" C26 WEV K 901 " pdb=" C27 WEV K 901 " pdb=" O41 WEV K 901 " ideal model delta sinusoidal sigma weight residual 74.97 -93.97 168.94 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 13728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 3663 0.100 - 0.201: 62 0.201 - 0.301: 16 0.301 - 0.402: 10 0.402 - 0.502: 4 Chirality restraints: 3755 Sorted by residual: chirality pdb=" C02 WEV K 901 " pdb=" C01 WEV K 901 " pdb=" C03 WEV K 901 " pdb=" C18 WEV K 901 " both_signs ideal model delta sigma weight residual False 2.36 2.86 -0.50 2.00e-01 2.50e+01 6.30e+00 chirality pdb=" C02 WEV D 201 " pdb=" C01 WEV D 201 " pdb=" C03 WEV D 201 " pdb=" C18 WEV D 201 " both_signs ideal model delta sigma weight residual False 2.36 2.82 -0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" C02 WEV I 201 " pdb=" C01 WEV I 201 " pdb=" C03 WEV I 201 " pdb=" C18 WEV I 201 " both_signs ideal model delta sigma weight residual False 2.36 2.78 -0.42 2.00e-01 2.50e+01 4.48e+00 ... (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: 233 2.67 - 3.23: 22601 3.23 - 3.78: 38164 3.78 - 4.34: 51086 4.34 - 4.90: 84387 Nonbonded interactions: 196471 Sorted by model distance: nonbonded pdb=" OH TYR A 31 " pdb=" OE1 GLU A 316 " model vdw 2.109 3.040 nonbonded pdb=" ND2 ASN A 480 " pdb=" O LEU A 518 " model vdw 2.145 3.120 nonbonded pdb=" OH TYR H 142 " pdb=" O19 WEV H 201 " model vdw 2.175 3.040 nonbonded pdb=" OH TYR J 142 " pdb=" O19 WEV J 201 " model vdw 2.177 3.040 nonbonded pdb=" ND2 ASN B 106 " pdb=" O HIS B 128 " model vdw 2.186 3.120 ... (remaining 196466 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 59.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 57.170 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.560 ------------------------------------------------------------------------------- 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 : 0.006 0.116 22955 Z= 0.315 Angle : 0.700 12.739 31207 Z= 0.316 Chirality : 0.048 0.502 3755 Planarity : 0.004 0.064 3841 Dihedral : 18.174 176.944 8476 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 Details of bonding type rmsd hydrogen bonds : bond 0.12574 ( 1726) hydrogen bonds : angle 5.06929 ( 5082) SS BOND : bond 0.01085 ( 1) SS BOND : angle 3.06273 ( 2) covalent geometry : bond 0.00634 (22954) covalent geometry : angle 0.69919 (31205) *********************** 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 to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 3.428 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: 0.6431 (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: 0.4021 time to fit residues: 182.2296 Evaluate side-chains 246 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 2.289 ------------------------------------------------------------------------------- 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: 2.9990 chunk 212 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 220 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 163 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN M 29 ASN F 151 ASN ** H 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.161588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.118108 restraints weight = 21861.881| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.50 r_work: 0.3069 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22955 Z= 0.218 Angle : 0.610 11.377 31207 Z= 0.303 Chirality : 0.043 0.343 3755 Planarity : 0.004 0.042 3841 Dihedral : 17.260 177.286 3731 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.02 % Allowed : 7.13 % Favored : 91.84 % 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: 1.74 (0.16), residues: 2881 helix: 1.69 (0.11), residues: 2133 sheet: -1.07 (0.94), residues: 29 loop : -0.27 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 77 HIS 0.005 0.001 HIS A 801 PHE 0.047 0.002 PHE I 88 TYR 0.017 0.001 TYR A 328 ARG 0.010 0.000 ARG B 218 Details of bonding type rmsd hydrogen bonds : bond 0.04996 ( 1726) hydrogen bonds : angle 4.39807 ( 5082) SS BOND : bond 0.00926 ( 1) SS BOND : angle 3.25711 ( 2) covalent geometry : bond 0.00511 (22954) covalent geometry : angle 0.60939 (31205) *********************** 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 308 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 284 time to evaluate : 2.279 Fit