Starting phenix.real_space_refine on Wed May 21 05:54:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xp0_38546/05_2025/8xp0_38546_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xp0_38546/05_2025/8xp0_38546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xp0_38546/05_2025/8xp0_38546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xp0_38546/05_2025/8xp0_38546.map" model { file = "/net/cci-nas-00/data/ceres_data/8xp0_38546/05_2025/8xp0_38546_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xp0_38546/05_2025/8xp0_38546_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.025 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 87 5.16 5 C 13329 2.51 5 N 3768 2.21 5 O 3972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21156 Number of models: 1 Model: "" Number of chains: 4 Chain: "M" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2462 Classifications: {'peptide': 315} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 307} Chain breaks: 1 Chain: "N" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 224 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "a" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2341 Classifications: {'peptide': 289} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 267} Chain: "c" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 675 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Restraints were copied for chains: T, Z, b, d, Q, P, R, W, V, X, O, U, S, Y Time building chain proxies: 10.87, per 1000 atoms: 0.51 Number of scatterers: 21156 At special positions: 0 Unit cell: (150.7, 168.3, 172.7, 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 87 16.00 O 3972 8.00 N 3768 7.00 C 13329 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=0, symmetry=0 Time building additional restraints: 4.89 Conformation dependent library (CDL) restraints added in 2.5 seconds 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5052 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 14 sheets defined 54.4% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'M' and resid 5 through 18 removed outlier: 3.867A pdb=" N GLY M 18 " --> pdb=" O LEU M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 28 removed outlier: 3.626A pdb=" N HIS M 28 " --> pdb=" O GLU M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 43 removed outlier: 3.720A pdb=" N ASN M 43 " --> pdb=" O THR M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 66 removed outlier: 3.566A pdb=" N GLN M 65 " --> pdb=" O GLN M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 99 removed outlier: 8.114A pdb=" N GLU M 87 " --> pdb=" O LYS M 83 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N GLU M 88 " --> pdb=" O ALA M 84 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG M 89 " --> pdb=" O LEU M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 112 Processing helix chain 'M' and resid 114 through 124 removed outlier: 3.787A pdb=" N ASP M 124 " --> pdb=" O ASP M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 138 through 148 removed outlier: 3.613A pdb=" N LEU M 148 " --> pdb=" O ASP M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 162 Processing helix chain 'M' and resid 168 through 183 Processing helix chain 'M' and resid 196 through 205 Processing helix chain 'M' and resid 207 through 221 Processing helix chain 'M' and resid 223 through 233 Processing helix chain 'M' and resid 235 through 242 removed outlier: 3.832A pdb=" N VAL M 240 " --> pdb=" O GLU M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 254 Processing helix chain 'M' and resid 255 through 266 Processing helix chain 'M' and resid 267 through 278 Processing helix chain 'M' and resid 279 through 293 Processing helix chain 'M' and resid 297 through 318 Processing helix chain 'N' and resid 533 through 541 removed outlier: 4.402A pdb=" N ARG N 537 " --> pdb=" O SER N 533 " (cutoff:3.500A) Processing helix chain 'N' and resid 543 through 558 Processing helix chain 'O' and resid 51 through 74 Processing helix chain 'O' and resid 89 through 95 removed outlier: 3.690A pdb=" N ASN O 95 " --> pdb=" O GLU O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 131 Processing helix chain 'O' and resid 147 through 171 removed outlier: 3.676A pdb=" N LEU O 160 " --> pdb=" O ARG O 156 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA O 171 " --> pdb=" O ASP O 167 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 189 Processing helix chain 'O' and resid 221 through 225 Processing helix chain 'O' and resid 227 through 233 removed outlier: 3.675A pdb=" N ASN O 233 " --> pdb=" O GLU O 229 " (cutoff:3.500A) Processing helix chain 'O' and resid 239 through 255 Processing helix chain 'O' and resid 272 through 276 Processing helix chain 'P' and resid 52 through 59 Processing helix chain 'P' and resid 75 through 81 Processing helix chain 'P' and resid 127 through 137 removed outlier: 3.585A pdb=" N ARG P 137 " --> pdb=" O ARG P 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 59 Processing helix chain 'Q' and resid 74 through 81 Processing helix chain 'Q' and resid 127 through 137 removed outlier: 3.585A pdb=" N ARG Q 137 " --> pdb=" O ARG Q 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 59 Processing helix chain 'R' and resid 75 through 81 Processing helix chain 'R' and resid 127 through 137 removed outlier: 3.584A pdb=" N ARG R 137 " --> pdb=" O ARG R 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 18 removed outlier: 3.867A pdb=" N GLY S 18 " --> pdb=" O LEU S 14 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 28 removed outlier: 3.626A pdb=" N HIS S 28 " --> pdb=" O GLU S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 43 removed outlier: 3.720A pdb=" N ASN S 43 " --> pdb=" O THR S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 66 removed outlier: 3.566A pdb=" N GLN S 65 " --> pdb=" O GLN S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 99 removed outlier: 8.114A pdb=" N GLU S 87 " --> pdb=" O LYS S 83 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N GLU S 88 " --> pdb=" O ALA S 84 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG S 89 " --> pdb=" O LEU S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 112 Processing helix chain 'S' and resid 114 through 124 removed outlier: 3.786A pdb=" N ASP S 124 " --> pdb=" O ASP S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 138 through 148 removed outlier: 3.613A pdb=" N LEU S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 162 Processing helix chain 'S' and resid 168 through 183 Processing helix chain 'S' and resid 196 through 205 Processing helix chain 'S' and resid 207 through 221 Processing helix chain 'S' and resid 223 through 233 Processing helix chain 'S' and resid 235 through 242 removed outlier: 3.832A pdb=" N VAL S 240 " --> pdb=" O GLU S 237 " (cutoff:3.500A) Processing helix chain 'S' and resid 243 through 254 Processing helix chain 'S' and resid 255 through 266 Processing helix chain 'S' and resid 267 through 278 Processing helix chain 'S' and resid 279 through 293 Processing helix chain 'S' and resid 297 through 318 Processing helix chain 'T' and resid 533 through 541 removed outlier: 4.403A pdb=" N ARG T 537 " --> pdb=" O SER T 533 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 558 Processing helix chain 'U' and resid 51 through 74 Processing helix chain 'U' and resid 89 through 95 removed outlier: 3.690A pdb=" N ASN U 95 " --> pdb=" O GLU U 91 " (cutoff:3.500A) Processing helix chain 'U' and resid 119 through 131 Processing helix chain 'U' and resid 147 through 171 removed outlier: 3.676A pdb=" N LEU U 160 " --> pdb=" O ARG U 156 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA U 171 " --> pdb=" O ASP U 167 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 189 Processing helix chain 'U' and resid 221 through 225 Processing helix chain 'U' and resid 227 through 233 removed outlier: 3.675A pdb=" N ASN U 233 " --> pdb=" O GLU U 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 239 through 255 Processing helix chain 'U' and resid 272 through 276 Processing helix chain 'V' and resid 52 through 59 Processing helix chain 'V' and resid 75 through 81 Processing helix chain 'V' and resid 127 through 137 removed outlier: 3.584A pdb=" N ARG V 137 " --> pdb=" O ARG V 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 59 Processing helix chain 'W' and resid 74 through 81 Processing helix chain 'W' and resid 127 through 137 removed outlier: 3.585A pdb=" N ARG W 137 " --> pdb=" O ARG W 133 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 59 Processing helix chain 'X' and resid 75 through 81 Processing helix chain 'X' and resid 127 through 137 removed outlier: 3.585A pdb=" N ARG X 137 " --> pdb=" O ARG X 133 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 18 removed outlier: 3.867A pdb=" N GLY Y 18 " --> pdb=" O LEU Y 14 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 28 removed outlier: 3.626A pdb=" N HIS Y 28 " --> pdb=" O GLU Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 30 through 43 removed outlier: 3.719A pdb=" N ASN Y 43 " --> pdb=" O THR Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 66 removed outlier: 3.565A pdb=" N GLN Y 65 " --> pdb=" O GLN Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 72 through 99 removed outlier: 8.114A pdb=" N GLU Y 87 " --> pdb=" O LYS Y 83 " (cutoff:3.500A) removed outlier: 9.524A pdb=" N GLU Y 88 " --> pdb=" O ALA Y 84 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG Y 89 " --> pdb=" O LEU Y 