Starting phenix.real_space_refine on Thu Feb 5 14:24:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v7k_64816/02_2026/9v7k_64816_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v7k_64816/02_2026/9v7k_64816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v7k_64816/02_2026/9v7k_64816_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v7k_64816/02_2026/9v7k_64816_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v7k_64816/02_2026/9v7k_64816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v7k_64816/02_2026/9v7k_64816.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.037 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 71 5.16 5 C 11385 2.51 5 N 3003 2.21 5 O 3428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 143 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17887 Number of models: 1 Model: "" Number of chains: 28 Chain: "1" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1679 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain: "Z" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 204 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "A" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1223 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain: "B" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1210 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1209 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1210 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1223 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain: "F" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1210 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1223 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain: "H" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1210 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1223 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain: "J" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1210 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1223 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain: "L" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1210 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 529 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "X" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 375 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.23, per 1000 atoms: 0.24 Number of scatterers: 17887 At special positions: 0 Unit cell: (127.5, 90, 145, 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 71 16.00 O 3428 8.00 N 3003 7.00 C 11385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 606.1 milliseconds 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4164 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 1 sheets defined 82.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain '1' and resid 950 through 957 removed outlier: 3.683A pdb=" N GLY 1 956 " --> pdb=" O PHE 1 952 " (cutoff:3.500A) Processing helix chain '1' and resid 989 through 1005 removed outlier: 3.517A pdb=" N ALA 1 996 " --> pdb=" O GLU 1 992 " (cutoff:3.500A) Processing helix chain '1' and resid 1018 through 1027 Processing helix chain '1' and resid 1031 through 1042 Processing helix chain '1' and resid 1042 through 1049 Processing helix chain '1' and resid 1054 through 1066 Processing helix chain '1' and resid 1073 through 1087 Processing helix chain '1' and resid 1089 through 1099 Processing helix chain '1' and resid 1099 through 1106 Processing helix chain '1' and resid 1122 through 1133 Processing helix chain 'Z' and resid 315 through 329 Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 19 through 46 removed outlier: 4.684A pdb=" N GLU A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 62 Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 74 through 99 Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 111 through 120 Processing helix chain 'A' and resid 122 through 141 Processing helix chain 'A' and resid 142 through 160 removed outlier: 3.857A pdb=" N TYR A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 20 through 47 removed outlier: 4.357A pdb=" N ALA B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 59 Processing helix chain 'B' and resid 74 through 99 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 111 through 120 Processing helix chain 'B' and resid 122 through 142 Processing helix chain 'B' and resid 142 through 161 removed outlier: 4.006A pdb=" N GLU B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 19 through 32 Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 46 through 62 Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 74 through 99 Processing helix chain 'C' and resid 101 through 109 Processing helix chain 'C' and resid 111 through 120 Processing helix chain 'C' and resid 122 through 139 removed outlier: 5.723A pdb=" N GLU C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 160 removed outlier: 3.905A pdb=" N TYR C 152 " --> pdb=" O GLU C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 16 Processing helix chain 'D' and resid 20 through 47 removed outlier: 4.393A pdb=" N ALA D 35 " --> pdb=" O PHE D 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL D 36 " --> pdb=" O THR D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 59 Processing helix chain 'D' and resid 74 through 99 Processing helix chain 'D' and resid 101 through 108 Processing helix chain 'D' and resid 111 through 120 Processing helix chain 'D' and resid 122 through 142 Processing helix chain 'D' and resid 142 through 161 removed outlier: 4.018A pdb=" N GLU D 148 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 15 Processing helix chain 'E' and resid 19 through 46 removed outlier: 4.489A pdb=" N GLU E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ARG E 35 " --> pdb=" O ALA E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 Processing helix chain 'E' and resid 63 through 67 Processing helix chain 'E' and resid 74 through 99 Processing helix chain 'E' and resid 101 through 109 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 122 through 141 Processing helix chain 'E' and resid 142 through 160 removed outlier: 3.833A pdb=" N TYR E 152 " --> pdb=" O GLU E 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 16 removed outlier: 3.862A pdb=" N GLN F 15 " --> pdb=" O ASN F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 47 removed outlier: 3.657A pdb=" N THR F 33 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL F 36 " --> pdb=" O THR F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 60 Processing helix chain 'F' and resid 74 through 99 Processing helix chain 'F' and resid 101 through 108 Processing helix chain 'F' and resid 111 through 120 Processing helix chain 'F' and resid 122 through 142 removed outlier: 3.802A pdb=" N GLY F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU F 140 " --> pdb=" O VAL F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 161 removed outlier: 4.815A pdb=" N LYS F 147 " --> pdb=" O PRO F 143 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU F 148 " --> pdb=" O ASP F 144 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE F 151 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR F 152 " --> pdb=" O GLU F 148 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 15 Processing helix chain 'G' and resid 19 through 46 removed outlier: 4.555A pdb=" N GLU G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ARG G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 62 Processing helix chain 'G' and resid 63 through 67 Processing helix chain 'G' and resid 74 through 99 Processing helix chain 'G' and resid 101 through 109 removed outlier: 3.604A pdb=" N ILE G 107 " --> pdb=" O PRO G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 120 Processing helix chain 'G' and resid 122 through 141 Processing helix chain 'G' and resid 142 through 160 removed outlier: 3.815A pdb=" N TYR G 152 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 16 Processing helix chain 'H' and resid 20 through 47 removed outlier: 4.412A pdb=" N ALA H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL H 36 " --> pdb=" O THR H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 59 Processing helix chain 'H' and resid 74 through 99 Processing helix