side-chains REVERT: E 129 MET cc_start: 0.7342 (ttp) cc_final: 0.7057 (ttp) REVERT: F 81 LYS cc_start: 0.9299 (mttp) cc_final: 0.9094 (mttt) REVERT: I 153 ARG cc_start: 0.8855 (ttm-80) cc_final: 0.8612 (ttm-80) REVERT: A 300 TYR cc_start: 0.7402 (m-80) cc_final: 0.7182 (m-80) outliers start: 24 outliers final: 17 residues processed: 299 average time/residue: 0.3702 time to fit residues: 171.8857 Evaluate side-chains 284 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 267 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 152 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 L residue 151 ASN Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 ASN 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 243 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 257 optimal weight: 0.7980 chunk 210 optimal weight: 0.0050 chunk 171 optimal weight: 0.8980 chunk 264 optimal weight: 6.9990 chunk 232 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.164855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121068 restraints weight = 21662.596| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.47 r_work: 0.3123 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22955 Z= 0.135 Angle : 0.529 8.339 31207 Z= 0.264 Chirality : 0.039 0.322 3755 Planarity : 0.004 0.040 3841 Dihedral : 16.797 178.358 3731 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.11 % Allowed : 9.14 % Favored : 89.75 % 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: 2.05 (0.16), residues: 2881 helix: 1.91 (0.11), residues: 2125 sheet: -0.88 (0.97), residues: 29 loop : -0.13 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 312 HIS 0.003 0.001 HIS A 499 PHE 0.026 0.001 PHE C 80 TYR 0.007 0.001 TYR H 142 ARG 0.005 0.000 ARG M 63 Details of bonding type rmsd hydrogen bonds : bond 0.04473 ( 1726) hydrogen bonds : angle 4.19155 ( 5082) SS BOND : bond 0.01344 ( 1) SS BOND : angle 1.85550 ( 2) covalent geometry : bond 0.00292 (22954) covalent geometry : angle 0.52871 (31205) *********************** 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 311 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 285 time to evaluate : 2.378 Fit side-chains REVERT: G 129 MET cc_start: 0.7999 (ttp) cc_final: 0.7701 (ttm) REVERT: I 153 ARG cc_start: 0.8806 (ttm-80) cc_final: 0.8531 (ttm-80) REVERT: B 149 TYR cc_start: 0.6500 (t80) cc_final: 0.6267 (t80) REVERT: B 193 TYR cc_start: 0.7817 (t80) cc_final: 0.7559 (t80) REVERT: A 20 TYR cc_start: 0.8459 (m-80) cc_final: 0.8231 (m-80) REVERT: A 144 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8108 (mt) REVERT: A 201 GLN cc_start: 0.8141 (tt0) cc_final: 0.7835 (tt0) REVERT: A 300 TYR cc_start: 0.7377 (m-80) cc_final: 0.7039 (m-80) outliers start: 26 outliers final: 20 residues processed: 298 average time/residue: 0.3660 time to fit residues: 169.5779 Evaluate side-chains 286 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 265 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain O residue 75 LEU 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 155 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 454 ILE Chi-restraints excluded: chain A residue 484 SER 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 265 optimal weight: 0.6980 chunk 196 optimal weight: 10.0000 chunk 188 optimal weight: 0.4980 chunk 217 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 159 optimal weight: 0.7980 chunk 171 optimal weight: 0.6980 chunk 246 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.169300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.123253 restraints weight = 21519.621| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.87 r_work: 0.3143 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22955 Z= 0.135 Angle : 0.516 8.577 31207 Z= 0.257 Chirality : 0.039 0.322 3755 Planarity : 0.003 0.038 3841 Dihedral : 16.537 179.793 3731 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.49 % Allowed : 11.14 % Favored : 87.36 % 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: 2.12 (0.16), residues: 2881 helix: 1.97 (0.11), residues: 2138 sheet: -0.92 (0.97), residues: 29 loop : -0.15 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 243 HIS 0.003 0.001 HIS A 801 PHE 0.024 0.001 PHE C 80 TYR 0.007 0.001 TYR H 142 ARG 0.005 0.000 ARG M 63 