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 105 through 112 Processing helix chain 'Y' and resid 114 through 124 removed outlier: 3.787A pdb=" N ASP Y 124 " --> pdb=" O ASP Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 126 through 137 Processing helix chain 'Y' and resid 138 through 148 removed outlier: 3.613A pdb=" N LEU Y 148 " --> pdb=" O ASP Y 144 " (cutoff:3.500A) Processing helix chain 'Y' and resid 150 through 162 Processing helix chain 'Y' and resid 168 through 183 Processing helix chain 'Y' and resid 196 through 205 Processing helix chain 'Y' and resid 207 through 221 Processing helix chain 'Y' and resid 223 through 233 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.832A pdb=" N VAL Y 240 " --> pdb=" O GLU Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 243 through 254 Processing helix chain 'Y' and resid 255 through 266 Processing helix chain 'Y' and resid 267 through 278 Processing helix chain 'Y' and resid 279 through 293 Processing helix chain 'Y' and resid 297 through 318 Processing helix chain 'Z' and resid 533 through 541 removed outlier: 4.403A pdb=" N ARG Z 537 " --> pdb=" O SER Z 533 " (cutoff:3.500A) Processing helix chain 'Z' and resid 543 through 558 Processing helix chain 'a' and resid 51 through 74 Processing helix chain 'a' and resid 89 through 95 removed outlier: 3.690A pdb=" N ASN a 95 " --> pdb=" O GLU a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 119 through 131 Processing helix chain 'a' and resid 147 through 171 removed outlier: 3.676A pdb=" N LEU a 160 " --> pdb=" O ARG a 156 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA a 171 " --> pdb=" O ASP a 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 189 Processing helix chain 'a' and resid 221 through 225 Processing helix chain 'a' and resid 227 through 233 removed outlier: 3.675A pdb=" N ASN a 233 " --> pdb=" O GLU a 229 " (cutoff:3.500A) Processing helix chain 'a' and resid 239 through 255 Processing helix chain 'a' and resid 272 through 276 Processing helix chain 'b' and resid 52 through 59 Processing helix chain 'b' and resid 75 through 81 Processing helix chain 'b' and resid 127 through 137 removed outlier: 3.585A pdb=" N ARG b 137 " --> pdb=" O ARG b 133 " (cutoff:3.500A) Processing helix chain 'c' and resid 52 through 59 Processing helix chain 'c' and resid 74 through 81 Processing helix chain 'c' and resid 127 through 137 removed outlier: 3.584A pdb=" N ARG c 137 " --> pdb=" O ARG c 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 59 Processing helix chain 'd' and resid 75 through 81 Processing helix chain 'd' and resid 127 through 137 removed outlier: 3.585A pdb=" N ARG d 137 " --> pdb=" O ARG d 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 35 through 37 removed outlier: 7.797A pdb=" N ILE d 106 " --> pdb=" O ILE d 125 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE d 125 " --> pdb=" O ILE d 106 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN d 108 " --> pdb=" O THR d 123 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TYR d 118 " --> pdb=" O LEU c 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 35 through 37 removed outlier: 7.111A pdb=" N ILE d 99 " --> pdb=" O ILE d 106 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLN d 108 " --> pdb=" O LEU d 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU d 97 " --> pdb=" O GLN d 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP d 98 " --> pdb=" O GLU d 67 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL d 62 " --> pdb=" O MET c 73 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET c 73 " --> pdb=" O VAL d 62 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY c 69 " --> pdb=" O VAL d 66 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU d 68 " --> pdb=" O GLU c 67 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLU c 67 " --> pdb=" O LEU d 68 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ARG d 70 " --> pdb=" O THR c 65 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR c 65 " --> pdb=" O ARG d 70 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ARG d 72 " --> pdb=" O LYS c 63 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LYS c 63 " --> pdb=" O ARG d 72 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR d 74 " --> pdb=" O PRO c 61 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP c 98 " --> pdb=" O GLU c 67 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU c 97 " --> pdb=" O GLN c 108 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN c 108 " --> pdb=" O LEU c 97 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE c 99 " --> pdb=" O ILE c 106 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE c 106 " --> pdb=" O ILE c 125 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE c 125 " --> pdb=" O ILE c 106 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN c 108 " --> pdb=" O THR c 123 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL c 120 " --> pdb=" O VAL d 87 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL d 87 " --> pdb=" O VAL c 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 78 through 81 Processing sheet with id=AA4, first strand: chain 'O' and resid 78 through 81 removed outlier: 3.560A pdb=" N ASN O 101 " --> pdb=" O PHE O 118 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU O 102 " --> pdb=" O SER O 182 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER O 182 " --> pdb=" O LEU O 102 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU O 104 " --> pdb=" O VAL O 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 282 through 285 removed outlier: 3.552A pdb=" N ASP O 282 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN P 108 " --> pdb=" O THR P 123 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE P 125 " --> pdb=" O ILE P 106 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE P 106 " --> pdb=" O ILE P 125 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE P 99 " --> pdb=" O ILE P 106 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLN P 108 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU P 97 " --> pdb=" O GLN P 108 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP P 98 " --> pdb=" O GLU P 67 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA O 266 " --> pdb=" O VAL P 66 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU P 68 " --> pdb=" O ASN O 264 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ASN O 264 " --> pdb=" O LEU P 68 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ARG P 70 " --> pdb=" O VAL O 262 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL O 262 " --> pdb=" O ARG P 70 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ARG P 72 " --> pdb=" O GLU O 260 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLU O 260 " --> pdb=" O ARG P 72 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR P 74 " --> pdb=" O GLU O 258 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU O 258 " --> pdb=" O THR P 74 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN O 264 " --> pdb=" O ILE O 293 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE O 293 " --> pdb=" O ASN O 264 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU O 302 " --> pdb=" O ALA O 294 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL O 296 " --> pdb=" O PRO O 300 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL O 301 " --> pdb=" O LEU O 320 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU O 320 " --> pdb=" O VAL O 301 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR O 303 " --> pdb=" O GLU O 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Q' and resid 86 through 92 removed outlier: 5.476A pdb=" N TYR R 118 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN R 108 " --> pdb=" O THR R 123 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE R 125 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE R 106 " --> pdb=" O ILE R 125 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE R 99 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLN R 108 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU R 97 " --> pdb=" O GLN R 108 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP R 98 " --> pdb=" O GLU R 67 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL R 62 " --> pdb=" O MET Q 73 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET Q 73 " --> pdb=" O VAL R 62 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY Q 69 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU R 68 " --> pdb=" O GLU Q 67 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU Q 67 " --> pdb=" O LEU R 68 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ARG R 70 " --> pdb=" O THR Q 65 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR Q 65 " --> pdb=" O ARG R 70 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ARG R 72 " --> pdb=" O LYS Q 63 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LYS Q 63 " --> pdb=" O ARG R 72 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR R 74 " --> pdb=" O PRO Q 61 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP Q 98 " --> pdb=" O GLU Q 67 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU Q 97 " --> pdb=" O GLN Q 108 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN Q 108 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE Q 99 " --> pdb=" O ILE Q 106 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE Q 106 " --> pdb=" O ILE Q 125 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE Q 125 " --> pdb=" O ILE Q 106 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLN Q 108 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL Q 120 " --> pdb=" O VAL R 87 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL R 87 " --> pdb=" O VAL Q 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 86 through 92 removed outlier: 5.476A pdb=" N TYR R 118 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN R 108 " --> pdb=" O THR R 123 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE R 125 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE R 106 " --> pdb=" O ILE R 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'U' and resid 78 through 81 Processing sheet with id=AA9, first strand: chain 'U' and resid 78 through 81 removed outlier: 3.560A pdb=" N ASN U 101 " --> pdb=" O PHE U 118 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU U 102 " --> pdb=" O SER U 182 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER U 182 " --> pdb=" O LEU U 102 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU U 104 " --> pdb=" O VAL U 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 282 through 285 removed outlier: 3.551A pdb=" N ASP U 282 " --> pdb=" O ILE V 122 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN V 108 " --> pdb=" O THR V 123 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE V 125 " --> pdb=" O ILE V 106 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE V 106 " --> pdb=" O ILE V 125 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE V 99 " --> pdb=" O ILE V 106 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN V 108 " --> pdb=" O LEU V 97 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU V 97 " --> pdb=" O GLN V 108 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP V 98 " --> pdb=" O GLU V 67 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA U 266 " --> pdb=" O VAL V 66 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU V 68 " --> pdb=" O ASN U 264 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ASN U 264 " --> pdb=" O LEU V 68 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ARG V 70 " --> pdb=" O VAL U 262 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL U 262 " --> pdb=" O ARG V 70 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG V 72 " --> pdb=" O GLU U 260 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU U 260 " --> pdb=" O ARG V 72 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR V 74 " --> pdb=" O GLU U 258 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU U 258 " --> pdb=" O THR V 74 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN U 264 " --> pdb=" O ILE U 293 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE U 293 " --> pdb=" O ASN U 264 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU U 302 " --> pdb=" O ALA U 294 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL U 296 " --> pdb=" O PRO U 300 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL U 301 " --> pdb=" O LEU U 320 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU U 320 " --> pdb=" O VAL U 301 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR U 303 " --> pdb=" O GLU U 318 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'W' and resid 86 through 92 removed outlier: 5.477A pdb=" N TYR X 118 " --> pdb=" O LEU W 89 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN X 108 " --> pdb=" O THR X 123 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N ILE X 125 " --> pdb=" O ILE X 106 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE X 106 " --> pdb=" O ILE X 125 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE X 99 " --> pdb=" O ILE X 106 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLN X 108 " --> pdb=" O LEU X 97 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU X 97 " --> pdb=" O GLN X 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP X 98 " --> pdb=" O GLU X 67 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL X 62 " --> pdb=" O MET W 73 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET W 73 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY W 69 " --> pdb=" O VAL X 66 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU X 68 " --> pdb=" O GLU W 67 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLU W 67 " --> pdb=" O LEU X 68 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ARG X 70 " --> pdb=" O THR W 65 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR W 65 " --> pdb=" O ARG X 70 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ARG X 72 " --> pdb=" O LYS W 63 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LYS W 63 " --> pdb=" O ARG X 72 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR X 74 " --> pdb=" O PRO W 61 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP W 98 " --> pdb=" O GLU W 67 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU W 97 " --> pdb=" O GLN W 108 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN W 108 " --> pdb=" O LEU W 97 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE W 99 " --> pdb=" O ILE W 106 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE W 106 " --> pdb=" O ILE W 125 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE W 125 " --> pdb=" O ILE W 106 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN W 108 " --> pdb=" O THR W 123 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL W 120 " --> pdb=" O VAL X 87 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL X 87 " --> pdb=" O VAL W 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 78 through 81 Processing sheet with id=AB4, first strand: chain 'a' and resid 78 through 81 removed outlier: 3.560A pdb=" N ASN a 101 " --> pdb=" O PHE a 118 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU a 102 " --> pdb=" O SER a 182 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER a 182 " --> pdb=" O LEU a 102 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU a 104 " --> pdb=" O VAL a 180 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 282 through 285 removed outlier: 3.551A pdb=" N ASP a 282 " --> pdb=" O ILE b 122 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLN b 108 " --> pdb=" O THR b 123 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ILE b 125 " --> pdb=" O ILE b 106 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE b 106 " --> pdb=" O ILE b 125 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE b 99 " --> pdb=" O ILE b 106 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN b 108 " --> pdb=" O LEU b 97 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU b 97 " --> pdb=" O GLN b 108 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP b 98 " --> pdb=" O GLU b 67 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA a 266 " --> pdb=" O VAL b 66 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU b 68 " --> pdb=" O ASN a 264 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ASN a 264 " --> pdb=" O LEU b 68 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ARG b 70 " --> pdb=" O VAL a 262 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL a 262 " --> pdb=" O ARG b 70 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG b 72 " --> pdb=" O GLU a 260 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU a 260 " --> pdb=" O ARG b 72 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR b 74 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU a 258 " --> pdb=" O THR b 74 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN a 264 " --> pdb=" O ILE a 293 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ILE a 293 " --> pdb=" O ASN a 264 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU a 302 " --> pdb=" O ALA a 294 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL a 296 " --> pdb=" O PRO a 300 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL a 301 " --> pdb=" O LEU a 320 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU a 320 " --> pdb=" O VAL a 301 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR a 303 " --> pdb=" O GLU a 318 " (cutoff:3.500A) 1241 hydrogen bonds defined for protein. 3540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.18 Time building geometry restraints manager: 5.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4605 1.33 - 1.45: 3971 1.45 - 1.57: 12664 1.57 - 1.69: 0 1.69 - 1.81: 171 Bond restraints: 21411 Sorted by residual: bond pdb=" C GLN Y 209 " pdb=" O GLN Y 209 " ideal model delta sigma weight residual 1.237 1.275 -0.039 1.17e-02 7.31e+03 1.09e+01 bond pdb=" C GLN S 209 " pdb=" O GLN S 209 " ideal model delta sigma weight residual 1.237 1.275 -0.039 1.17e-02 7.31e+03 1.09e+01 bond pdb=" N PHE M 221 " pdb=" CA PHE M 221 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.07e+01 bond pdb=" N PHE Y 221 " pdb=" CA PHE Y 221 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.07e+01 bond pdb=" N PHE S 221 " pdb=" CA PHE S 221 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.07e+01 ... (remaining 21406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 28699 2.56 - 5.12: 236 5.12 - 7.69: 21 7.69 - 10.25: 0 10.25 - 12.81: 3 Bond angle restraints: 28959 Sorted by residual: angle pdb=" C PHE S 66 " pdb=" N ALA S 67 " pdb=" CA ALA S 67 " ideal model delta sigma weight residual 121.70 134.51 -12.81 1.80e+00 3.09e-01 5.06e+01 angle pdb=" C PHE M 66 " pdb=" N ALA M 67 " pdb=" CA ALA M 67 " ideal model delta sigma weight residual 121.70 134.50 -12.80 1.80e+00 3.09e-01 5.06e+01 angle pdb=" C PHE Y 66 " pdb=" N ALA Y 67 " pdb=" CA ALA Y 67 " ideal model delta sigma weight residual 121.70 134.49 -12.79 1.80e+00 3.09e-01 5.05e+01 angle pdb=" N VAL O 186 " pdb=" CA VAL