Starting phenix.real_space_refine on Sun Oct 12 04:16:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xp0_38546/10_2025/8xp0_38546_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xp0_38546/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xp0_38546/10_2025/8xp0_38546_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xp0_38546/10_2025/8xp0_38546_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xp0_38546/10_2025/8xp0_38546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xp0_38546/10_2025/8xp0_38546.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: "O" 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: "P" 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: S, Y, T, Z, U, a, Q, R, V, W, X, b, c, d Time building chain proxies: 3.98, per 1000 atoms: 0.19 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: 1.51 Conformation dependent library (CDL) restraints added in 998.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.78 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: 4.32 Time building geometry restraints manager: 2.09 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: 0.06 Found NCS groups: ncs_group { reference = chain 'M' selection = chain 'S' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = chain 'T' selection = chain 'Z' } ncs_group { reference = chain 'O' selection = chain 'U' selection = chain 'a' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 19.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.250 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.370 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG S 219 TYR 0.006 0.001 TYR a 179 PHE 0.009 0.001 PHE a 215 TRP 0.006 0.001 TRP a 246 HIS 0.002 0.000 HIS O 241 Details of bonding type rmsd covalent geometry : bond 0.00250 (21411) covalent geometry : angle 0.53043 (28959) hydrogen bonds : bond 0.18833 ( 1217) hydrogen bonds : angle 5.88960 ( 3540) *********************** 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 : 0.973 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: S 124 ASP cc_start: 0.6522 (OUTLIER) cc_final: 0.6043 (t0) REVERT: V 51 MET cc_start: 0.3201 (ptt) cc_final: 0.1873 (ptm) REVERT: W 51 MET cc_start: 0.1352 (ptt) cc_final: 0.0977 (ptm) REVERT: W 59 ASP cc_start: 0.7571 (m-30) cc_final: 0.7185 (t0) REVERT: Y 193 MET cc_start: 0.2419 (mpt) cc_final: 0.0608 (ttp) REVERT: Y 208 THR cc_start: 0.8069 (p) cc_final: 0.7658 (p) REVERT: a 39 ASP cc_start: 0.6116 (t0) cc_final: 0.5055 (t0) outliers start: 63 outliers final: 17 residues processed: 606 average time/residue: 0.2331 time to fit residues: 194.3121 Evaluate side-chains 265 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 162 LEU 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 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 0.0770 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.1340 ------------------------------------------------------------------------------- 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** N 542 ASN 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** 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: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.064895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.053569 restraints weight = 303919.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.054247 restraints weight = 246545.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.054837 restraints weight = 191171.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.055078 restraints weight = 162191.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.055203 restraints weight = 143860.305| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.3926 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= 0.142 Angle : 0.700 13.525 28959 Z= 0.354 Chirality : 0.044 0.216 3468 Planarity : 0.005 0.063 3768 Dihedral : 5.121 58.222 2958 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.83 % Favored : 95.60 % Rotamer: Outliers : 2.55 % Allowed : 10.80 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.17), residues: 2634 helix: 2.13 (0.14), residues: 1392 sheet: 0.52 (0.36), residues: 228 loop : -0.05 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 156 TYR 0.018 0.001 TYR a 165 PHE 0.022 0.001 PHE U 221 TRP 0.014 0.002 TRP O 169 HIS 0.009 0.001 HIS O 319 Details of bonding type rmsd covalent geometry : bond 0.00305 (21411) covalent geometry : angle 0.70006 (28959) hydrogen bonds : bond 0.03820 ( 1217) hydrogen bonds : angle 4.90532 ( 3540) *********************** 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 333 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 273 time to evaluate : 0.903 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: M 41 MET cc_start: 0.2837 (ttm) cc_final: 0.2597 (ttt) REVERT: M 321 MET cc_start: 0.7348 (ttt) cc_final: 0.6445 (mmp) REVERT: S 112 PHE cc_start: 0.4833 (OUTLIER) cc_final: 0.4433 (t80) REVERT: S 124 ASP cc_start: 0.7945 (m-30) cc_final: 0.7314 (t0) REVERT: T 532 MET cc_start: 0.5167 (OUTLIER) cc_final: 0.3339 (mpp) REVERT: U 113 THR cc_start: 0.6090 (OUTLIER) cc_final: 0.5851 (p) REVERT: U 145 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8722 (tp30) REVERT: U 184 MET cc_start: 