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 1726) hydrogen bonds : angle 4.10015 ( 5082) SS BOND : bond 0.01541 ( 1) SS BOND : angle 1.77294 ( 2) covalent geometry : bond 0.00293 (22954) covalent geometry : angle 0.51545 (31205) *********************** 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 312 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 2.228 Fit side-chains REVERT: C 99 LYS cc_start: 0.9134 (ttpp) cc_final: 0.8845 (ttpp) REVERT: G 129 MET cc_start: 0.7913 (ttp) cc_final: 0.7601 (ttm) REVERT: I 77 SER cc_start: 0.8943 (t) cc_final: 0.8691 (t) REVERT: I 153 ARG cc_start: 0.8736 (ttm-80) cc_final: 0.8406 (ttm-80) REVERT: B 149 TYR cc_start: 0.6375 (t80) cc_final: 0.6121 (t80) REVERT: B 150 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7854 (mt-10) REVERT: B 193 TYR cc_start: 0.7804 (t80) cc_final: 0.7566 (t80) REVERT: A 201 GLN cc_start: 0.7829 (tt0) cc_final: 0.7485 (tt0) REVERT: A 300 TYR cc_start: 0.7264 (m-80) cc_final: 0.6905 (m-80) REVERT: A 611 MET cc_start: 0.7494 (ttp) cc_final: 0.7213 (ttt) REVERT: A 759 PHE cc_start: 0.8093 (m-10) cc_final: 0.7622 (m-80) REVERT: A 794 MET cc_start: 0.8491 (ttp) cc_final: 0.7916 (ttp) outliers start: 35 outliers final: 22 residues processed: 294 average time/residue: 0.3553 time to fit residues: 164.5941 Evaluate side-chains 286 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 264 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain O residue 75 LEU 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 155 THR Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 484 SER 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 23 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 147 optimal weight: 3.9990 chunk 271 optimal weight: 0.6980 chunk 262 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 267 optimal weight: 8.9990 chunk 269 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.166026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.123376 restraints weight = 21682.520| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.25 r_work: 0.3145 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22955 Z= 0.157 Angle : 0.530 8.929 31207 Z= 0.265 Chirality : 0.040 0.321 3755 Planarity : 0.003 0.038 3841 Dihedral : 16.440 178.481 3731 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.75 % Allowed : 12.30 % Favored : 85.95 % 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: 2.06 (0.16), residues: 2881 helix: 1.94 (0.11), residues: 2131 sheet: -1.00 (0.98), residues: 29 loop : -0.21 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 312 HIS 0.004 0.001 HIS A 801 PHE 0.027 0.001 PHE C 80 TYR 0.018 0.001 TYR A 69 ARG 0.004 0.000 ARG M 63 Details of bonding type rmsd hydrogen bonds : bond 0.04390 ( 1726) hydrogen bonds : angle 4.13346 ( 5082) SS BOND : bond 0.00933 ( 1) SS BOND : angle 1.55967 ( 2) covalent geometry : bond 0.00357 (22954) covalent geometry : angle 0.52961 (31205) *********************** 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 324 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 283 time to evaluate : 2.517 Fit side-chains REVERT: M 24 MET cc_start: 0.7066 (ppp) cc_final: 0.6425 (ppp) REVERT: G 129 MET cc_start: 0.7890 (ttp) cc_final: 0.7617 (ttm) REVERT: I 77 SER cc_start: 0.8943 (t) cc_final: 0.8688 (t) REVERT: I 153 ARG cc_start: 0.8789 (ttm-80) cc_final: 0.8419 (ttm-80) REVERT: L 46 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8369 (mmm-85) REVERT: B 138 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7651 (p) REVERT: B 149 TYR cc_start: 0.6654 (t80) cc_final: 0.6380 (t80) REVERT: B 193 TYR cc_start: 0.7921 (t80) cc_final: 0.7649 (t80) REVERT: A 201 GLN cc_start: 0.7949 (tt0) cc_final: 0.7571 (tt0) REVERT: A 231 LYS cc_start: 0.8694 (mtmt) cc_final: 0.8430 (pttt) REVERT: A 300 TYR cc_start: 0.7343 (m-80) cc_final: 0.6959 (m-80) REVERT: A 611 MET cc_start: 0.7702 (ttp) cc_final: 0.7405 (ttt) REVERT: A 712 MET cc_start: 0.8181 (tpt) cc_final: 0.7857 (tpp) REVERT: A 759 PHE cc_start: 0.8193 (m-10) cc_final: 0.7686 (m-80) REVERT: A 794 MET cc_start: 0.8590 (ttp) cc_final: 0.8014 (ttp) outliers start: 41 outliers final: 30 residues processed: 307 average time/residue: 0.3639 time to fit residues: 174.0084 Evaluate side-chains 299 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 268 