O 186 " pdb=" C VAL O 186 " ideal model delta sigma weight residual 113.00 106.50 6.50 1.30e+00 5.92e-01 2.50e+01 angle pdb=" N VAL U 186 " pdb=" CA VAL U 186 " pdb=" C VAL U 186 " ideal model delta sigma weight residual 113.00 106.51 6.49 1.30e+00 5.92e-01 2.50e+01 ... (remaining 28954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.76: 12518 11.76 - 23.52: 583 23.52 - 35.28: 160 35.28 - 47.04: 39 47.04 - 58.80: 41 Dihedral angle restraints: 13341 sinusoidal: 5595 harmonic: 7746 Sorted by residual: dihedral pdb=" CA THR U 189 " pdb=" C THR U 189 " pdb=" N ASN U 190 " pdb=" CA ASN U 190 " ideal model delta harmonic sigma weight residual -180.00 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA THR O 189 " pdb=" C THR O 189 " pdb=" N ASN O 190 " pdb=" CA ASN O 190 " ideal model delta harmonic sigma weight residual 180.00 -156.86 -23.14 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA THR a 189 " pdb=" C THR a 189 " pdb=" N ASN a 190 " pdb=" CA ASN a 190 " ideal model delta harmonic sigma weight residual -180.00 -156.89 -23.11 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 13338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2982 0.058 - 0.116: 406 0.116 - 0.174: 68 0.174 - 0.232: 6 0.232 - 0.290: 6 Chirality restraints: 3468 Sorted by residual: chirality pdb=" CA ILE Y 215 " pdb=" N ILE Y 215 " pdb=" C ILE Y 215 " pdb=" CB ILE Y 215 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ILE M 215 " pdb=" N ILE M 215 " pdb=" C ILE M 215 " pdb=" CB ILE M 215 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ILE S 215 " pdb=" N ILE S 215 " pdb=" C ILE S 215 " pdb=" CB ILE S 215 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 3465 not shown) Planarity restraints: 3768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET Y 206 " -0.036 2.00e-02 2.50e+03 7.07e-02 5.00e+01 pdb=" C MET Y 206 " 0.122 2.00e-02 2.50e+03 pdb=" O MET Y 206 " -0.047 2.00e-02 2.50e+03 pdb=" N LYS Y 207 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET M 206 " -0.036 2.00e-02 2.50e+03 7.07e-02 4.99e+01 pdb=" C MET M 206 " 0.122 2.00e-02 2.50e+03 pdb=" O MET M 206 " -0.047 2.00e-02 2.50e+03 pdb=" N LYS M 207 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET S 206 " -0.036 2.00e-02 2.50e+03 7.06e-02 4.99e+01 pdb=" C MET S 206 " 0.122 2.00e-02 2.50e+03 pdb=" O MET S 206 " -0.047 2.00e-02 2.50e+03 pdb=" N LYS S 207 " -0.040 2.00e-02 2.50e+03 ... (remaining 3765 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 100 2.57 - 3.15: 16975 3.15 - 3.74: 32273 3.74 - 4.32: 42627 4.32 - 4.90: 70867 Nonbonded interactions: 162842 Sorted by model distance: nonbonded pdb=" OH TYR M 76 " pdb=" O LEU Y 14 " model vdw 1.990 3.040 nonbonded pdb=" O LEU M 14 " pdb=" OH TYR S 76 " model vdw 1.990 3.040 nonbonded pdb=" O ASP O 34 " pdb=" N ALA d 115 " model vdw 2.278 3.120 nonbonded pdb=" N ALA R 115 " pdb=" O ASP U 34 " model vdw 2.278 3.120 nonbonded pdb=" OG1 THR O 193 " pdb=" NE2 GLN d 83 " model vdw 2.299 3.120 ... (remaining 162837 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: 0.15 Found NCS groups: ncs_group { reference = chain 'N' selection = chain 'T' selection = chain 'Z' } ncs_group { reference = chain 'c' selection = chain 'b' selection = chain 'd' selection = chain 'Q' selection = chain 'P' selection = chain 'R' selection = chain 'W' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'a' selection = chain 'O' selection = chain 'U' } ncs_group { reference = chain 'M' selection = chain 'S' selection = chain 'Y' } 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 group one per residue 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: 10.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 43.540 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4949 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 : 0.002 0.042 21411 Z= 0.178 Angle : 0.530 12.809 28959 Z= 0.328 Chirality : 0.043 0.290 3468 Planarity : 0.007 0.205 3768 Dihedral : 8.472 58.801 8289 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.80 % Allowed : 3.64 % Favored : 95.56 % Rotamer: Outliers : 2.68 % Allowed : 2.81 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.18), residues: 2634 helix: 2.14 (0.14), residues: 1410 sheet: 1.28 (0.40), residues: 207 loop : 0.03 (0.22), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 246 HIS 0.002 0.000 HIS O 241 PHE 0.009 0.001 PHE a 215 TYR 0.006 0.001 TYR a 179 ARG 0.005 0.000 ARG S 219 Details of bonding type rmsd hydrogen bonds : bond 0.18833 ( 1217) hydrogen bonds : angle 5.88960 ( 3540) covalent geometry : bond 0.00250 (21411) covalent geometry : angle 0.53043 (28959) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 558 time to evaluate : 2.470 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 124 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.6043 (t0) REVERT: V 51 MET cc_start: 0.3201 (ptt) cc_final: 0.1872 (ptm) REVERT: W 59 ASP cc_start: 0.7571 (m-30) cc_final: 0.7179 (t0) REVERT: Y 193 MET cc_start: 0.2419 (mpt) cc_final: 0.0635 (ttp) REVERT: Y 208 THR cc_start: 0.8069 (p) cc_final: 0.7655 (p) REVERT: a 39 ASP cc_start: 0.6116 (t0) cc_final: 0.5055 (t0) outliers start: 63 outliers final: 16 residues processed: 606 average time/residue: 0.4458 time to fit residues: 370.0172 Evaluate side-chains 267 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 250 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 112 PHE Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain O residue 85 ARG Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain S residue 124 ASP Chi-restraints excluded: chain U residue 155 ASN Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 112 PHE Chi-restraints excluded: chain a residue 155 ASN Chi-restraints excluded: chain a residue 211 LEU Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 120 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 215 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 121 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 35 GLN M 46 GLN M 49 ASN M 168 GLN ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 148 HIS O 190 ASN Q 102 ASN R 83 GLN S 35 GLN S 46 GLN ** S 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 238 ASN U 155 ASN U 190 ASN V 102 ASN ** W 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 GLN Y 46 GLN Y 49 ASN Z 542 ASN a 148 HIS a 155 ASN c 102 ASN d 83 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.064900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.053473 restraints weight = 302364.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.054302 restraints weight = 241164.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.054817 restraints weight = 178949.403| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21411 Z= 0.143 Angle : 0.698 13.531 28959 Z= 0.353 Chirality : 0.044 0.215 3468 Planarity : 0.005 0.060 3768 Dihedral : 4.996 52.984 2956 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.87 % Favored : 95.56 % Rotamer: Outliers : 2.55 % Allowed : 10.88 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.17), residues: 2634 helix: 2.09 (0.14), residues: 1395 sheet: 0.52 (0.36), residues: 228 loop : -0.04 (0.21), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 169 HIS 0.010 0.001 HIS O 319 PHE 0.023 0.001 PHE U 221 TYR 0.019 0.001 TYR a 165 ARG 0.006 0.001 ARG a 156 Details of bonding type rmsd hydrogen bonds : bond 0.03788 ( 1217) hydrogen bonds : angle 4.88739 ( 3540) covalent geometry : bond 0.00304 (21411) covalent geometry : angle 0.69799 (28959) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 271 time to evaluate : 2.763 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 321 MET cc_start: 0.7260 (ttt) cc_final: 0.6057 (mmp) REVERT: S 112 PHE cc_start: 0.4908 (OUTLIER) cc_final: 0.4473 (t80) REVERT: S 124 ASP cc_start: 0.7884 (m-30) cc_final: 0.7203 (t0) REVERT: T 532 MET cc_start: 0.5063 (OUTLIER) cc_final: 0.3203 (mpp) REVERT: U 113 THR cc_start: 0.6438 (OUTLIER) cc_final: 0.6179 (p) REVERT: U 145 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8707 (tp30) REVERT: U 184 MET cc_start: 0.8259 (mmm) cc_final: 0.7944 (tpp) REVERT: V 51 MET cc_start: 0.6746 (ptt) cc_final: 0.6005 (ptm) REVERT: W 59 ASP cc_start: 0.8929 (m-30) cc_final: 0.8602 (t0) REVERT: Y 193 MET cc_start: 0.3725 (mpt) cc_final: 0.2297 (ttp) REVERT: Y 293 ARG cc_start: 0.7776 (ttt180) cc_final: 0.7303 (ptp-170) REVERT: a 184 MET cc_start: 0.8797 (tmm) cc_final: 0.8264 (tmm) REVERT: b 58 MET cc_start: 0.4499 (mmt) cc_final: 0.4219 (mmt) REVERT: c 73 MET cc_start: 0.7442 (ppp) cc_final: 0.7156 (ppp) outliers start: 60 outliers final: 30 residues processed: 318 average time/residue: 0.4127 time to fit residues: 186.9188 Evaluate side-chains 239 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 112 PHE Chi-restraints excluded: chain N residue 532 MET Chi-restraints excluded: chain O residue 85 ARG Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain T residue 532 MET Chi-restraints excluded: chain U residue 113 THR Chi-restraints excluded: chain U residue 155 ASN Chi-restraints excluded: chain U residue 162 LEU Chi-restraints excluded: chain U residue 167 ASP Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 254 VAL Chi-restraints excluded: chain V residue 58 MET Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 122 ILE Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 155 ASN Chi-restraints excluded: chain a residue 169 TRP Chi-restraints excluded: chain a residue 211 LEU Chi-restraints excluded: chain b residue 120 VAL Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain d residue 78 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 201 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 214 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 542 ASN O 58 ASN O 129 ASN S 28 HIS ** U 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 HIS U 190 ASN ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 102 ASN Y 141 GLN Y 180 ASN a 58 ASN a 129 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.060313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.049714 restraints weight = 295261.