chain 'H' and resid 101 through 108 Processing helix chain 'H' and resid 111 through 120 Processing helix chain 'H' and resid 122 through 142 Processing helix chain 'H' and resid 142 through 161 removed outlier: 4.032A pdb=" N GLU H 148 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE H 151 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR H 152 " --> pdb=" O GLU H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 15 Processing helix chain 'I' and resid 19 through 46 removed outlier: 4.605A pdb=" N GLU I 34 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ARG I 35 " --> pdb=" O ALA I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 62 Processing helix chain 'I' and resid 63 through 67 Processing helix chain 'I' and resid 74 through 99 Processing helix chain 'I' and resid 101 through 109 Processing helix chain 'I' and resid 111 through 120 Processing helix chain 'I' and resid 122 through 141 Processing helix chain 'I' and resid 142 through 160 removed outlier: 3.831A pdb=" N TYR I 152 " --> pdb=" O GLU I 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 16 Processing helix chain 'J' and resid 20 through 47 removed outlier: 4.478A pdb=" N ALA J 35 " --> pdb=" O PHE J 31 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL J 36 " --> pdb=" O THR J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 59 Processing helix chain 'J' and resid 74 through 99 Processing helix chain 'J' and resid 101 through 108 Processing helix chain 'J' and resid 111 through 120 Processing helix chain 'J' and resid 122 through 142 Processing helix chain 'J' and resid 142 through 161 removed outlier: 3.989A pdb=" N GLU J 148 " --> pdb=" O ASP J 144 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE J 151 " --> pdb=" O LYS J 147 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR J 152 " --> pdb=" O GLU J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 15 Processing helix chain 'K' and resid 19 through 46 removed outlier: 4.512A pdb=" N GLU K 34 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ARG K 35 " --> pdb=" O ALA K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 62 Processing helix chain 'K' and resid 63 through 67 Processing helix chain 'K' and resid 74 through 99 Processing helix chain 'K' and resid 101 through 109 Processing helix chain 'K' and resid 111 through 120 Processing helix chain 'K' and resid 122 through 141 Processing helix chain 'K' and resid 142 through 160 removed outlier: 3.834A pdb=" N TYR K 152 " --> pdb=" O GLU K 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 16 Processing helix chain 'L' and resid 20 through 47 removed outlier: 4.454A pdb=" N ALA L 35 " --> pdb=" O PHE L 31 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL L 36 " --> pdb=" O THR L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 59 Processing helix chain 'L' and resid 74 through 99 Processing helix chain 'L' and resid 101 through 108 Processing helix chain 'L' and resid 111 through 120 Processing helix chain 'L' and resid 122 through 142 Processing helix chain 'L' and resid 142 through 161 removed outlier: 3.990A pdb=" N GLU L 148 " --> pdb=" O ASP L 144 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE L 151 " --> pdb=" O LYS L 147 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR L 152 " --> pdb=" O GLU L 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 27 Processing helix chain 'M' and resid 34 through 47 removed outlier: 4.307A pdb=" N PHE M 38 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N THR M 39 " --> pdb=" O GLU M 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 53 Processing sheet with id=AA1, first strand: chain 'M' and resid 30 through 33 removed outlier: 6.388A pdb=" N TYR M 4 " --> pdb=" O PHE M 57 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N CYS M 10 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL M 51 " --> pdb=" O CYS M 10 " (cutoff:3.500A) 1365 hydrogen bonds defined for protein. 4047 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: 2.27 Time building geometry restraints manager: 1.75 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: 3144 1.32 - 1.44: 4622 1.44 - 1.57: 10291 1.57 - 1.70: 3 1.70 - 1.82: 129 Bond restraints: 18189 Sorted by residual: bond pdb=" C GLY D 70 " pdb=" N MEN D 71 " ideal model delta sigma weight residual 1.329 1.438 -0.109 1.40e-02 5.10e+03 6.09e+01 bond pdb=" C GLY H 70 " pdb=" N MEN H 71 " ideal model delta sigma weight residual 1.329 1.431 -0.102 1.40e-02 5.10e+03 5.35e+01 bond pdb=" C4A CYC H 201 " pdb=" CHB CYC H 201 " ideal model delta sigma weight residual 1.437 1.303 0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C4A CYC B 201 " pdb=" CHB CYC B 201 " ideal model delta sigma weight residual 1.437 1.318 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C GLY J 70 " pdb=" N MEN J 71 " ideal model delta sigma weight residual 1.329 1.405 -0.076 1.40e-02 5.10e+03 2.94e+01 ... (remaining 18184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 23011 3.17 - 6.34: 1468 6.34 - 9.51: 176 9.51 - 12.68: 31 12.68 - 15.85: 2 Bond angle restraints: 24688 Sorted by residual: angle pdb=" C TYR 11116 " pdb=" CA TYR 11116 " pdb=" CB TYR 11116 " ideal model delta sigma weight residual 110.65 100.08 10.57 1.04e+00 9.25e-01 1.03e+02 angle pdb=" CA PHE M 28 " pdb=" CB PHE M 28 " pdb=" CG PHE M 28 " ideal model delta sigma weight residual 113.80 121.71 -7.91 1.00e+00 1.00e+00 6.25e+01 angle pdb=" CA PHE 11008 " pdb=" CB PHE 11008 " pdb=" CG PHE 11008 " ideal model delta sigma weight residual 113.80 121.30 -7.50 1.00e+00 1.00e+00 5.62e+01 angle pdb=" N LEU 11067 " pdb=" CA LEU 11067 " pdb=" CB LEU 11067 " ideal model delta sigma weight residual 110.49 123.01 -12.52 1.69e+00 3.50e-01 5.49e+01 angle pdb=" N ALA Z 335 " pdb=" CA ALA Z 335 " pdb=" CB ALA Z 335 " ideal model delta sigma weight residual 110.49 122.98 -12.49 1.69e+00 3.50e-01 5.46e+01 ... (remaining 24683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 9334 17.82 - 35.64: 1140 35.64 - 53.45: 512 53.45 - 71.27: 147 71.27 - 89.09: 57 Dihedral angle restraints: 11190 sinusoidal: 4630 harmonic: 6560 Sorted by residual: dihedral pdb=" CD ARG A 36 " pdb=" NE ARG A 36 " pdb=" CZ ARG A 36 " pdb=" NH1 ARG A 36 " ideal model delta sinusoidal sigma weight residual 0.00 71.75 -71.75 1 1.00e+01 1.00e-02 6.59e+01 dihedral pdb=" CD ARG I 36 " pdb=" NE ARG I 36 " pdb=" CZ ARG I 36 " pdb=" NH1 ARG I 36 " ideal model delta sinusoidal sigma weight residual 0.00 70.83 -70.83 1 1.00e+01 1.00e-02 6.45e+01 dihedral pdb=" CD ARG 1 975 " pdb=" NE ARG 1 975 " pdb=" CZ ARG 1 975 " pdb=" NH1 ARG 1 975 " ideal model delta sinusoidal sigma weight residual 0.00 68.41 -68.41 1 1.00e+01 1.00e-02 6.07e+01 ... (remaining 11187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2289 0.113 - 0.227: 448 0.227 - 0.340: 25 0.340 - 0.453: 2 0.453 - 0.566: 3 Chirality restraints: 2767 Sorted by residual: chirality pdb=" CA LEU 11067 " pdb=" N LEU 11067 " pdb=" C LEU 11067 " pdb=" CB LEU 11067 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.02e+00 chirality pdb=" CA MET F 72 " pdb=" N MET F 72 " pdb=" C MET F 72 " pdb=" CB MET F 72 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CA ASN 11028 " pdb=" N ASN 11028 " pdb=" C ASN 11028 " pdb=" CB ASN 11028 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+00 ... (remaining 2764 not shown) Planarity restraints: 3165 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A CYC C 201 " 0.037 2.00e-02 2.50e+03 2.06e-01 9.54e+02 pdb=" C2A CYC C 201 " 0.037 2.00e-02 2.50e+03 pdb=" C3A CYC C 201 " 0.183 2.00e-02 2.50e+03 pdb=" C4A CYC C 201 " 0.058 2.00e-02 2.50e+03 pdb=" CAA CYC C 201 " -0.332 2.00e-02 2.50e+03 pdb=" CHA CYC C 201 " 0.022 2.00e-02 2.50e+03 pdb=" CHB CYC C 201 " -0.394 2.00e-02 2.50e+03 pdb=" CMA CYC C 201 " 0.186 2.00e-02 2.50e+03 pdb=" NA CYC C 201 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYC J 201 " 0.028 2.00e-02 2.50e+03 2.05e-01 9.44e+02 pdb=" OB CYC J 201 " 0.205 2.00e-02 2.50e+03 pdb=" C1B CYC J 201 " -0.064 2.00e-02 2.50e+03 pdb=" C2B CYC J 201 " 0.046 2.00e-02 2.50e+03 pdb=" C3B CYC J 201 " -0.048 2.00e-02 2.50e+03 pdb=" C4B CYC J 201 " 0.068 2.00e-02 2.50e+03 pdb=" CAB CYC J 201 " -0.369 2.00e-02 2.50e+03 pdb=" CHB CYC J 201 " -0.230 