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 138 VAL 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 131 LEU Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 484 SER 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 107 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 142 optimal weight: 0.2980 chunk 118 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 204 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 270 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.166888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.124851 restraints weight = 21528.903| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.21 r_work: 0.3165 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22955 Z= 0.133 Angle : 0.515 8.863 31207 Z= 0.257 Chirality : 0.039 0.318 3755 Planarity : 0.003 0.037 3841 Dihedral : 16.293 177.962 3731 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.88 % Allowed : 12.89 % Favored : 85.23 % 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: 2.20 (0.16), residues: 2881 helix: 2.05 (0.11), residues: 2130 sheet: -1.10 (0.99), residues: 29 loop : -0.18 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 312 HIS 0.003 0.000 HIS A 801 PHE 0.023 0.001 PHE C 80 TYR 0.018 0.001 TYR A 69 ARG 0.004 0.000 ARG J 153 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 1726) hydrogen bonds : angle 4.05658 ( 5082) SS BOND : bond 0.01753 ( 1) SS BOND : angle 1.42841 ( 2) covalent geometry : bond 0.00289 (22954) covalent geometry : angle 0.51532 (31205) *********************** 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 328 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 2.272 Fit side-chains REVERT: C 99 LYS cc_start: 0.9129 (ttpp) cc_final: 0.8881 (ttpp) REVERT: M 24 MET cc_start: 0.7078 (ppp) cc_final: 0.6545 (ppp) REVERT: G 129 MET cc_start: 0.7859 (ttp) cc_final: 0.7591 (ttm) REVERT: I 77 SER cc_start: 0.8906 (t) cc_final: 0.8663 (t) REVERT: I 153 ARG cc_start: 0.8767 (ttm-80) cc_final: 0.8374 (ttm-80) REVERT: L 8 TYR cc_start: 0.9081 (p90) cc_final: 0.8555 (p90) REVERT: L 46 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8393 (mmm-85) REVERT: B 138 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7645 (p) REVERT: B 149 TYR cc_start: 0.6635 (t80) cc_final: 0.6350 (t80) REVERT: B 150 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7981 (mt-10) REVERT: B 193 TYR cc_start: 0.7952 (t80) cc_final: 0.7681 (t80) REVERT: A 201 GLN cc_start: 0.7987 (tt0) cc_final: 0.7638 (tt0) REVERT: A 231 LYS cc_start: 0.8695 (mtmt) cc_final: 0.8438 (pttt) REVERT: A 300 TYR cc_start: 0.7350 (m-80) cc_final: 0.7003 (m-80) REVERT: A 611 MET cc_start: 0.7690 (ttp) cc_final: 0.7413 (ttt) REVERT: A 739 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8613 (mp) REVERT: A 794 MET cc_start: 0.8540 (ttp) cc_final: 0.7975 (ttp) outliers start: 44 outliers final: 30 residues processed: 310 average time/residue: 0.3403 time to fit residues: 164.5295 Evaluate side-chains 303 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 271 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain N residue 218 ILE 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 155 THR Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain K residue 155 THR Chi-restraints excluded: chain L residue 19 SER Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 188 THR 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 379 THR Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 739 LEU 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 115 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 159 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.165289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.121889 restraints weight = 21670.657| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.22 r_work: 0.3128 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22955 Z= 0.177 Angle : 0.554 10.393 31207 Z= 0.275 Chirality : 0.041 0.323 3755 Planarity : 0.004 0.038 3841 Dihedral : 16.275 176.411 3731 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.96 % Allowed : 13.66 % Favored : 84.37 % 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: 1.88 (0.11), residues: 2129 sheet: -1.20 (0.97), residues: 29 loop : -0.25 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 494 HIS 0.005 0.001 