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.050572 restraints weight = 205270.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.051186 restraints weight = 155977.498| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21411 Z= 0.214 Angle : 0.783 15.162 28959 Z= 0.402 Chirality : 0.045 0.228 3468 Planarity : 0.006 0.059 3768 Dihedral : 5.408 58.847 2948 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.02 % Favored : 95.41 % Rotamer: Outliers : 3.61 % Allowed : 11.69 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.16), residues: 2634 helix: 1.31 (0.13), residues: 1392 sheet: 0.29 (0.38), residues: 207 loop : -0.49 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP a 246 HIS 0.009 0.002 HIS S 28 PHE 0.016 0.002 PHE M 59 TYR 0.018 0.002 TYR a 38 ARG 0.009 0.001 ARG Y 152 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 1217) hydrogen bonds : angle 5.31583 ( 3540) covalent geometry : bond 0.00456 (21411) covalent geometry : angle 0.78259 (28959) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 200 time to evaluate : 2.560 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: 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: M 45 ARG cc_start: 0.5472 (OUTLIER) cc_final: 0.4933 (tpm170) REVERT: M 112 PHE cc_start: 0.6914 (OUTLIER) cc_final: 0.6641 (t80) REVERT: M 158 MET cc_start: 0.9052 (tmm) cc_final: 0.8680 (ppp) REVERT: M 321 MET cc_start: 0.7109 (ttt) cc_final: 0.5794 (mmp) REVERT: S 112 PHE cc_start: 0.5160 (OUTLIER) cc_final: 0.4896 (t80) REVERT: S 124 ASP cc_start: 0.8397 (m-30) cc_final: 0.7620 (p0) REVERT: S 233 MET cc_start: 0.7805 (ptt) cc_final: 0.6923 (mtp) REVERT: T 532 MET cc_start: 0.5071 (mmp) cc_final: 0.1880 (mpp) REVERT: U 145 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8958 (tp30) REVERT: U 184 MET cc_start: 0.7920 (mmm) cc_final: 0.7429 (mmm) REVERT: U 306 TYR cc_start: 0.1489 (OUTLIER) cc_final: -0.0242 (p90) REVERT: V 51 MET cc_start: 0.7070 (ptt) cc_final: 0.6435 (ptm) REVERT: W 132 MET cc_start: 0.9255 (ptp) cc_final: 0.9035 (ptp) REVERT: Y 112 PHE cc_start: 0.4995 (OUTLIER) cc_final: 0.4638 (t80) REVERT: Y 193 MET cc_start: 0.3019 (mpt) cc_final: 0.1901 (ttp) REVERT: Y 207 LYS cc_start: 0.5125 (mmtm) cc_final: 0.4911 (mtmm) REVERT: Y 293 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7025 (ptm160) REVERT: a 184 MET cc_start: 0.8165 (tmm) cc_final: 0.7785 (tmm) REVERT: a 306 TYR cc_start: 0.1965 (OUTLIER) cc_final: 0.1074 (p90) REVERT: b 51 MET cc_start: 0.2937 (ptt) cc_final: 0.2693 (ptm) REVERT: c 73 MET cc_start: 0.8263 (ppp) cc_final: 0.7953 (ppp) REVERT: c 132 MET cc_start: 0.9272 (mmm) cc_final: 0.8994 (mpp) REVERT: d 51 MET cc_start: 0.7913 (ttp) cc_final: 0.7620 (tmm) outliers start: 85 outliers final: 45 residues processed: 265 average time/residue: 0.3624 time to fit residues: 142.9398 Evaluate side-chains 222 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 171 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 112 PHE Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain N residue 555 MET Chi-restraints excluded: chain O residue 85 ARG Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain O residue 306 TYR Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain U residue 162 LEU Chi-restraints excluded: chain U residue 167 ASP Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 306 TYR Chi-restraints excluded: chain V residue 77 GLU Chi-restraints excluded: chain V residue 80 ARG Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 122 ILE Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 108 GLU Chi-restraints excluded: chain Y residue 112 PHE Chi-restraints excluded: chain Y residue 188 LEU Chi-restraints excluded: chain Y residue 208 THR Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 155 ASN Chi-restraints excluded: chain a residue 169 TRP Chi-restraints excluded: chain a residue 208 ILE Chi-restraints excluded: chain a residue 290 ASP Chi-restraints excluded: chain a residue 306 TYR Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain b residue 77 GLU Chi-restraints excluded: chain b residue 92 LEU Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 ILE Chi-restraints excluded: chain d residue 78 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 109 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 222 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 102 ASN U 87 GLN U 310 ASN ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 28 HIS d 83 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.060861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.050171 restraints weight = 298245.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.051072 restraints weight = 204878.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.051707 restraints weight = 154181.868| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21411 Z= 0.135 Angle : 0.667 14.417 28959 Z= 0.336 Chirality : 0.042 0.190 3468 Planarity : 0.005 0.051 3768 Dihedral : 5.073 58.040 2944 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.80 % Favored : 95.63 % Rotamer: Outliers : 2.76 % Allowed : 13.35 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 2634 helix: 1.56 (0.14), residues: 1395 sheet: 0.45 (0.37), residues: 201 loop : -0.44 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 169 HIS 0.005 0.001 HIS O 319 PHE 0.013 0.001 PHE U 221 TYR 0.009 0.001 TYR U 165 ARG 0.005 0.000 ARG a 66 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 1217) hydrogen bonds : angle 4.88786 ( 3540) covalent geometry : bond 0.00285 (21411) covalent geometry : angle 0.66679 (28959) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 2.701 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: 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: M 112 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.6272 (t80) REVERT: M 158 MET cc_start: 0.8981 (tmm) cc_final: 0.8662 (ppp) REVERT: M 321 MET cc_start: 0.6962 (ttt) cc_final: 0.5565 (mmp) REVERT: S 112 PHE cc_start: 0.5596 (OUTLIER) cc_final: 0.5006 (t80) REVERT: S 124 ASP cc_start: 0.8246 (m-30) cc_final: 0.7429 (p0) REVERT: S 233 MET cc_start: 0.7900 (ptt) cc_final: 0.6992 (mtp) REVERT: T 532 MET cc_start: 0.5365 (OUTLIER) cc_final: 0.2008 (mpp) REVERT: U 145 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8951 (tp30) REVERT: U 184 MET cc_start: 0.8225 (mmm) cc_final: 0.7614 (mmm) REVERT: V 51 MET cc_start: 0.7211 (ptt) cc_final: 0.5590 (tmm) REVERT: W 51 MET cc_start: 0.4142 (ppp) cc_final: 0.3900 (ppp) REVERT: W 132 MET cc_start: 0.9225 (ptp) cc_final: 0.9007 (ptp) REVERT: Y 112 PHE cc_start: 0.5246 (OUTLIER) cc_final: 0.4841 (t80) REVERT: Y 193 MET cc_start: 0.3062 (mpt) cc_final: 0.2059 (ttp) REVERT: a 184 MET cc_start: 0.8516 (tmm) cc_final: 0.8150 (tmm) REVERT: a 306 TYR cc_start: 0.1355 (OUTLIER) cc_final: 0.0285 (p90) REVERT: b 51 MET cc_start: 0.2340 (ptt) cc_final: 0.2107 (ptm) REVERT: b 77 GLU cc_start: 0.9291 (tt0) cc_final: 0.9019 (tp30) REVERT: c 73 MET cc_start: 0.8140 (ppp) cc_final: 0.7761 (ppp) REVERT: c 132 MET cc_start: 0.9290 (mmm) cc_final: 0.9038 (mpp) REVERT: d 51 MET cc_start: 0.7654 (ttp) cc_final: 0.7351 (ttp) REVERT: d 132 MET cc_start: 0.7904 (mpp) cc_final: 0.7655 (mpp) outliers start: 65 outliers final: 32 residues processed: 240 average time/residue: 0.3624 time to fit residues: 130.8393 Evaluate side-chains 206 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 112 PHE Chi-restraints excluded: chain O residue 85 ARG Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain O residue 306 TYR Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain T residue 532 MET Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain U residue 155 ASN Chi-restraints excluded: chain U residue 162 LEU Chi-restraints excluded: chain U residue 167 ASP Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain V residue 77 GLU Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 122 ILE Chi-restraints excluded: chain Y residue 112 PHE Chi-restraints excluded: chain a residue 38 TYR Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 155 ASN Chi-restraints excluded: chain a residue 169 TRP Chi-restraints excluded: chain a residue 208 ILE Chi-restraints excluded: chain a residue 290 ASP Chi-restraints excluded: chain a residue 306 TYR Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 125 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 82 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN ** O 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.059254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.048997 restraints weight = 298567.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.049834 restraints weight = 207316.