0.8174 (mmm) cc_final: 0.7846 (tpp) REVERT: V 51 MET cc_start: 0.6735 (ptt) cc_final: 0.6048 (ptm) REVERT: W 51 MET cc_start: 0.4112 (ptt) cc_final: 0.3605 (ptt) REVERT: W 59 ASP cc_start: 0.8883 (m-30) cc_final: 0.8565 (t0) REVERT: Y 193 MET cc_start: 0.3717 (mpt) cc_final: 0.2296 (ttp) REVERT: Y 293 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7410 (ptp-170) REVERT: b 58 MET cc_start: 0.4601 (mmt) cc_final: 0.4317 (mmt) REVERT: c 73 MET cc_start: 0.7481 (ppp) cc_final: 0.7228 (ppp) REVERT: c 118 TYR cc_start: 0.9083 (m-10) cc_final: 0.8831 (m-10) outliers start: 60 outliers final: 29 residues processed: 320 average time/residue: 0.2058 time to fit residues: 93.9609 Evaluate side-chains 246 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 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 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 162 LEU 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 74 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 247 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 chunk 144 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 19 optimal weight: 0.5980 chunk 133 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** W 102 ASN Y 28 HIS Z 542 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.063992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.052820 restraints weight = 306727.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.053608 restraints weight = 251564.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.054084 restraints weight = 188164.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.054277 restraints weight = 167963.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.054439 restraints weight = 151655.994| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21411 Z= 0.121 Angle : 0.650 11.347 28959 Z= 0.324 Chirality : 0.042 0.194 3468 Planarity : 0.005 0.051 3768 Dihedral : 4.855 53.167 2950 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.91 % Favored : 95.52 % Rotamer: Outliers : 2.64 % Allowed : 11.52 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.17), residues: 2634 helix: 2.00 (0.14), residues: 1398 sheet: 0.75 (0.38), residues: 204 loop : -0.17 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 228 TYR 0.008 0.001 TYR V 118 PHE 0.018 0.001 PHE Y 26 TRP 0.014 0.001 TRP a 246 HIS 0.006 0.001 HIS O 319 Details of bonding type rmsd covalent geometry : bond 0.00254 (21411) covalent geometry : angle 0.64970 (28959) hydrogen bonds : bond 0.03418 ( 1217) hydrogen bonds : angle 4.65147 ( 3540) *********************** 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 289 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 227 time to evaluate : 0.919 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: M 110 LEU cc_start: 0.9053 (mm) cc_final: 0.8835 (mm) REVERT: M 158 MET cc_start: 0.9031 (tmm) cc_final: 0.8584 (ppp) REVERT: M 241 ASP cc_start: 0.7463 (t0) cc_final: 0.7067 (p0) REVERT: M 321 MET cc_start: 0.7297 (ttt) cc_final: 0.6445 (mmp) REVERT: O 156 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.8228 (mtt180) REVERT: P 116 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8031 (p0) REVERT: S 112 PHE cc_start: 0.4929 (OUTLIER) cc_final: 0.4681 (t80) REVERT: S 124 ASP cc_start: 0.7989 (m-30) cc_final: 0.7291 (t0) REVERT: S 233 MET cc_start: 0.7829 (ptt) cc_final: 0.6862 (mtp) REVERT: T 532 MET cc_start: 0.5165 (mmp) cc_final: 0.3128 (mpp) REVERT: U 145 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8718 (tp30) REVERT: U 169 TRP cc_start: 0.7527 (OUTLIER) cc_final: 0.7149 (t60) REVERT: U 184 MET cc_start: 0.8130 (mmm) cc_final: 0.7764 (tpp) REVERT: V 51 MET cc_start: 0.6811 (ptt) cc_final: 0.6078 (ptm) REVERT: W 51 MET cc_start: 0.4187 (ptt) cc_final: 0.3696 (ptm) REVERT: W 59 ASP cc_start: 0.8824 (m-30) cc_final: 0.8436 (t0) REVERT: X 106 ILE cc_start: 0.7974 (tp) cc_final: 0.7743 (mm) REVERT: Y 60 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6549 (tp30) REVERT: Y 193 MET cc_start: 0.3931 (mpt) cc_final: 0.2545 (ttp) REVERT: Y 293 ARG cc_start: 0.7733 (ttt180) cc_final: 0.7347 (ptm-80) REVERT: c 118 TYR cc_start: 0.9048 (m-10) cc_final: 0.8747 (m-10) outliers start: 62 outliers final: 33 residues processed: 272 average time/residue: 0.1895 time to fit residues: 75.8072 Evaluate side-chains 234 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 112 PHE Chi-restraints excluded: chain M residue 187 ASN Chi-restraints excluded: chain M residue 214 VAL 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 224 ILE 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 P residue 74 THR Chi-restraints excluded: chain P residue 116 ASP 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 S residue 298 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 169 TRP Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 254 VAL 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 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 b residue 92 LEU Chi-restraints excluded: chain c residue 105 LEU Chi-restraints excluded: chain c residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 84 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 91 optimal weight: 0.1980 chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 241 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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** ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 HIS U 190 ASN U 310 ASN W 83 GLN a 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.062181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.051117 restraints weight = 312418.