HIS A 801 PHE 0.028 0.001 PHE C 80 TYR 0.016 0.001 TYR A 69 ARG 0.009 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 1726) hydrogen bonds : angle 4.16818 ( 5082) SS BOND : bond 0.02594 ( 1) SS BOND : angle 0.97365 ( 2) covalent geometry : bond 0.00411 (22954) covalent geometry : angle 0.55354 (31205) *********************** 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 325 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 279 time to evaluate : 2.593 Fit side-chains REVERT: C 99 LYS cc_start: 0.9145 (ttpp) cc_final: 0.8795 (ttpp) REVERT: M 24 MET cc_start: 0.7098 (ppp) cc_final: 0.6557 (ppp) REVERT: G 35 SER cc_start: 0.7961 (m) cc_final: 0.7710 (m) REVERT: G 129 MET cc_start: 0.7915 (ttp) cc_final: 0.7638 (ttm) REVERT: I 77 SER cc_start: 0.8926 (t) cc_final: 0.8656 (t) REVERT: I 153 ARG cc_start: 0.8804 (ttm-80) cc_final: 0.8423 (ttm-80) REVERT: L 8 TYR cc_start: 0.9114 (p90) cc_final: 0.8598 (p90) REVERT: B 149 TYR cc_start: 0.6694 (t80) cc_final: 0.6420 (t80) REVERT: B 150 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7858 (mt-10) REVERT: B 193 TYR cc_start: 0.7973 (t80) cc_final: 0.7688 (t80) REVERT: A 201 GLN cc_start: 0.8017 (tt0) cc_final: 0.7620 (tt0) REVERT: A 231 LYS cc_start: 0.8646 (mtmt) cc_final: 0.8371 (pttt) REVERT: A 300 TYR cc_start: 0.7300 (m-80) cc_final: 0.6920 (m-80) REVERT: A 453 GLU cc_start: 0.7321 (tp30) cc_final: 0.7094 (tp30) REVERT: A 455 PHE cc_start: 0.8043 (t80) cc_final: 0.7659 (t80) REVERT: A 611 MET cc_start: 0.7732 (ttp) cc_final: 0.7441 (ttt) REVERT: A 739 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8645 (mp) outliers start: 46 outliers final: 36 residues processed: 307 average time/residue: 0.3615 time to fit residues: 174.5022 Evaluate side-chains 304 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 138 VAL 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 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 65 ILE Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 510 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 739 LEU 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 81 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 117 optimal weight: 0.0370 chunk 74 optimal weight: 0.4980 chunk 222 optimal weight: 0.2980 chunk 182 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.169144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126290 restraints weight = 21465.399| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.32 r_work: 0.3172 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22955 Z= 0.119 Angle : 0.511 9.542 31207 Z= 0.256 Chirality : 0.039 0.312 3755 Planarity : 0.003 0.037 3841 Dihedral : 16.114 177.042 3731 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.49 % Allowed : 14.35 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.16), residues: 2881 helix: 2.13 (0.11), residues: 2123 sheet: -1.21 (0.97), residues: 29 loop : -0.17 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 494 HIS 0.004 0.000 HIS A 79 PHE 0.020 0.001 PHE C 80 TYR 0.014 0.001 TYR F 76 ARG 0.007 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 1726) hydrogen bonds : angle 4.01124 ( 5082) SS BOND : bond 0.00283 ( 1) SS BOND : angle 4.18160 ( 2) covalent geometry : bond 0.00248 (22954) covalent geometry : angle 0.51032 (31205) *********************** 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 317 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 2.372 Fit side-chains REVERT: D 87 THR cc_start: 0.9054 (p) cc_final: 0.8849 (p) REVERT: C 99 LYS cc_start: 0.9099 (ttpp) cc_final: 0.8794 (ttpp) REVERT: M 24 MET cc_start: 0.7078 (ppp) cc_final: 0.6616 (ppp) REVERT: I 77 SER cc_start: 0.8886 (t) cc_final: 0.8670 (t) REVERT: I 153 ARG cc_start: 0.8756 (ttm-80) cc_final: 0.8516 (ttm-80) REVERT: J 75 CYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7267 (m) REVERT: L 8 TYR cc_start: 0.9065 (p90) cc_final: 0.8538 (p90) REVERT: B 149 TYR cc_start: 0.6666 (t80) cc_final: 0.6383 (t80) REVERT: B 193 TYR cc_start: 0.7936 (t80) cc_final: 0.7669 (t80) REVERT: A 14 MET cc_start: 0.8091 (mmm) cc_final: 0.7434 (mtt) REVERT: A 201 GLN cc_start: 0.7964 (tt0) cc_final: 0.7563 (tt0) REVERT: A 231 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8370 (pttt) REVERT: A 300 TYR cc_start: 0.7320 (m-80) cc_final: 0.6966 (m-80) REVERT: A 453 GLU cc_start: 0.7404 (tp30) cc_final: 0.7149 (tp30) REVERT: A 611 MET cc_start: 0.7694 (ttp) cc_final: 0.7404 (ttt) REVERT: A 739 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8658 (mp) REVERT: A 759 PHE cc_start: 0.8120 (m-10) cc_final: 0.7726 (m-80) REVERT: A 794 MET cc_start: 0.8523 (ttp) cc_final: 0.7972 (ttp) outliers start: 35 outliers final: 29 residues processed: 303 average time/residue: 0.3429 time to fit residues: 162.1781 Evaluate side-chains 303 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 272 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 138 VAL 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 19 SER Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 765 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 250 optimal weight: 0.7980 chunk 259 optimal weight: 0.5980 chunk 164 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 200 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN B 303 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** 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 = 0.3842 r_free = 0.3842 target = 0.166628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.122155 restraints weight = 21626.058| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.36 r_work: 0.3157 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22955 Z= 0.141 Angle : 0.527 9.862 31207 Z= 0.263 Chirality : 0.040 0.318 3755 Planarity : 0.004 0.037 3841 Dihedral : 16.085 175.925 3731 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.58 % Allowed : 14.73 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.16), residues: 2881 helix: 2.09 (0.11), residues: 2123 sheet: -1.19 (0.98), residues: 29 loop : -0.23 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 494 HIS 0.004 0.001 HIS A 801 PHE 0.024 0.001 PHE C 80 TYR 0.016 0.001 TYR A 69 ARG 0.008 0.000 ARG A 332 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 1726) hydrogen bonds : angle 4.04474 ( 5082) SS BOND : bond 0.00002 ( 1) SS BOND : angle 3.87053 ( 2) covalent geometry : bond 0.00315 (22954) covalent geometry : angle 0.52591 (31205) *********************** 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 315 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 278 time to evaluate : 2.407 Fit side-chains REVERT: C 99 LYS cc_start: 0.9107 (ttpp) cc_final: 0.8785 (ttpp) REVERT: M 24 MET cc_start: 0.7146 (ppp) cc_final: 0.6686 (ppp) REVERT: I 77 SER cc_start: 0.8867 (t) cc_final: 0.8656 (t) REVERT: I 153 ARG cc_start: 0.8763 (ttm-80) cc_final: 0.8549 (ttm-80) REVERT: J 75 CYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7320 (m) REVERT: L 8 TYR cc_start: 0.9084 (p90) cc_final: 0.8557 (p90) REVERT: B 149 TYR cc_start: 0.6752 (t80) cc_final: 0.6470 (t80) REVERT: B 150 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7862 (mt-10) REVERT: B 193 TYR cc_start: 0.8030 (t80) cc_final: 0.7771 (t80) REVERT: B 208 MET cc_start: 0.7404 (mmm) cc_final: 0.7056 (mmm) REVERT: A 14 MET cc_start: 0.8229 (mmm) cc_final: 0.7542 (mtt) REVERT: A 201 GLN cc_start: 0.7994 (tt0) cc_final: 0.7601 (tt0) REVERT: A 231 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8397 (pttt) REVERT: A 300 TYR cc_start: 0.7353 (m-80) cc_final: 0.6961 (m-80) REVERT: A 332 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6637 (mtm180) REVERT: A 453 GLU cc_start: 0.7448 (tp30) cc_final: 0.7156 (tp30) REVERT: A 611 MET cc_start: 0.7830 (ttp) cc_final: 0.7528 (ttt) REVERT: A 739 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8672 (mp) REVERT: A 759 PHE cc_start: 0.8157 (m-10) cc_final: 0.7809 (m-10) REVERT: A 794 MET cc_start: 0.8600 (ttp) cc_final: 0.8066 (ttp) outliers start: 37 outliers final: 33 residues processed: 301 average time/residue: 0.3573 time to fit residues: 169.5563 Evaluate side-chains 311 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 275 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 138 VAL 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 19 SER Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 765 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 195 optimal weight: 0.2980 chunk 263 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 220 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 54 optimal weight: 0.0970 chunk 119 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 