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.050438 restraints weight = 157305.865| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.7053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21411 Z= 0.177 Angle : 0.711 14.601 28959 Z= 0.364 Chirality : 0.043 0.187 3468 Planarity : 0.005 0.058 3768 Dihedral : 5.298 56.757 2941 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.40 % Favored : 95.03 % Rotamer: Outliers : 2.93 % Allowed : 13.90 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2634 helix: 1.26 (0.14), residues: 1395 sheet: -0.44 (0.29), residues: 318 loop : -0.53 (0.22), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 246 HIS 0.005 0.001 HIS a 148 PHE 0.020 0.002 PHE Y 66 TYR 0.012 0.002 TYR b 104 ARG 0.006 0.001 ARG N 537 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 1217) hydrogen bonds : angle 5.08297 ( 3540) covalent geometry : bond 0.00362 (21411) covalent geometry : angle 0.71112 (28959) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 182 time to evaluate : 2.432 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 112 PHE cc_start: 0.6850 (OUTLIER) cc_final: 0.6412 (t80) REVERT: M 113 MET cc_start: 0.6370 (mmt) cc_final: 0.6151 (mmm) REVERT: M 158 MET cc_start: 0.8815 (tmm) cc_final: 0.8380 (ptp) REVERT: M 193 MET cc_start: 0.6245 (tpt) cc_final: 0.5670 (mmp) REVERT: M 321 MET cc_start: 0.6285 (ttt) cc_final: 0.4731 (mmp) REVERT: S 112 PHE cc_start: 0.6039 (OUTLIER) cc_final: 0.5446 (t80) REVERT: S 124 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7364 (p0) REVERT: S 233 MET cc_start: 0.7964 (ptt) cc_final: 0.6971 (mtp) REVERT: T 532 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.0375 (pmm) REVERT: U 184 MET cc_start: 0.8321 (mmm) cc_final: 0.8011 (mmm) REVERT: U 306 TYR cc_start: 0.2144 (OUTLIER) cc_final: -0.0287 (p90) REVERT: V 51 MET cc_start: 0.7417 (ptt) cc_final: 0.5659 (tmm) REVERT: Y 112 PHE cc_start: 0.5393 (OUTLIER) cc_final: 0.4894 (t80) REVERT: Z 532 MET cc_start: 0.4000 (mpp) cc_final: 0.3080 (mtm) REVERT: Z 539 MET cc_start: 0.0952 (ptp) cc_final: -0.0466 (ptp) REVERT: a 184 MET cc_start: 0.8564 (tmm) cc_final: 0.8088 (tmm) REVERT: a 306 TYR cc_start: 0.2784 (OUTLIER) cc_final: 0.1145 (p90) REVERT: b 51 MET cc_start: 0.2374 (ptt) cc_final: 0.2151 (ptm) REVERT: b 77 GLU cc_start: 0.9233 (tt0) cc_final: 0.8988 (tp30) REVERT: c 73 MET cc_start: 0.7839 (ppp) cc_final: 0.7480 (ppp) REVERT: d 132 MET cc_start: 0.7955 (mpp) cc_final: 0.7668 (mpp) outliers start: 69 outliers final: 42 residues processed: 239 average time/residue: 0.3585 time to fit residues: 131.2623 Evaluate side-chains 215 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 112 PHE Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain M residue 187 ASN Chi-restraints excluded: chain N residue 532 MET Chi-restraints excluded: chain O residue 85 ARG Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain O residue 306 TYR Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain S residue 124 ASP Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain T residue 532 MET Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain U residue 155 ASN Chi-restraints excluded: chain U residue 167 ASP Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 275 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 306 TYR Chi-restraints excluded: chain V residue 77 GLU Chi-restraints excluded: chain V residue 80 ARG Chi-restraints excluded: chain V residue 106 ILE Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 122 ILE Chi-restraints excluded: chain Y residue 112 PHE Chi-restraints excluded: chain a residue 38 TYR Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 155 ASN Chi-restraints excluded: chain a residue 169 TRP Chi-restraints excluded: chain a residue 208 ILE Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 290 ASP Chi-restraints excluded: chain a residue 306 TYR Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 ILE Chi-restraints excluded: chain d residue 73 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 77 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 6 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 542 ASN ** U 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 141 GLN Z 542 ASN ** a 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.058947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.048700 restraints weight = 296609.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.049545 restraints weight = 204652.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.050153 restraints weight = 154663.665| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.7567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21411 Z= 0.151 Angle : 0.689 16.643 28959 Z= 0.346 Chirality : 0.043 0.232 3468 Planarity : 0.005 0.055 3768 Dihedral : 5.229 57.775 2941 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.18 % Favored : 95.25 % Rotamer: Outliers : 2.98 % Allowed : 14.88 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.17), residues: 2634 helix: 1.28 (0.14), residues: 1407 sheet: -0.39 (0.34), residues: 237 loop : -0.53 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP U 246 HIS 0.004 0.001 HIS Y 28 PHE 0.014 0.001 PHE Y 26 TYR 0.010 0.001 TYR U 89 ARG 0.007 0.001 ARG V 131 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 1217) hydrogen bonds : angle 4.98683 ( 3540) covalent geometry : bond 0.00322 (21411) covalent geometry : angle 0.68895 (28959) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 172 time to evaluate : 2.693 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 15 MET cc_start: 0.7852 (mmp) cc_final: 0.7617 (mmp) REVERT: M 45 ARG cc_start: 0.5276 (OUTLIER) cc_final: 0.4690 (tpm170) REVERT: M 158 MET cc_start: 0.8852 (tmm) cc_final: 0.8344 (ptp) REVERT: M 321 MET cc_start: 0.6595 (ttt) cc_final: 0.5159 (mmp) REVERT: O 157 MET cc_start: 0.8657 (mmm) cc_final: 0.8002 (mtm) REVERT: O 240 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8238 (tpp-160) REVERT: S 112 PHE cc_start: 0.6113 (OUTLIER) cc_final: 0.5457 (t80) REVERT: S 124 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7545 (p0) REVERT: S 233 MET cc_start: 0.8079 (ptt) cc_final: 0.7774 (ptp) REVERT: U 169 TRP cc_start: 0.8086 (OUTLIER) cc_final: 0.7807 (t60) REVERT: U 306 TYR cc_start: 0.2098 (OUTLIER) cc_final: -0.0170 (p90) REVERT: V 51 MET cc_start: 0.7498 (ptt) cc_final: 0.5709 (ttm) REVERT: W 132 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8762 (ptp) REVERT: Y 112 PHE cc_start: 0.5389 (OUTLIER) cc_final: 0.4906 (t80) REVERT: Z 532 MET cc_start: 0.3517 (mpp) cc_final: 0.2697 (mtm) REVERT: a 184 MET cc_start: 0.8580 (tmm) cc_final: 0.8087 (tmm) REVERT: a 306 TYR cc_start: 0.2939 (OUTLIER) cc_final: 0.1183 (p90) REVERT: c 73 MET cc_start: 0.7897 (ppp) cc_final: 0.7527 (ppp) REVERT: c 118 TYR cc_start: 0.8853 (m-10) cc_final: 0.8565 (m-10) REVERT: d 132 MET cc_start: 0.8046 (mpp) cc_final: 0.7767 (mpp) outliers start: 70 outliers final: 40 residues processed: 229 average time/residue: 0.3444 time to fit residues: 121.0778 Evaluate side-chains 207 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain M residue 187 ASN Chi-restraints excluded: chain O residue 85 ARG Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 180 VAL Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 240 ARG Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 306 TYR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain S residue 124 ASP Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain U residue 155 ASN Chi-restraints excluded: chain U residue 163 GLU Chi-restraints excluded: chain U residue 167 ASP Chi-restraints excluded: chain U residue 169 TRP Chi-restraints excluded: chain U residue 275 ILE Chi-restraints excluded: chain U residue 306 TYR Chi-restraints excluded: chain V residue 77 GLU Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain W residue 132 MET Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 122 ILE Chi-restraints excluded: chain Y residue 112 PHE Chi-restraints excluded: chain a residue 38 TYR Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 155 ASN Chi-restraints excluded: chain a residue 169 TRP Chi-restraints excluded: chain a residue 208 ILE Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 290 ASP Chi-restraints excluded: chain a residue 306 TYR Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 ILE Chi-restraints excluded: chain d residue 73 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 221 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN ** O 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 ASN ** U 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 173 ASN ** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.058790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.048200 restraints weight = 302553.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.049066 restraints weight = 205379.