2.00e-02 2.50e+03 pdb=" CMB CYC J 201 " 0.364 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYC B 201 " 0.123 2.00e-02 2.50e+03 1.98e-01 8.85e+02 pdb=" OB CYC B 201 " 0.087 2.00e-02 2.50e+03 pdb=" C1B CYC B 201 " -0.033 2.00e-02 2.50e+03 pdb=" C2B CYC B 201 " 0.071 2.00e-02 2.50e+03 pdb=" C3B CYC B 201 " 0.004 2.00e-02 2.50e+03 pdb=" C4B CYC B 201 " 0.094 2.00e-02 2.50e+03 pdb=" CAB CYC B 201 " -0.358 2.00e-02 2.50e+03 pdb=" CHB CYC B 201 " -0.301 2.00e-02 2.50e+03 pdb=" CMB CYC B 201 " 0.313 2.00e-02 2.50e+03 ... (remaining 3162 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 130 2.56 - 3.14: 15275 3.14 - 3.73: 30948 3.73 - 4.31: 43281 4.31 - 4.90: 67259 Nonbonded interactions: 156893 Sorted by model distance: nonbonded pdb=" O PRO 11117 " pdb=" OG1 THR 11118 " model vdw 1.974 3.040 nonbonded pdb=" O ARG 11114 " pdb=" O ARG 11115 " model vdw 2.006 3.040 nonbonded pdb=" NH2 ARG M 18 " pdb=" OE1 GLU M 22 " model vdw 2.155 3.120 nonbonded pdb=" O ARG 11114 " pdb=" C ARG 11115 " model vdw 2.227 3.270 nonbonded pdb=" O ILE C 123 " pdb=" N ALA C 125 " model vdw 2.230 3.120 ... (remaining 156888 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 'A' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 160 or resid 201)) selection = chain 'C' selection = (chain 'E' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 160 or resid 201)) selection = (chain 'G' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 160 or resid 201)) selection = (chain 'I' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 160 or resid 201)) selection = (chain 'K' and (resid 2 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 160 or resid 201)) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' 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: 21.910 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.990 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.134 18201 Z= 0.705 Angle : 1.753 15.851 24688 Z= 1.111 Chirality : 0.085 0.566 2767 Planarity : 0.044 0.467 3165 Dihedral : 20.436 89.089 7026 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.49 % Allowed : 2.56 % Favored : 96.94 % Rotamer: Outliers : 19.51 % Allowed : 11.68 % Favored : 68.81 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.16), residues: 2225 helix: 1.65 (0.11), residues: 1747 sheet: 1.78 (1.36), residues: 14 loop : -1.19 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.070 0.009 ARG D 107 TYR 0.091 0.010 TYR 11116 PHE 0.057 0.008 PHE M 38 TRP 0.040 0.009 TRP M 37 HIS 0.012 0.008 HIS 1 980 Details of bonding type rmsd covalent geometry : bond 0.01104 (18189) covalent geometry : angle 1.75290 (24688) hydrogen bonds : bond 0.20684 ( 1365) hydrogen bonds : angle 5.83672 ( 4047) Misc. bond : bond 0.06740 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 349 poor density : 555 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 969 VAL cc_start: 0.7995 (OUTLIER) cc_final: 0.7294 (t) REVERT: A 66 VAL cc_start: 0.8026 (OUTLIER) cc_final: 0.7723 (m) REVERT: A 102 THR cc_start: 0.7785 (OUTLIER) cc_final: 0.7382 (m) REVERT: C 145 ASP cc_start: 0.5892 (m-30) cc_final: 0.5479 (m-30) REVERT: F 61 ILE cc_start: 0.7324 (pt) cc_final: 0.6836 (pt) REVERT: G 100 ASP cc_start: 0.5867 (OUTLIER) cc_final: 0.5462 (m-30) REVERT: I 76 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7230 (tttt) REVERT: I 91 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7336 (mt) REVERT: J 3 ASP cc_start: 0.6742 (OUTLIER) cc_final: 0.6297 (p0) REVERT: K 64 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7788 (p0) REVERT: K 118 SER cc_start: 0.8031 (OUTLIER) cc_final: 0.7735 (p) REVERT: M 25 ASN cc_start: 0.7563 (m-40) cc_final: 0.7043 (m-40) REVERT: X 37 GLU cc_start: 0.0189 (OUTLIER) cc_final: -0.1052 (mp0) outliers start: 349 outliers final: 28 residues processed: 761 average time/residue: 0.6111 time to fit residues: 514.9934 Evaluate side-chains 320 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 282 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 958 SER Chi-restraints excluded: chain 1 residue 969 VAL Chi-restraints excluded: chain 1 residue 1097 VAL Chi-restraints excluded: chain 1 residue 1119 LEU Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain G residue 47 ARG Chi-restraints excluded: chain G residue 75 GLU Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain I residue 121 THR Chi-restraints excluded: chain I residue 144 ASP Chi-restraints excluded: chain J residue 3 ASP Chi-restraints excluded: chain J residue 135 GLU Chi-restraints excluded: chain J residue 151 ILE Chi-restraints excluded: chain J residue 157 SER Chi-restraints excluded: chain K residue 25 ARG Chi-restraints excluded: chain K residue 64 ASP Chi-restraints excluded: chain K residue 118 SER Chi-restraints excluded: chain K residue 142 SER Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain X residue 15 ILE Chi-restraints excluded: chain X residue 16 LYS Chi-restraints excluded: chain X residue 37 GLU Chi-restraints excluded: chain X residue 42 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 965 GLN 11028 ASN 11074 GLN 11131 ASN 11151 GLN A 10 ASN B 110 ASN C 120 GLN D 131 GLN E 53 GLN E 60 GLN F 110 ASN G 41 GLN H 47 ASN H 131 GLN I 41 GLN I 60 GLN I 71 ASN I 120 GLN L 11 ASN L 15 GLN L 131 GLN M 25 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.061373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.049897 restraints weight = 60506.193| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.75 r_work: 0.2843 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18201 Z= 0.192 Angle : 0.829 10.333 24688 Z= 0.423 Chirality : 0.043 0.188 2767 Planarity : 0.005 0.059 3165 Dihedral : 10.318 89.443 3160 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.75 % Favored : 98.07 % Rotamer: Outliers : 5.98 % Allowed : 25.21 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.17), residues: 2225 helix: 2.09 (0.11), residues: 1777 sheet: 1.45 (1.30), residues: 17 loop : -1.05 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 131 TYR 0.039 0.002 TYR C 155 PHE 0.022 0.002 PHE M 28 TRP 0.006 0.002 TRP Z 318 HIS 0.002 0.001 HIS 11065 Details of bonding type rmsd covalent geometry : bond 0.00408 (18189) covalent geometry : angle 0.82897 (24688) hydrogen bonds : bond 0.05391 ( 1365) hydrogen bonds : angle 4.55713 ( 4047) Misc. bond : bond 0.00039 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 327 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 959 PHE cc_start: 0.8009 (m-80) cc_final: 0.7714 (m-10) REVERT: 1 992 GLU cc_start: 0.8122 (tt0) cc_final: 0.7912 (tm-30) REVERT: 1 1150 TYR cc_start: 0.7723 (m-10) cc_final: 0.7243 (m-10) REVERT: 1 1151 GLN cc_start: 0.8926 (mm-40) cc_final: 0.8725 (mm110) REVERT: Z 324 ASP cc_start: 0.8654 (m-30) cc_final: 0.8423 (m-30) REVERT: Z 325 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8419 (pp) REVERT: Z 331 TYR cc_start: 0.6671 (m-80) cc_final: 0.6393 (m-80) REVERT: A 102 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7682 (p) REVERT: A 160 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7359 (pmm) REVERT: B 2 GLN cc_start: 0.8422 (mt0) cc_final: 0.7805 (mt0) REVERT: B 64 ASP cc_start: 0.8596 (m-30) cc_final: 0.7808 (t70) REVERT: B 100 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7271 (t70) REVERT: B 105 ASP cc_start: 0.7335 (m-30) cc_final: 0.7090 (m-30) REVERT: B 154 ASP cc_start: 0.9078 (m-30) cc_final: 0.8779 (m-30) REVERT: C 6 LYS cc_start: 0.8736 (mmmm) cc_final: 0.8534 (mmmm) REVERT: C 53 GLN cc_start: 0.7372 (mm110) cc_final: 0.6745 (mp10) REVERT: C 100 ASP cc_start: 0.6144 (p0) cc_final: 0.5892 (p0) REVERT: C 113 LYS cc_start: 0.8397 (tppp) cc_final: 0.7921 (mptt) REVERT: D 10 ASN cc_start: 0.8167 (t0) cc_final: 0.7730 (t0) REVERT: D 133 MET cc_start: 0.8146 (mtm) cc_final: 0.7901 (mtp) REVERT: E 6 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.6930 (mptt) REVERT: F 96 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7874 (ttp) REVERT: F 114 GLU cc_start: 0.8440 (mp0) cc_final: 0.8174 (mp0) REVERT: G 41 GLN cc_start: 0.8649 (tp40) cc_final: 0.8298 (tp-100) REVERT: G 100 ASP cc_start: 0.7163 (t0) cc_final: 0.6289 (m-30) REVERT: G 106 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6438 (mp0) REVERT: G 115 MET cc_start: 0.9444 (ttp) cc_final: 0.9053 (ttp) REVERT: H 77 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7351 (mtp85) REVERT: H 96 MET cc_start: 0.9059 (ptm) cc_final: 0.8755 (tmm) REVERT: H 147 LYS cc_start: 0.8524 (ptpt) cc_final: 0.8254 (ptpp) REVERT: I 76 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.6713 (tttt) REVERT: I 148 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: I 161 GLN cc_start: 0.7701 (mt0) cc_final: 0.7339 (mt0) REVERT: K 39 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7773 (mm) REVERT: K 61 LYS cc_start: 0.9497 (mmmm) cc_final: 0.9190 (mmpt) REVERT: L 30 TYR cc_start: 0.7868 (t80) cc_final: 0.7536 (t80) REVERT: L 86 ASP cc_start: 0.8110 (t0) cc_final: 0.7839 (t0) REVERT: L 100 ASP cc_start: 0.6859 (OUTLIER) cc_final: 0.6161 (m-30) REVERT: M 64 ASN cc_start: 0.4829 (OUTLIER) cc_final: 0.4589 (m110) outliers start: 107 outliers final: 24 residues processed: 399 average time/residue: 0.5599 time to fit residues: 248.9241 Evaluate side-chains 287 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 1028 ASN Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain E residue 6 LYS Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain G residue 47 ARG Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain I residue 64 ASP Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 106 GLU Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain J residue 100 ASP Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 100 ASP Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain M residue 13 SER Chi-restraints excluded: chain M residue 64 ASN Chi-restraints excluded: chain X residue 12 ILE Chi-restraints excluded: chain X residue 36 ILE Chi-restraints excluded: chain X residue 42 VAL Chi-restraints excluded: chain X residue 45 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 200 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 149 optimal weight: 0.1980 chunk 136 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 980 HIS 11065 HIS ** 11123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 10 ASN B 110 ASN C 117 ASN E 57 GLN H 11 ASN I 120 GLN M 25 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.059678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.048735 restraints weight = 60874.500| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.57 r_work: 0.2874 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.7144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 18201 Z= 0.202 Angle : 0.784 11.928 24688 Z= 0.402 Chirality : 0.042 0.277 2767 Planarity : 0.005 0.066 3165 Dihedral : 9.057 88.025 3097 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.34 % Favored : 97.48 % Rotamer: Outliers : 5.20 % Allowed : 25.82 % Favored : 68.98 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.17), residues: 2225 helix: 2.13 (0.12), residues: 1770 sheet: 1.13 (1.22), residues: 17 loop : -1.23 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 131 TYR 0.033 0.002 TYR G 155 PHE 0.013 0.002 PHE 11066 TRP 0.009 0.002 TRP Z 318 HIS 0.012 0.004 HIS 11065 Details of bonding type rmsd covalent geometry : bond 0.00459 (18189) covalent geometry : angle 0.78368 (24688) hydrogen bonds : bond 0.05405 ( 1365) hydrogen bonds : angle 4.51417 ( 4047) Misc. bond : bond 0.00040 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 287 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 959 PHE cc_start: 0.8040 (m-80) cc_final: 0.7807 (m-10) REVERT: 1 978 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9251 (tp) REVERT: 1 1087 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7882 (mttm) REVERT: 1 1138 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8614 (tt0) REVERT: Z 324 ASP cc_start: 0.8727 (m-30) cc_final: 0.8512 (m-30) REVERT: A 10 ASN cc_start: 0.8996 (OUTLIER) cc_final: 0.8743 (t0) REVERT: A 14 GLU cc_start: 0.8254 (tp30) cc_final: 0.7987 (tm-30) REVERT: A 41 GLN cc_start: 0.8410 (pt0) cc_final: 0.7983 (pt0) REVERT: A 47 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8567 (tmm-80) REVERT: B 28 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9173 (tppp) REVERT: B 47 ASN cc_start: 0.8028 (m-40) cc_final: 0.7762 (m-40) REVERT: B 54 GLU cc_start: 0.8785 (mp0) cc_final: 0.8254 (mp0) REVERT: B 96 MET cc_start: 0.9224 (ptm) cc_final: 0.8978 (ttp) REVERT: C 113 LYS cc_start: 0.8845 (tppp) cc_final: 0.8563 (tptt) REVERT: E 133 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8871 (mtm) REVERT: E 134 LYS cc_start: 0.8878 (tttp) cc_final: 0.8638 (tppp) REVERT: F 51 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8518 (mp) REVERT: F 96 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8388 (ttp) REVERT: F 114 GLU cc_start: 0.8789 (mp0) cc_final: 0.8505 (mp0) REVERT: G 41 GLN cc_start: 0.8919 (tp40) cc_final: 0.8482 (tp-100) REVERT: G 61 LYS cc_start: 0.8773 (tppp) cc_final: 0.8448 (tptp) REVERT: G 73 TYR cc_start: 0.7956 (t80) cc_final: 0.7746 (t80) REVERT: G 77 MET cc_start: 0.8308 (mmm) cc_final: 0.8059 (mmm) REVERT: G 104 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8713 (pt) REVERT: G 106 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6862 (pm20) REVERT: H 47 ASN cc_start: 0.7932 (m110) cc_final: 0.7639 (m-40) REVERT: H 147 LYS cc_start: 0.8832 (ptpt) cc_final: 0.8446 (ptpp) REVERT: I 52 LYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6779 (tmtt) REVERT: I 59 PHE cc_start: 0.9100 (m-10) cc_final: 0.8800 (m-10) REVERT: I 76 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7017 (tttt) REVERT: I 100 ASP cc_start: 0.7576 (m-30) cc_final: 0.7345 (p0) REVERT: I 148 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7952 (mt-10) REVERT: J 58 LYS cc_start: 0.9070 (mmpt) cc_final: 0.8862 (mmpt) REVERT: K 6 LYS cc_start: 0.8415 (mmmt) cc_final: 0.7897 (mttt) REVERT: K 61 LYS cc_start: 0.9527 (mmmm) cc_final: 0.9295 (mmpt) REVERT: K 88 TYR cc_start: 0.8733 (m-80) cc_final: 0.8170 (m-80) REVERT: K 100 ASP cc_start: 0.7639 (p0) cc_final: 0.7229 (p0) REVERT: L 85 MET cc_start: 0.9072 (mmm) cc_final: 0.8845 (mmp) REVERT: M 3 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7662 (mtm180) outliers start: 93 outliers final: 16 residues processed: 347 average time/residue: 0.5649 time to fit residues: 217.6328 Evaluate side-chains 264 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 978 LEU Chi-restraints excluded: chain 1 residue 1087 LYS Chi-restraints excluded: chain 1 residue 1119 LEU Chi-restraints excluded: chain 1 residue 1138 GLN Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 61 ILE Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain G residue 47 ARG Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain I residue 52 LYS Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 148 GLU Chi-restraints excluded: chain J residue 141 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain L residue 135 GLU Chi-restraints excluded: chain M residue 3 ARG Chi-restraints excluded: chain X residue 42 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 208 optimal weight: 0.3980 chunk 159 optimal weight: 0.8980 chunk 220 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11151 GLN A 53 GLN B 2 GLN E 57 GLN H 11 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.057849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.046745 restraints weight = 61117.998| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.59 r_work: 0.2820 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.8527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18201 Z= 0.178 Angle : 0.737 11.011 24688 Z= 0.374 Chirality : 0.041 0.189 2767 Planarity : 0.004 0.060 3165 Dihedral : 8.814 86.565 3095 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.43 % Favored : 97.39 % Rotamer: Outliers : 3.52 % Allowed : 27.05 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.17), residues: 2225 helix: 2.14 (0.12), residues: 1775 sheet: 1.58 (1.11), residues: 17 loop : -1.32 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Z 323 TYR 0.021 0.002 TYR G 155 PHE 0.011 0.001 PHE A 29 TRP 0.008 0.002 TRP Z 318 HIS 0.002 0.001 HIS 1 980 Details of bonding type rmsd covalent geometry : bond 0.00396 (18189) covalent geometry : angle 0.73685 (24688) hydrogen bonds : bond 0.04893 ( 1365) hydrogen