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 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.167221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.122226 restraints weight = 21693.296| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.56 r_work: 0.3158 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22955 Z= 0.141 Angle : 0.535 10.296 31207 Z= 0.267 Chirality : 0.040 0.317 3755 Planarity : 0.003 0.037 3841 Dihedral : 16.042 175.953 3731 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.71 % Allowed : 14.65 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.16), residues: 2881 helix: 2.08 (0.11), residues: 2124 sheet: -0.65 (0.95), residues: 33 loop : -0.23 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 494 HIS 0.003 0.001 HIS A 801 PHE 0.024 0.001 PHE C 80 TYR 0.015 0.001 TYR C 57 ARG 0.006 0.000 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 1726) hydrogen bonds : angle 4.04661 ( 5082) SS BOND : bond 0.00024 ( 1) SS BOND : angle 3.39385 ( 2) covalent geometry : bond 0.00316 (22954) covalent geometry : angle 0.53396 (31205) ********************** 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 319 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 2.283 Fit side-chains REVERT: C 99 LYS cc_start: 0.9099 (ttpp) cc_final: 0.8742 (ttpp) REVERT: M 24 MET cc_start: 0.7072 (ppp) cc_final: 0.6585 (ppp) REVERT: I 77 SER cc_start: 0.8953 (t) cc_final: 0.8703 (t) REVERT: I 153 ARG cc_start: 0.8703 (ttm-80) cc_final: 0.8449 (ttm-80) REVERT: J 75 CYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7158 (m) REVERT: L 8 TYR cc_start: 0.9033 (p90) cc_final: 0.8471 (p90) REVERT: B 149 TYR cc_start: 0.6602 (t80) cc_final: 0.6313 (t80) REVERT: B 150 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7659 (mt-10) REVERT: A 201 GLN cc_start: 0.7992 (tt0) cc_final: 0.7610 (tt0) REVERT: A 231 LYS cc_start: 0.8603 (mtmt) cc_final: 0.8369 (pttt) REVERT: A 234 ASN cc_start: 0.7181 (m-40) cc_final: 0.6926 (m-40) REVERT: A 300 TYR cc_start: 0.7394 (m-80) cc_final: 0.6956 (m-80) REVERT: A 453 GLU cc_start: 0.7303 (tp30) cc_final: 0.7031 (tp30) REVERT: A 611 MET cc_start: 0.7568 (ttp) cc_final: 0.7292 (ttt) REVERT: A 739 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8634 (mp) REVERT: A 759 PHE cc_start: 0.8122 (m-10) cc_final: 0.7759 (m-10) REVERT: A 794 MET cc_start: 0.8461 (ttp) cc_final: 0.7861 (ttp) outliers start: 40 outliers final: 34 residues processed: 305 average time/residue: 0.3737 time to fit residues: 181.9111 Evaluate side-chains 308 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 152 SER Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 138 VAL 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 19 SER Chi-restraints excluded: chain L residue 65 ILE Chi-restraints excluded: chain L residue 151 ASN Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 765 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 164 optimal weight: 0.9980 chunk 141 optimal weight: 0.5980 chunk 174 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 257 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 GLN ** A 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.168203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124538 restraints weight = 21595.655| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.36 r_work: 0.3168 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22955 Z= 0.124 Angle : 0.521 9.884 31207 Z= 0.260 Chirality : 0.039 0.315 3755 Planarity : 0.003 0.037 3841 Dihedral : 15.939 176.000 3731 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.54 % Allowed : 15.03 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.16), residues: 2881 helix: 2.04 (0.11), residues: 2173 sheet: -0.61 (0.97), residues: 33 loop : -0.31 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 494 HIS 0.004 0.001 HIS A 79 PHE 0.022 0.001 PHE C 80 TYR 0.012 0.001 TYR A 69 ARG 0.005 0.000 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 1726) hydrogen bonds : angle 3.97668 ( 5082) SS BOND : bond 0.00011 ( 1) SS BOND : angle 3.05366 ( 2) covalent geometry : bond 0.00266 (22954) covalent geometry : angle 0.52042 (31205) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13169.53 seconds wall clock time: 230 minutes 19.05 seconds (13819.05 seconds total)