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.049687 restraints weight = 154073.148| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21411 Z= 0.139 Angle : 0.678 15.639 28959 Z= 0.342 Chirality : 0.043 0.247 3468 Planarity : 0.004 0.052 3768 Dihedral : 5.066 56.666 2939 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.48 % Favored : 94.95 % Rotamer: Outliers : 3.10 % Allowed : 15.94 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2634 helix: 1.29 (0.14), residues: 1407 sheet: -0.39 (0.34), residues: 237 loop : -0.53 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP U 246 HIS 0.004 0.001 HIS O 319 PHE 0.014 0.001 PHE Y 26 TYR 0.008 0.001 TYR U 89 ARG 0.004 0.000 ARG a 66 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 1217) hydrogen bonds : angle 4.89811 ( 3540) covalent geometry : bond 0.00297 (21411) covalent geometry : angle 0.67760 (28959) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 168 time to evaluate : 2.623 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: symmetry clash REVERT: M 45 ARG cc_start: 0.5378 (OUTLIER) cc_final: 0.4853 (tpm170) REVERT: M 158 MET cc_start: 0.8986 (tmm) cc_final: 0.8439 (ptp) REVERT: M 193 MET cc_start: 0.6939 (tpp) cc_final: 0.6694 (ttt) REVERT: M 233 MET cc_start: 0.7997 (mmt) cc_final: 0.7765 (mmm) REVERT: M 321 MET cc_start: 0.6948 (ttt) cc_final: 0.6238 (mmp) REVERT: R 137 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8159 (mtt180) REVERT: S 112 PHE cc_start: 0.5767 (OUTLIER) cc_final: 0.5369 (t80) REVERT: S 124 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7452 (p0) REVERT: S 233 MET cc_start: 0.8105 (ptt) cc_final: 0.7802 (ptp) REVERT: U 306 TYR cc_start: 0.1704 (OUTLIER) cc_final: -0.0099 (p90) REVERT: V 51 MET cc_start: 0.7571 (ptt) cc_final: 0.6838 (ttm) REVERT: W 132 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8899 (ptp) REVERT: Y 71 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7144 (tp) REVERT: Y 112 PHE cc_start: 0.5312 (OUTLIER) cc_final: 0.4936 (t80) REVERT: Z 532 MET cc_start: 0.3536 (mpp) cc_final: 0.2994 (mtm) REVERT: a 184 MET cc_start: 0.8397 (tmm) cc_final: 0.7934 (tmm) REVERT: a 306 TYR cc_start: 0.2841 (OUTLIER) cc_final: 0.1359 (p90) REVERT: c 73 MET cc_start: 0.8290 (ppp) cc_final: 0.7980 (ppp) REVERT: c 118 TYR cc_start: 0.9036 (m-10) cc_final: 0.8804 (m-10) REVERT: d 132 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7753 (mpp) outliers start: 73 outliers final: 47 residues processed: 230 average time/residue: 0.3639 time to fit residues: 127.3543 Evaluate side-chains 212 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 155 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 214 VAL Chi-restraints excluded: chain O residue 85 ARG Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 180 VAL Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 251 VAL Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 302 LEU Chi-restraints excluded: chain O residue 306 TYR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain R residue 137 ARG Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain S residue 124 ASP Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain U residue 115 LEU Chi-restraints excluded: chain U residue 155 ASN Chi-restraints excluded: chain U residue 163 GLU Chi-restraints excluded: chain U residue 167 ASP Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 275 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 306 TYR Chi-restraints excluded: chain V residue 77 GLU Chi-restraints excluded: chain V residue 80 ARG Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain W residue 132 MET Chi-restraints excluded: chain X residue 72 ARG Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 122 ILE Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Y residue 112 PHE Chi-restraints excluded: chain a residue 38 TYR Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 155 ASN Chi-restraints excluded: chain a residue 169 TRP Chi-restraints excluded: chain a residue 208 ILE Chi-restraints excluded: chain a residue 211 LEU Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 290 ASP Chi-restraints excluded: chain a residue 306 TYR Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain c residue 125 ILE Chi-restraints excluded: chain d residue 132 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 85 optimal weight: 20.0000 chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 chunk 191 optimal weight: 0.9980 chunk 176 optimal weight: 0.0010 chunk 12 optimal weight: 0.9990 chunk 245 optimal weight: 0.0050 chunk 92 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 238 ASN O 310 ASN ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 83 GLN ** a 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.059622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.048780 restraints weight = 299023.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.049644 restraints weight = 203654.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.050286 restraints weight = 153051.919| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.7892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 21411 Z= 0.119 Angle : 0.694 15.504 28959 Z= 0.341 Chirality : 0.043 0.217 3468 Planarity : 0.004 0.056 3768 Dihedral : 4.869 57.595 2939 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.99 % Favored : 95.44 % Rotamer: Outliers : 2.38 % Allowed : 16.84 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.17), residues: 2634 helix: 1.47 (0.14), residues: 1404 sheet: -0.22 (0.34), residues: 237 loop : -0.44 (0.22), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP U 246 HIS 0.005 0.001 HIS O 319 PHE 0.019 0.001 PHE Y 26 TYR 0.008 0.001 TYR U 179 ARG 0.004 0.000 ARG a 66 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 1217) hydrogen bonds : angle 4.71411 ( 3540) covalent geometry : bond 0.00249 (21411) covalent geometry : angle 0.69389 (28959) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 2.737 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 158 MET cc_start: 0.8998 (tmm) cc_final: 0.8426 (ptp) REVERT: M 193 MET cc_start: 0.7224 (tpp) cc_final: 0.6114 (mpp) REVERT: M 233 MET cc_start: 0.7956 (mmt) cc_final: 0.7659 (mmm) REVERT: M 321 MET cc_start: 0.6968 (ttt) cc_final: 0.6131 (mmp) REVERT: O 157 MET cc_start: 0.8419 (mmm) cc_final: 0.7859 (mtm) REVERT: R 80 ARG cc_start: 0.9145 (mtt180) cc_final: 0.8760 (mtp85) REVERT: R 137 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8103 (mtt180) REVERT: S 124 ASP cc_start: 0.8281 (m-30) cc_final: 0.7521 (p0) REVERT: S 177 GLU cc_start: 0.9336 (tp30) cc_final: 0.8881 (mt-10) REVERT: S 233 MET cc_start: 0.8090 (ptt) cc_final: 0.7794 (ptp) REVERT: U 67 MET cc_start: 0.9329 (ppp) cc_final: 0.8842 (pmm) REVERT: U 278 LEU cc_start: 0.8402 (tt) cc_final: 0.8103 (mt) REVERT: U 306 TYR cc_start: 0.1655 (OUTLIER) cc_final: -0.0124 (p90) REVERT: V 51 MET cc_start: 0.6332 (ptt) cc_final: 0.5852 (ttm) REVERT: W 132 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8905 (ptp) REVERT: Y 112 PHE cc_start: 0.5268 (OUTLIER) cc_final: 0.4869 (t80) REVERT: Z 532 MET cc_start: 0.3466 (mpp) cc_final: 0.2959 (mtm) REVERT: a 184 MET cc_start: 0.8548 (tmm) cc_final: 0.8341 (tmm) REVERT: b 73 MET cc_start: 0.7401 (ppp) cc_final: 0.6690 (tmm) REVERT: b 81 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7185 (mt) REVERT: b 105 LEU cc_start: 0.9126 (pt) cc_final: 0.8746 (tp) REVERT: c 52 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.5719 (pm20) REVERT: c 118 TYR cc_start: 0.9026 (m-10) cc_final: 0.8800 (m-10) REVERT: d 132 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7749 (mpp) outliers start: 56 outliers final: 36 residues processed: 217 average time/residue: 0.3550 time to fit residues: 117.1130 Evaluate side-chains 206 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 163 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain O residue 85 ARG Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain R residue 137 ARG Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain U residue 155 ASN Chi-restraints excluded: chain U residue 163 GLU Chi-restraints excluded: chain U residue 167 ASP Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 275 ILE Chi-restraints excluded: chain U residue 306 TYR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain W residue 132 MET Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 15 MET Chi-restraints excluded: chain Y residue 112 PHE Chi-restraints excluded: chain a residue 38 TYR Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 155 ASN Chi-restraints excluded: chain a residue 169 TRP Chi-restraints excluded: chain a residue 208 ILE Chi-restraints excluded: chain a residue 211 LEU Chi-restraints excluded: chain a residue 223 MET Chi-restraints excluded: chain a residue 290 ASP Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain c residue 52 GLN Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain d residue 132 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 47 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 214 optimal weight: 9.9990 chunk 168 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.058730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.047993 restraints weight = 301659.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.048868 restraints weight = 204328.