bonds : angle 4.40373 ( 4047) Misc. bond : bond 0.00076 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 246 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 959 PHE cc_start: 0.8109 (m-80) cc_final: 0.7892 (m-10) REVERT: 1 977 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8848 (pt0) REVERT: 1 1087 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8090 (mttm) REVERT: Z 324 ASP cc_start: 0.8841 (m-30) cc_final: 0.8518 (m-30) REVERT: A 41 GLN cc_start: 0.8492 (pt0) cc_final: 0.7970 (pp30) REVERT: A 60 GLN cc_start: 0.9191 (tm-30) cc_final: 0.8776 (pp30) REVERT: A 88 TYR cc_start: 0.9194 (m-80) cc_final: 0.8989 (m-80) REVERT: A 160 MET cc_start: 0.7615 (ptp) cc_final: 0.6369 (ptp) REVERT: B 28 LYS cc_start: 0.9416 (tppt) cc_final: 0.9148 (tppp) REVERT: B 54 GLU cc_start: 0.8868 (mp0) cc_final: 0.8379 (mp0) REVERT: C 73 TYR cc_start: 0.8464 (t80) cc_final: 0.8244 (t80) REVERT: C 151 PHE cc_start: 0.8311 (m-10) cc_final: 0.8090 (m-10) REVERT: D 1 MET cc_start: 0.7067 (ptm) cc_final: 0.6818 (tmt) REVERT: E 133 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8930 (mtm) REVERT: E 154 ASP cc_start: 0.8841 (m-30) cc_final: 0.8511 (m-30) REVERT: F 45 SER cc_start: 0.8325 (m) cc_final: 0.8109 (t) REVERT: F 54 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8722 (mm-30) REVERT: F 114 GLU cc_start: 0.8826 (mp0) cc_final: 0.8563 (mp0) REVERT: G 41 GLN cc_start: 0.8897 (tp40) cc_final: 0.8470 (tp-100) REVERT: G 61 LYS cc_start: 0.8897 (tppp) cc_final: 0.8685 (tptp) REVERT: G 77 MET cc_start: 0.8469 (mmm) cc_final: 0.8126 (mmm) REVERT: G 115 MET cc_start: 0.9548 (ttp) cc_final: 0.9243 (ttp) REVERT: G 133 MET cc_start: 0.8649 (mtm) cc_final: 0.8440 (mmm) REVERT: H 1 MET cc_start: 0.8742 (ptm) cc_final: 0.8141 (ppp) REVERT: H 15 GLN cc_start: 0.7616 (tt0) cc_final: 0.7335 (tm-30) REVERT: H 17 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8149 (mmmm) REVERT: H 54 GLU cc_start: 0.9063 (mp0) cc_final: 0.8667 (mp0) REVERT: H 147 LYS cc_start: 0.8929 (ptpt) cc_final: 0.8615 (ptpp) REVERT: I 76 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7308 (tttt) REVERT: I 154 ASP cc_start: 0.9039 (m-30) cc_final: 0.8802 (m-30) REVERT: K 6 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8155 (mttp) REVERT: K 61 LYS cc_start: 0.9555 (mmmm) cc_final: 0.9296 (mmpt) REVERT: K 144 ASP cc_start: 0.8720 (p0) cc_final: 0.8431 (p0) REVERT: M 22 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7258 (mm-30) outliers start: 63 outliers final: 19 residues processed: 292 average time/residue: 0.7195 time to fit residues: 231.8583 Evaluate side-chains 239 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 977 GLN Chi-restraints excluded: chain 1 residue 1087 LYS Chi-restraints excluded: chain 1 residue 1119 LEU Chi-restraints excluded: chain Z residue 325 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain G residue 47 ARG Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain I residue 64 ASP Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain X residue 42 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 180 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11123 ASN 11151 GLN B 2 GLN B 117 ASN E 57 GLN E 120 GLN H 11 ASN I 135 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.057162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.045546 restraints weight = 62239.511| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.79 r_work: 0.2768 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.8999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18201 Z= 0.148 Angle : 0.697 11.351 24688 Z= 0.352 Chirality : 0.039 0.183 2767 Planarity : 0.004 0.048 3165 Dihedral : 8.704 87.093 3094 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.38 % Favored : 97.39 % Rotamer: Outliers : 3.63 % Allowed : 26.94 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.18), residues: 2225 helix: 2.27 (0.12), residues: 1775 sheet: 1.49 (1.17), residues: 17 loop : -1.36 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Z 323 TYR 0.025 0.002 TYR E 73 PHE 0.009 0.001 PHE 1 952 TRP 0.005 0.001 TRP Z 318 HIS 0.002 0.001 HIS 1 980 Details of bonding type rmsd covalent geometry : bond 0.00319 (18189) covalent geometry : angle 0.69689 (24688) hydrogen bonds : bond 0.04546 ( 1365) hydrogen bonds : angle 4.28752 ( 4047) Misc. bond : bond 0.00053 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 251 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 959 PHE cc_start: 0.8170 (m-80) cc_final: 0.7849 (m-10) REVERT: 1 960 LYS cc_start: 0.8209 (tppp) cc_final: 0.7993 (ttpp) REVERT: 1 968 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: 1 977 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8902 (pt0) REVERT: 1 1075 GLN cc_start: 0.8917 (tp40) cc_final: 0.8597 (tp-100) REVERT: 1 1087 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8167 (mtpp) REVERT: Z 324 ASP cc_start: 0.8748 (m-30) cc_final: 0.8504 (m-30) REVERT: A 41 GLN cc_start: 0.8499 (pt0) cc_final: 0.7789 (pp30) REVERT: A 45 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8436 (mm-30) REVERT: A 88 TYR cc_start: 0.9137 (m-80) cc_final: 0.8869 (m-80) REVERT: A 154 ASP cc_start: 0.8751 (m-30) cc_final: 0.8538 (m-30) REVERT: A 160 MET cc_start: 0.7774 (ptp) cc_final: 0.6569 (ptp) REVERT: B 28 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9102 (tppp) REVERT: B 54 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: B 106 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8530 (mt-10) REVERT: B 114 GLU cc_start: 0.8607 (mp0) cc_final: 0.8381 (pm20) REVERT: C 47 ARG cc_start: 0.7085 (OUTLIER) cc_final: 0.6682 (ppt170) REVERT: C 73 TYR cc_start: 0.8380 (t80) cc_final: 0.8005 (t80) REVERT: C 154 ASP cc_start: 0.8493 (m-30) cc_final: 0.8245 (m-30) REVERT: D 28 LYS cc_start: 0.8721 (pttt) cc_final: 0.8514 (pttt) REVERT: E 133 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8884 (mtm) REVERT: E 154 ASP cc_start: 0.8928 (m-30) cc_final: 0.8690 (m-30) REVERT: F 54 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8802 (mm-30) REVERT: F 114 GLU cc_start: 0.8865 (mp0) cc_final: 0.8563 (mp0) REVERT: G 41 GLN cc_start: 0.8868 (tp40) cc_final: 0.8374 (tp-100) REVERT: G 61 LYS cc_start: 0.8943 (tppp) cc_final: 0.8696 (tptp) REVERT: G 77 MET cc_start: 0.8827 (mmm) cc_final: 0.8456 (mmm) REVERT: G 106 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7053 (pm20) REVERT: H 1 MET cc_start: 0.8084 (ptm) cc_final: 0.7661 (OUTLIER) REVERT: H 15 GLN cc_start: 0.7710 (tt0) cc_final: 0.7248 (tm-30) REVERT: H 17 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8108 (mmmm) REVERT: H 147 LYS cc_start: 0.8827 (ptpt) cc_final: 0.8455 (ptpp) REVERT: I 59 PHE cc_start: 0.9361 (m-10) cc_final: 0.9031 (m-10) REVERT: I 76 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7219 (tttt) REVERT: J 17 LYS cc_start: 0.7558 (mmpt) cc_final: 0.7345 (mmtt) REVERT: J 58 LYS cc_start: 0.9176 (mmpt) cc_final: 0.8877 (ttmm) REVERT: K 6 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8148 (mttt) REVERT: K 61 LYS cc_start: 0.9581 (mmmm) cc_final: 0.9246 (mmpt) REVERT: K 77 MET cc_start: 0.8443 (mmm) cc_final: 0.8187 (mmm) REVERT: K 135 ASN cc_start: 0.9254 (t0) cc_final: 0.8892 (m110) REVERT: K 144 ASP cc_start: 0.8799 (p0) cc_final: 0.8554 (p0) REVERT: L 30 TYR cc_start: 0.8519 (t80) cc_final: 0.8310 (t80) REVERT: M 22 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7277 (mm-30) outliers start: 65 outliers final: 17 residues processed: 304 average time/residue: 0.6707 time to fit residues: 224.9638 Evaluate side-chains 237 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 968 GLU Chi-restraints excluded: chain 1 residue 977 GLN Chi-restraints excluded: chain 1 residue 1072 ILE Chi-restraints excluded: chain 1 residue 1087 LYS Chi-restraints excluded: chain 1 residue 1119 LEU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain G residue 47 ARG Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain X residue 42 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 95 optimal weight: 0.8980 chunk 139 optimal weight: 0.0170 chunk 16 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 171 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11151 GLN B 117 ASN E 57 GLN E 71 ASN H 11 