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.049500 restraints weight = 153171.107| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.8224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21411 Z= 0.138 Angle : 0.718 17.419 28959 Z= 0.356 Chirality : 0.043 0.224 3468 Planarity : 0.004 0.060 3768 Dihedral : 4.962 57.533 2939 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.52 % Favored : 94.91 % Rotamer: Outliers : 2.47 % Allowed : 16.92 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.17), residues: 2634 helix: 1.37 (0.14), residues: 1410 sheet: -0.19 (0.28), residues: 345 loop : -0.48 (0.23), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP U 246 HIS 0.004 0.001 HIS O 319 PHE 0.019 0.001 PHE Y 26 TYR 0.011 0.001 TYR U 165 ARG 0.006 0.000 ARG W 72 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 1217) hydrogen bonds : angle 4.82602 ( 3540) covalent geometry : bond 0.00294 (21411) covalent geometry : angle 0.71753 (28959) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 2.486 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: M 113 MET cc_start: 0.7351 (tpp) cc_final: 0.6988 (tpp) REVERT: M 158 MET cc_start: 0.9008 (tmm) cc_final: 0.8459 (ptp) REVERT: M 193 MET cc_start: 0.7113 (tpp) cc_final: 0.6027 (mpp) REVERT: M 321 MET cc_start: 0.6953 (ttt) cc_final: 0.6359 (mmp) REVERT: O 157 MET cc_start: 0.8447 (mmm) cc_final: 0.7896 (mtm) REVERT: R 137 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8074 (mtt180) REVERT: S 124 ASP cc_start: 0.8367 (m-30) cc_final: 0.7630 (p0) REVERT: S 177 GLU cc_start: 0.9326 (tp30) cc_final: 0.8861 (mt-10) REVERT: S 233 MET cc_start: 0.8228 (ptt) cc_final: 0.7966 (ptp) REVERT: U 278 LEU cc_start: 0.8292 (tt) cc_final: 0.8048 (mt) REVERT: U 306 TYR cc_start: 0.1615 (OUTLIER) cc_final: -0.0123 (p90) REVERT: W 80 ARG cc_start: 0.9262 (mtt180) cc_final: 0.9031 (mmt-90) REVERT: W 132 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8860 (ptp) REVERT: Y 71 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7348 (tp) REVERT: Y 112 PHE cc_start: 0.5221 (OUTLIER) cc_final: 0.4859 (t80) REVERT: Z 532 MET cc_start: 0.3633 (mpp) cc_final: 0.3185 (mtm) REVERT: a 184 MET cc_start: 0.8500 (tmm) cc_final: 0.8054 (tmm) REVERT: a 306 TYR cc_start: 0.3026 (OUTLIER) cc_final: 0.1574 (p90) REVERT: b 105 LEU cc_start: 0.9069 (pt) cc_final: 0.8693 (tp) REVERT: c 118 TYR cc_start: 0.9024 (m-10) cc_final: 0.8794 (m-10) REVERT: d 132 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7803 (mpp) outliers start: 58 outliers final: 43 residues processed: 211 average time/residue: 0.3336 time to fit residues: 108.0807 Evaluate side-chains 208 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 158 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain M residue 187 ASN Chi-restraints excluded: chain O residue 85 ARG Chi-restraints excluded: chain O residue 104 LEU Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 306 TYR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain R residue 58 MET Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain R residue 137 ARG Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain U residue 155 ASN Chi-restraints excluded: chain U residue 163 GLU Chi-restraints excluded: chain U residue 167 ASP Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 275 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 306 TYR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 99 ILE Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain W residue 132 MET Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 15 MET Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Y residue 112 PHE Chi-restraints excluded: chain a residue 38 TYR Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 155 ASN Chi-restraints excluded: chain a residue 169 TRP Chi-restraints excluded: chain a residue 208 ILE Chi-restraints excluded: chain a residue 223 MET Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 290 ASP Chi-restraints excluded: chain a residue 306 TYR Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain d residue 132 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 98 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 253 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 234 optimal weight: 1.9990 chunk 170 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 557 ASN ** a 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.059242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.048458 restraints weight = 300018.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.049341 restraints weight = 202778.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.049972 restraints weight = 151398.718| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.8342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21411 Z= 0.122 Angle : 0.713 17.256 28959 Z= 0.351 Chirality : 0.043 0.180 3468 Planarity : 0.004 0.060 3768 Dihedral : 4.838 58.518 2939 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.10 % Favored : 95.33 % Rotamer: Outliers : 2.38 % Allowed : 17.18 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.17), residues: 2634 helix: 1.46 (0.14), residues: 1407 sheet: 0.18 (0.29), residues: 315 loop : -0.57 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP U 246 HIS 0.005 0.001 HIS O 319 PHE 0.020 0.001 PHE Y 26 TYR 0.010 0.001 TYR X 104 ARG 0.004 0.000 ARG Y 152 Details of bonding type rmsd hydrogen bonds : bond 0.03306 ( 1217) hydrogen bonds : angle 4.69794 ( 3540) covalent geometry : bond 0.00261 (21411) covalent geometry : angle 0.71296 (28959) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 2.645 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: symmetry clash REVERT: M 113 MET cc_start: 0.6955 (tpp) cc_final: 0.6588 (tpp) REVERT: M 158 MET cc_start: 0.9017 (tmm) cc_final: 0.8418 (ptp) REVERT: M 193 MET cc_start: 0.7354 (tpp) cc_final: 0.6281 (mpp) REVERT: M 321 MET cc_start: 0.6972 (ttt) cc_final: 0.6336 (mmp) REVERT: O 157 MET cc_start: 0.8457 (mmm) cc_final: 0.7929 (mtm) REVERT: R 80 ARG cc_start: 0.9108 (mtt180) cc_final: 0.8727 (mtp85) REVERT: R 137 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8059 (mtt180) REVERT: S 124 ASP cc_start: 0.8396 (m-30) cc_final: 0.7681 (p0) REVERT: S 233 MET cc_start: 0.8101 (ptt) cc_final: 0.7850 (ptp) REVERT: U 223 MET cc_start: 0.7535 (tpt) cc_final: 0.7313 (tpt) REVERT: U 278 LEU cc_start: 0.8431 (tt) cc_final: 0.8109 (mt) REVERT: U 306 TYR cc_start: 0.1343 (OUTLIER) cc_final: -0.0364 (p90) REVERT: W 132 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8849 (ptp) REVERT: Y 71 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7302 (tp) REVERT: Y 112 PHE cc_start: 0.5522 (OUTLIER) cc_final: 0.5119 (t80) REVERT: Z 532 MET cc_start: 0.3677 (mpp) cc_final: 0.3209 (mtm) REVERT: a 67 MET cc_start: 0.9504 (mmm) cc_final: 0.9301 (mmm) REVERT: a 184 MET cc_start: 0.8521 (tmm) cc_final: 0.8063 (tmm) REVERT: a 306 TYR cc_start: 0.3012 (OUTLIER) cc_final: 0.1603 (p90) REVERT: b 105 LEU cc_start: 0.9104 (pt) cc_final: 0.8722 (tp) REVERT: c 118 TYR cc_start: 0.8987 (m-10) cc_final: 0.8762 (m-10) REVERT: d 132 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7788 (mpp) outliers start: 56 outliers final: 41 residues processed: 207 average time/residue: 0.3427 time to fit residues: 108.4399 Evaluate side-chains 204 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 2.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 124 ASP Chi-restraints excluded: chain M residue 187 ASN Chi-restraints excluded: chain N residue 532 MET Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 236 LEU Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 306 TYR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain R residue 58 MET Chi-restraints excluded: chain R residue 106 ILE Chi-restraints excluded: chain R residue 137 ARG Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain U residue 155 ASN Chi-restraints excluded: chain U residue 163 GLU Chi-restraints excluded: chain U residue 167 ASP Chi-restraints excluded: chain U residue 275 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 306 TYR Chi-restraints excluded: chain W residue 53 ASP Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain W residue 132 MET Chi-restraints excluded: chain X residue 72 ARG Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain Y residue 15 MET Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Y residue 112 PHE Chi-restraints excluded: chain a residue 38 TYR Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 155 ASN Chi-restraints excluded: chain a residue 169 TRP Chi-restraints excluded: chain a residue 208 ILE Chi-restraints excluded: chain a residue 211 LEU Chi-restraints excluded: chain a residue 223 MET Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 290 ASP Chi-restraints excluded: chain a residue 306 TYR Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 120 VAL Chi-restraints excluded: chain d residue 132 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 44 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 125 optimal weight: 0.0170 chunk 199 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 168 optimal weight: 0.5980 chunk 215 optimal weight: 10.0000 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 HIS ** U 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.059014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.048189 restraints weight = 299647.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.049063 restraints weight = 203198.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.049690 restraints weight = 152241.357| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.8511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21411 Z= 0.128 Angle : 0.729 17.033 28959 Z= 0.359 Chirality : 0.043 0.341 3468 Planarity : 0.004 0.058 3768 Dihedral : 4.753 50.297 2935 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.25 % Favored : 95.22 % Rotamer: Outliers : 2.17 % Allowed : 17.56 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.17), residues: 2634 helix: 1.43 (0.14), residues: 1407 sheet: 0.17 (0.29), residues: 315 loop : -0.57 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 554 HIS 0.004 0.001 HIS O 319 PHE 0.015 0.001 PHE Y 26 TYR 0.009 0.001 TYR X 104 ARG 0.006 0.000 ARG O 85 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 1217) hydrogen bonds : angle 4.72359 ( 3540) covalent geometry : bond 0.00276 (21411) covalent geometry : angle 0.72884 (28959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8719.18 seconds wall clock time: 152 minutes 30.17 seconds (9150.17 seconds total)