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.057106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045438 restraints weight = 61789.170| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.78 r_work: 0.2764 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.9494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18201 Z= 0.144 Angle : 0.703 11.378 24688 Z= 0.352 Chirality : 0.038 0.179 2767 Planarity : 0.004 0.043 3165 Dihedral : 8.551 88.082 3092 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.70 % Favored : 97.08 % Rotamer: Outliers : 3.07 % Allowed : 27.00 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.18), residues: 2225 helix: 2.28 (0.12), residues: 1782 sheet: 1.14 (1.58), residues: 12 loop : -1.43 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 49 TYR 0.023 0.002 TYR E 73 PHE 0.009 0.001 PHE 1 952 TRP 0.004 0.001 TRP M 37 HIS 0.003 0.001 HIS 1 980 Details of bonding type rmsd covalent geometry : bond 0.00313 (18189) covalent geometry : angle 0.70255 (24688) hydrogen bonds : bond 0.04353 ( 1365) hydrogen bonds : angle 4.26272 ( 4047) Misc. bond : bond 0.00049 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 968 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8309 (mp0) REVERT: 1 1075 GLN cc_start: 0.8850 (tp40) cc_final: 0.8503 (tp-100) REVERT: 1 1087 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8219 (mmmt) REVERT: Z 324 ASP cc_start: 0.8779 (m-30) cc_final: 0.8521 (m-30) REVERT: A 41 GLN cc_start: 0.8488 (pt0) cc_final: 0.8118 (pp30) REVERT: A 60 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8793 (pp30) REVERT: A 86 ASP cc_start: 0.9086 (OUTLIER) cc_final: 0.8858 (t0) REVERT: A 88 TYR cc_start: 0.9111 (m-80) cc_final: 0.8736 (m-80) REVERT: A 154 ASP cc_start: 0.8790 (m-30) cc_final: 0.8559 (m-30) REVERT: B 28 LYS cc_start: 0.9404 (tppt) cc_final: 0.9122 (tppp) REVERT: B 52 ILE cc_start: 0.8975 (pt) cc_final: 0.8746 (mp) REVERT: B 54 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: B 114 GLU cc_start: 0.8662 (mp0) cc_final: 0.8373 (pm20) REVERT: B 148 GLU cc_start: 0.8801 (pp20) cc_final: 0.8420 (pm20) REVERT: C 53 GLN cc_start: 0.8187 (mm110) cc_final: 0.7685 (mp10) REVERT: C 73 TYR cc_start: 0.8683 (t80) cc_final: 0.8246 (t80) REVERT: C 154 ASP cc_start: 0.8712 (m-30) cc_final: 0.8437 (m-30) REVERT: D 28 LYS cc_start: 0.8763 (pttt) cc_final: 0.8539 (pttt) REVERT: D 96 MET cc_start: 0.9429 (ttp) cc_final: 0.8815 (ttt) REVERT: E 115 MET cc_start: 0.8900 (ttm) cc_final: 0.8661 (ttm) REVERT: E 133 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.8905 (mtm) REVERT: E 154 ASP cc_start: 0.8927 (m-30) cc_final: 0.8574 (m-30) REVERT: F 54 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8842 (mm-30) REVERT: F 114 GLU cc_start: 0.8930 (mp0) cc_final: 0.8626 (mp0) REVERT: G 41 GLN cc_start: 0.8877 (tp40) cc_final: 0.8387 (tp-100) REVERT: G 77 MET cc_start: 0.8790 (mmm) cc_final: 0.8400 (mmm) REVERT: G 106 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7202 (pm20) REVERT: G 115 MET cc_start: 0.9522 (ttp) cc_final: 0.9232 (ttp) REVERT: G 133 MET cc_start: 0.8672 (mtm) cc_final: 0.8469 (mmm) REVERT: H 1 MET cc_start: 0.7998 (ptm) cc_final: 0.7565 (OUTLIER) REVERT: H 15 GLN cc_start: 0.7804 (tt0) cc_final: 0.7311 (tm-30) REVERT: H 17 LYS cc_start: 0.8538 (mmmt) cc_final: 0.8046 (mmmm) REVERT: H 147 LYS cc_start: 0.8837 (ptpt) cc_final: 0.8490 (ptpp) REVERT: I 76 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7268 (tttt) REVERT: J 58 LYS cc_start: 0.9176 (mmpt) cc_final: 0.8875 (ttmm) REVERT: K 6 LYS cc_start: 0.8717 (mmmt) cc_final: 0.8249 (mmmm) REVERT: K 61 LYS cc_start: 0.9580 (mmmm) cc_final: 0.9227 (mmpt) REVERT: K 77 MET cc_start: 0.8494 (mmm) cc_final: 0.8201 (mmm) REVERT: L 135 GLU cc_start: 0.8310 (mp0) cc_final: 0.8064 (mp0) outliers start: 55 outliers final: 17 residues processed: 281 average time/residue: 0.6788 time to fit residues: 210.6794 Evaluate side-chains 228 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 968 GLU Chi-restraints excluded: chain 1 residue 1087 LYS Chi-restraints excluded: chain 1 residue 1119 LEU Chi-restraints excluded: chain Z residue 319 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain G residue 106 GLU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain X residue 42 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 32 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 11123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11151 GLN A 71 ASN B 117 ASN D 15 GLN E 41 GLN E 57 GLN I 135 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.055173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.043549 restraints weight = 63327.811| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.80 r_work: 0.2704 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 1.0004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18201 Z= 0.171 Angle : 0.718 11.536 24688 Z= 0.361 Chirality : 0.040 0.176 2767 Planarity : 0.004 0.046 3165 Dihedral : 8.412 89.237 3088 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.97 % Favored : 96.85 % Rotamer: Outliers : 3.24 % Allowed : 27.28 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.18), residues: 2225 helix: 2.27 (0.12), residues: 1782 sheet: 1.36 (1.63), residues: 12 loop : -1.54 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 49 TYR 0.024 0.002 TYR C 155 PHE 0.010 0.001 PHE 1 952 TRP 0.004 0.001 TRP M 37 HIS 0.002 0.001 HIS 1 980 Details of bonding type rmsd covalent geometry : bond 0.00388 (18189) covalent geometry : angle 0.71765 (24688) hydrogen bonds : bond 0.04735 ( 1365) hydrogen bonds : angle 4.30842 ( 4047) Misc. bond : bond 0.00074 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 224 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 968 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: 1 1075 GLN cc_start: 0.8861 (tp40) cc_final: 0.8450 (tp-100) REVERT: 1 1087 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8282 (mtpp) REVERT: Z 319 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8842 (pp) REVERT: A 41 GLN cc_start: 0.8565 (pt0) cc_final: 0.8191 (pp30) REVERT: A 86 ASP cc_start: 0.9153 (OUTLIER) cc_final: 0.8935 (t0) REVERT: A 154 ASP cc_start: 0.8798 (m-30) cc_final: 0.8534 (m-30) REVERT: A 160 MET cc_start: 0.8049 (ptp) cc_final: 0.7799 (ptt) REVERT: B 54 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8411 (mp0) REVERT: B 148 GLU cc_start: 0.8835 (pp20) cc_final: 0.8431 (pm20) REVERT: C 53 GLN cc_start: 0.8341 (mm110) cc_final: 0.7435 (mp10) REVERT: C 73 TYR cc_start: 0.8806 (t80) cc_final: 0.8298 (t80) REVERT: C 154 ASP cc_start: 0.8991 (m-30) cc_final: 0.8698 (m-30) REVERT: D 28 LYS cc_start: 0.8843 (pttt) cc_final: 0.8639 (pttt) REVERT: D 96 MET cc_start: 0.9514 (ttp) cc_final: 0.9167 (ttm) REVERT: E 133 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.8889 (mtm) REVERT: E 134 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8443 (tptp) REVERT: F 51 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9110 (mp) REVERT: F 54 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8861 (mm-30) REVERT: F 58 LYS cc_start: 0.8989 (tttt) cc_final: 0.8761 (ttmm) REVERT: F 114 GLU cc_start: 0.8960 (mp0) cc_final: 0.8685 (mp0) REVERT: G 41 GLN cc_start: 0.8895 (tp40) cc_final: 0.8405 (tp-100) REVERT: G 77 MET cc_start: 0.8930 (mmm) cc_final: 0.8633 (mmm) REVERT: H 1 MET cc_start: 0.8089 (ptm) cc_final: 0.7536 (OUTLIER) REVERT: H 15 GLN cc_start: 0.8089 (tt0) cc_final: 0.7619 (tm-30) REVERT: H 17 LYS cc_start: 0.8664 (mmmt) cc_final: 0.8220 (mmmm) REVERT: H 77 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.9003 (mtm180) REVERT: H 147 LYS cc_start: 0.8952 (ptpt) cc_final: 0.8593 (ptpp) REVERT: I 76 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7277 (tttt) REVERT: J 1 MET cc_start: 0.9178 (ppp) cc_final: 0.8828 (ptm) REVERT: J 58 LYS cc_start: 0.9202 (mmpt) cc_final: 0.8910 (ttmm) REVERT: J 135 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7881 (mp0) REVERT: K 41 GLN cc_start: 0.8805 (tt0) cc_final: 0.8367 (tp-100) REVERT: K 57 GLN cc_start: 0.9107 (mm110) cc_final: 0.8889 (mp-120) REVERT: K 61 LYS cc_start: 0.9569 (mmmm) cc_final: 0.9241 (mppt) REVERT: K 77 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8305 (mmm) REVERT: K 135 ASN cc_start: 0.9277 (t0) cc_final: 0.8912 (m110) REVERT: L 54 GLU cc_start: 0.8522 (mp0) cc_final: 0.8157 (mp0) REVERT: L 135 GLU cc_start: 0.8378 (mp0) cc_final: 0.8002 (mp0) REVERT: M 22 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7499 (mm-30) REVERT: M 60 VAL cc_start: 0.8974 (t) cc_final: 0.8774 (p) outliers start: 58 outliers final: 26 residues processed: 265 average time/residue: 0.6509 time to fit residues: 191.0036 Evaluate side-chains 240 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 968 GLU Chi-restraints excluded: chain 1 residue 987 ASP Chi-restraints excluded: chain 1 residue 1087 LYS Chi-restraints excluded: chain Z residue 319 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 151 PHE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 160 MET Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 77 ARG Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 144 ASP Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain X residue 42 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 77 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 3 optimal weight: 0.0030 chunk 55 optimal weight: 0.8980 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11123 ASN 11151 GLN C 10 ASN D 15 GLN E 57 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.055473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.044091 restraints weight = 61676.953| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.65 r_work: 0.2752 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 1.0398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18201 Z= 0.169 Angle : 0.730 12.536 24688 Z= 0.370 Chirality : 0.040 0.167 2767 Planarity : 0.004 0.047 3165 Dihedral : 8.330 88.601 3088 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.70 % Favored : 97.08 % Rotamer: Outliers : 2.68 % Allowed : 29.07 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.18), residues: 2225 helix: 2.19 (0.12), residues: 1777 sheet: 1.44 (1.65), residues: 12 loop : -1.55 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 323 TYR 0.023 0.002 TYR E 73 PHE 0.013 0.001 PHE 1 959 TRP 0.005 0.001 TRP Z 318 HIS 0.003 0.001 HIS 1 980 Details of bonding type rmsd covalent geometry : bond 0.00383 (18189) covalent geometry : angle 0.72952 (24688) hydrogen bonds : bond 0.04725 ( 1365) hydrogen bonds : angle 4.31696 ( 4047) Misc. bond : bond 0.00079 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 1075 GLN cc_start: 0.8750 (tp40) cc_final: 0.8199 (tp-100) REVERT: 1 1087 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8281 (mtpp) REVERT: A 41 GLN cc_start: 0.8561 (pt0) cc_final: 0.8309 (pp30) REVERT: A 60 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8781 (pp30) REVERT: A 86 ASP cc_start: 0.9104 (OUTLIER) cc_final: 0.8850 (t0) REVERT: A 154 ASP cc_start: 0.8810 (m-30) cc_final: 0.8550 (m-30) REVERT: B 54 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8462 (mp0) REVERT: C 53 GLN cc_start: 0.8554 (mm110) cc_final: 0.7683 (mp10) REVERT: C 73 TYR cc_start: 0.8915 (t80) cc_final: 0.8490 (t80) REVERT: C 154 ASP cc_start: 0.9046 (m-30) cc_final: 0.8837 (m-30) REVERT: D 28 LYS cc_start: 0.8900 (pttt) cc_final: 0.8661 (pttt) REVERT: D 96 MET cc_start: 0.9479 (ttp) cc_final: 0.9124 (ttm) REVERT: E 19 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8444 (p) REVERT: E 133 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.8972 (mtm) REVERT: E 134 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8775 (tptp) REVERT: F 1 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8160 (ttp) REVERT: F 51 ILE cc_start: 0.9568 (OUTLIER) cc_final: 0.9341 (mp) REVERT: F 54 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8883 (mm-30) REVERT: F 114 GLU cc_start: 0.8939 (mp0) cc_final: 0.8673 (mp0) REVERT: F 133 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.9060 (mtm) REVERT: G 41 GLN cc_start: 0.8916 (tp40) cc_final: 0.8412 (tp-100) REVERT: G 77 MET cc_start: 0.8850 (mmm) cc_final: 0.8541 (mmm) REVERT: H 15 GLN cc_start: 0.8206 (tt0) cc_final: 0.7757 (tm-30) REVERT: H 17 LYS cc_start: 0.8687 (mmmt) cc_final: 0.8354 (mmmm) REVERT: H 147 LYS cc_start: 0.9011 (ptpt) cc_final: 0.8631 (ptpp) REVERT: I 76 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7520 (tttt) REVERT: J 1 MET cc_start: 0.9302 (ppp) cc_final: 0.8853 (ptm) REVERT: K 6 LYS cc_start: 0.8868 (mmmm) cc_final: 0.8525 (mmmt) REVERT: K 41 GLN cc_start: 0.8903 (tt0) cc_final: 0.8520 (tp-100) REVERT: K 56 ASP cc_start: 0.8763 (m-30) cc_final: 0.8554 (m-30) REVERT: K 61 LYS cc_start: 0.9493 (mmmm) cc_final: 0.9167 (mppt) REVERT: K 77 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8383 (mmm) REVERT: K 133 MET cc_start: 0.8925 (ttp) cc_final: 0.8617 (mtt) REVERT: K 135 ASN cc_start: 0.9194 (t0) cc_final: 0.8916 (m110) REVERT: K 144 ASP cc_start: 0.8809 (p0) cc_final: 0.8578 (p0) REVERT: L 148 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8184 (tp30) outliers start: 48 outliers final: 19 residues processed: 251 average time/residue: 0.6437 time to fit residues: 178.7026 Evaluate side-chains 235 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 960 LYS Chi-restraints excluded: chain 1 residue 1087 LYS Chi-restraints excluded: chain Z residue 319 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain E residue 134 LYS Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain G residue 64 ASP Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain X residue 42 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 132 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 11151 GLN C 10 ASN D 15 GLN E 57 GLN ** M 41 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 = 0.3204 r_free = 0.3204 target = 0.055346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.043887 restraints weight = 61727.651| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.64 r_work: 0.2746 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 1.0545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18201 Z= 0.172 Angle : 0.744 13.138 24688 Z= 0.377 Chirality : 0.040 0.177 2767 Planarity : 0.004 0.046 3165 Dihedral : 8.307 86.980 3088 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.01 % Favored : 96.81 % Rotamer: Outliers : 2.63 % Allowed : 29.29 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.18), residues: 2225 helix: 2.20 (0.12), residues: 1777 sheet: 1.38 (1.62), residues: 12 loop : -1.58 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 323 TYR 0.025 0.002 TYR E 73 PHE 0.010 0.001 PHE 1 952 TRP 0.004 0.001 TRP M 37 HIS 0.002 0.001 HIS 1 980 Details of bonding type rmsd covalent geometry : bond 0.00395 (18189) covalent geometry : angle 0.74405 (24688) hydrogen bonds : bond 0.04745 ( 1365) hydrogen bonds : angle 4.36379 ( 4047) Misc. bond : bond 0.00081 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 216 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 975 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8897 (mtt-85) REVERT: 1 977 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8921 (pt0) REVERT: 1 1075 GLN cc_start: 0.8726 (tp40) cc_final: 0.8342 (tp-100) REVERT: 1 1087 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8321 (mtpp) REVERT: A 41 GLN cc_start: 0.8528 (pt0) cc_final: 0.8281 (pp30) REVERT: A 60 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8776 (pp30) REVERT: A 86 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8899 (t0) REVERT: A 154 ASP cc_start: 0.8842 (m-30) cc_final: 0.8632 (m-30) REVERT: B 54 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8490 (mp0) REVERT: B 148 GLU cc_start: 0.8853 (pp20) cc_final: 0.8430 (pm20) REVERT: C 53 GLN cc_start: 0.8529 (mm110) cc_final: 0.7703 (mp10) REVERT: C 73 TYR cc_start: 0.8862 (t80) cc_final: 0.8460 (t80) REVERT: C 154 ASP cc_start: 0.9162 (m-30) cc_final: 0.8906 (m-30) REVERT: D 28 LYS cc_start: 0.8938 (pttt) cc_final: 0.8695 (pttt) REVERT: D 96 MET cc_start: 0.9490 (ttp) cc_final: 0.9155 (ttm) REVERT: E 19 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8441 (p) REVERT: E 133 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8936 (mtm) REVERT: F 51 ILE cc_start: 0.9567 (OUTLIER) cc_final: 0.9342 (mp) REVERT: F 54 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8857 (mm-30) REVERT: F 114 GLU cc_start: 0.8926 (mp0) cc_final: 0.8665 (mp0) REVERT: F 133 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.9094 (mtm) REVERT: G 41 GLN cc_start: 0.8921 (tp40) cc_final: 0.8417 (tp-100) REVERT: G 77 MET cc_start: 0.8854 (mmm) cc_final: 0.8558 (mmm) REVERT: G 115 MET cc_start: 0.9378 (ttp) cc_final: 0.9100 (ttp) REVERT: H 15 GLN cc_start: 0.8288 (tt0) cc_final: 0.7799 (tm-30) REVERT: H 17 LYS cc_start: 0.8729 (mmmt) cc_final: 0.8415 (mmmm) REVERT: H 147 LYS cc_start: 0.9033 (ptpt) cc_final: 0.8681 (ptpp) REVERT: I 76 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7519 (tttt) REVERT: J 1 MET cc_start: 0.9299 (ppp) cc_final: 0.8847 (ptm) REVERT: J 135 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7942 (mp0) REVERT: K 6 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8453 (mmmt) REVERT: K 41 GLN cc_start: 0.8883 (tt0) cc_final: 0.8421 (tp-100) REVERT: K 61 LYS cc_start: 0.9511 (mmmm) cc_final: 0.9160 (mppt) REVERT: K 77 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8418 (mmm) REVERT: K 133 MET cc_start: 0.8909 (ttp) cc_final: 0.8558 (mtt) REVERT: K 135 ASN cc_start: 0.9249 (t0) cc_final: 0.8956 (m110) REVERT: K 144 ASP cc_start: 0.8905 (p0) cc_final: 0.8693 (p0) REVERT: L 147 LYS cc_start: 0.9142 (mtmp) cc_final: 0.8936 (mtmt) REVERT: L 148 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8217 (tp30) outliers start: 47 outliers final: 15 residues processed: 246 average time/residue: 0.6932 time to fit residues: 187.8436 Evaluate side-chains 231 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 975 ARG Chi-restraints excluded: chain 1 residue 977 GLN Chi-restraints excluded: chain 1 residue 1087 LYS Chi-restraints excluded: chain Z residue 319 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain E residue 19 SER Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain K residue 60 GLN Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain X residue 42 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 194 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 155 optimal weight: 0.0070 chunk 41 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 15 GLN E 57 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.056095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.044760 restraints weight = 61197.500| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.64 r_work: 0.2774 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 1.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18201 Z= 0.151 Angle : 0.732 13.735 24688 Z= 0.372 Chirality : 0.039 0.176 2767 Planarity : 0.004 0.044 3165 Dihedral : 8.278 84.768 3088 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.01 % Favored : 96.81 % Rotamer: Outliers : 1.62 % Allowed : 30.41 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.18), residues: 2225 helix: 2.21 (0.12), residues: 1777 sheet: 1.39 (1.62), residues: 12 loop : -1.57 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG X 39 TYR 0.023 0.002 TYR E 73 PHE 0.009 0.001 PHE 1 952 TRP 0.006 0.001 TRP X 43 HIS 0.002 0.001 HIS 1 980 Details of bonding type rmsd covalent geometry : bond 0.00337 (18189) covalent geometry : angle 0.73220 (24688) hydrogen bonds : bond 0.04446 ( 1365) hydrogen bonds : angle 4.30165 ( 4047) Misc. bond : bond 0.00061 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4450 Ramachandran restraints generated. 2225 Oldfield, 0 Emsley, 2225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 977 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8847 (pt0) REVERT: 1 1075 GLN cc_start: 0.8705 (tp40) cc_final: 0.8302 (tp-100) REVERT: 1 1087 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8299 (mtpp) REVERT: 1 1119 LEU cc_start: 0.7631 (tm) cc_final: 0.7416 (mt) REVERT: A 41 GLN cc_start: 0.8496 (pt0) cc_final: 0.8268 (pp30) REVERT: A 60 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8750 (pp30) REVERT: A 86 ASP cc_start: 0.9064 (OUTLIER) cc_final: 0.8842 (t0) REVERT: A 138 THR cc_start: 0.9468 (m) cc_final: 0.9240 (p) REVERT: A 154 ASP cc_start: 0.8781 (m-30) cc_final: 0.8556 (m-30) REVERT: B 54 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8508 (mp0) REVERT: B 148 GLU cc_start: 0.8847 (pp20) cc_final: 0.8380 (pm20) REVERT: C 53 GLN cc_start: 0.8560 (mm110) cc_final: 0.7945 (mp10) REVERT: C 73 TYR cc_start: 0.8818 (t80) cc_final: 0.8468 (t80) REVERT: C 139 SER cc_start: 0.9207 (p) cc_final: 0.9001 (p) REVERT: C 154 ASP cc_start: 0.9203 (m-30) cc_final: 0.8967 (m-30) REVERT: D 28 LYS cc_start: 0.8932 (pttt) cc_final: 0.8689 (pttt) REVERT: D 96 MET cc_start: 0.9466 (ttp) cc_final: 0.9121 (ttm) REVERT: E 133 MET cc_start: 0.9287 (OUTLIER) cc_final: 0.8988 (mtm) REVERT: F 51 ILE cc_start: 0.9527 (OUTLIER) cc_final: 0.9313 (mp) REVERT: F 54 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8845 (mm-30) REVERT: F 114 GLU cc_start: 0.8925 (mp0) cc_final: 0.8653 (mp0) REVERT: F 133 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8976 (mtm) REVERT: G 41 GLN cc_start: 0.8911 (tp40) cc_final: 0.8406 (tp-100) REVERT: G 77 MET cc_start: 0.8850 (mmm) cc_final: 0.8574 (mmm) REVERT: G 115 MET cc_start: 0.9337 (ttp) cc_final: 0.9048 (ttp) REVERT: H 1 MET cc_start: 0.8223 (ptm) cc_final: 0.7947 (ptm) REVERT: H 15 GLN cc_start: 0.8235 (tt0) cc_final: 0.7773 (tm-30) REVERT: H 17 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8347 (mmmm) REVERT: H 147 LYS cc_start: 0.9023 (ptpt) cc_final: 0.8645 (ptpp) REVERT: I 76 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7425 (tttt) REVERT: J 1 MET cc_start: 0.9318 (ppp) cc_final: 0.8755 (ptm) REVERT: J 135 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7899 (mp0) REVERT: J 147 LYS cc_start: 0.9020 (ptpp) cc_final: 0.8817 (mtmm) REVERT: K 6 LYS cc_start: 0.8917 (mmmm) cc_final: 0.8499 (mmmt) REVERT: K 41 GLN cc_start: 0.8884 (tt0) cc_final: 0.8419 (tp-100) REVERT: K 61 LYS cc_start: 0.9508 (mmmm) cc_final: 0.9184 (mppt) REVERT: K 77 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8423 (mmm) REVERT: K 100 ASP cc_start: 0.8243 (p0) cc_final: 0.7950 (p0) REVERT: K 135 ASN cc_start: 0.9210 (t0) cc_final: 0.8911 (m110) REVERT: L 148 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8176 (tp30) outliers start: 29 outliers final: 13 residues processed: 234 average time/residue: 0.6753 time to fit residues: 173.9335 Evaluate side-chains 228 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 977 GLN Chi-restraints excluded: chain 1 residue 1087 LYS Chi-restraints excluded: chain Z residue 319 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain C residue 57 GLN Chi-restraints excluded: chain E residue 133 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain K residue 60 GLN Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain L residue 135 GLU Chi-restraints excluded: chain X residue 42 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 223 random chunks: chunk 164 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 185 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN E 57 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.055892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.044561 restraints weight = 61739.661| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.64 r_work: 0.2768 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 1.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18201 Z= 0.157 Angle : 0.741 13.870 24688 Z= 0.377 Chirality : 0.039 0.174 2767 Planarity : 0.004 0.045 3165 Dihedral : 8.202 83.703 3088 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.06 % Favored : 96.76 % Rotamer: Outliers : 1.84 % Allowed : 30.30 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.18), residues: 2225 helix: 2.23 (0.12), residues: 1777 sheet: 1.38 (1.61), residues: 12 loop : -1.60 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 1 975 TYR 0.022 0.002 TYR E 73 PHE 0.009 0.001 PHE 1 952 TRP 0.012 0.001 TRP Z 318 HIS 0.002 0.001 HIS 1 980 Details of bonding type rmsd covalent geometry : bond 0.00353 (18189) covalent geometry : angle 0.74122 (24688) hydrogen bonds : bond 0.04489 ( 1365) hydrogen bonds : angle 4.30079 ( 4047) Misc. bond : bond 0.00065 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5834.01 seconds wall clock time: 100 minutes 29.32 seconds (6029.32 seconds total)