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.051779 restraints weight = 244683.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.052270 restraints weight = 201355.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.052648 restraints weight = 172957.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.052955 restraints weight = 153331.870| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21411 Z= 0.144 Angle : 0.666 13.366 28959 Z= 0.335 Chirality : 0.042 0.232 3468 Planarity : 0.005 0.044 3768 Dihedral : 4.864 58.715 2943 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.83 % Favored : 95.60 % Rotamer: Outliers : 3.27 % Allowed : 11.99 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.17), residues: 2634 helix: 1.83 (0.14), residues: 1395 sheet: 0.43 (0.37), residues: 207 loop : -0.25 (0.21), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG V 72 TYR 0.012 0.001 TYR U 165 PHE 0.009 0.001 PHE O 188 TRP 0.011 0.002 TRP O 246 HIS 0.006 0.001 HIS S 28 Details of bonding type rmsd covalent geometry : bond 0.00306 (21411) covalent geometry : angle 0.66585 (28959) hydrogen bonds : bond 0.03481 ( 1217) hydrogen bonds : angle 4.69016 ( 3540) *********************** 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 282 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 205 time to evaluate : 1.089 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: S 112 PHE cc_start: 0.5296 (OUTLIER) cc_final: 0.4884 (t80) REVERT: S 124 ASP cc_start: 0.8013 (m-30) cc_final: 0.7187 (t0) REVERT: S 233 MET cc_start: 0.7884 (ptt) cc_final: 0.6859 (mtp) REVERT: T 532 MET cc_start: 0.5672 (mmp) cc_final: 0.3155 (mpp) REVERT: U 145 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8904 (tp30) REVERT: U 184 MET cc_start: 0.7859 (mmm) cc_final: 0.7093 (mmm) REVERT: V 51 MET cc_start: 0.6977 (ptt) cc_final: 0.6310 (ptm) REVERT: W 51 MET cc_start: 0.4246 (ptt) cc_final: 0.3862 (ptt) REVERT: X 98 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8132 (t70) REVERT: Y 41 MET cc_start: 0.4397 (ttp) cc_final: 0.4194 (ttt) REVERT: Y 60 GLU cc_start: 0.6511 (mt-10) cc_final: 0.6190 (tp30) REVERT: Y 112 PHE cc_start: 0.5265 (OUTLIER) cc_final: 0.4843 (t80) REVERT: Y 193 MET cc_start: 0.3310 (mpt) cc_final: 0.2196 (ttp) REVERT: Y 293 ARG cc_start: 0.7956 (ttt180) cc_final: 0.7531 (ptm-80) REVERT: a 306 TYR cc_start: 0.0701 (OUTLIER) cc_final: -0.0194 (p90) REVERT: b 77 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8279 (pp20) REVERT: c 73 MET cc_start: 0.7885 (ppp) cc_final: 0.7653 (tpp) REVERT: c 118 TYR cc_start: 0.9077 (m-10) cc_final: 0.8827 (m-10) outliers start: 77 outliers final: 41 residues processed: 259 average time/residue: 0.1758 time to fit residues: 68.4835 Evaluate side-chains 232 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 555 MET Chi-restraints excluded: chain O residue 162 LEU Chi-restraints excluded: chain O residue 236 LEU 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 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 110 LEU 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 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 U residue 275 ILE Chi-restraints excluded: chain V residue 58 MET 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 92 LEU Chi-restraints excluded: chain X residue 98 ASP 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 112 PHE Chi-restraints excluded: chain Y residue 208 THR 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 b residue 77 GLU Chi-restraints excluded: chain b residue 92 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 125 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 203 optimal weight: 0.0050 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 28 HIS ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN O 87 GLN O 129 ASN ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 HIS Y 180 ASN ** Z 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 542 ASN a 129 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.058716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.048499 restraints weight = 299290.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.049304 restraints weight = 209063.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.049902 restraints weight = 159758.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.050311 restraints weight = 129581.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.050653 restraints weight = 110300.835| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.7064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21411 Z= 0.220 Angle : 0.789 10.201 28959 Z= 0.410 Chirality : 0.046 0.264 3468 Planarity : 0.006 0.066 3768 Dihedral : 5.450 49.950 2937 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.78 % Favored : 94.65 % Rotamer: Outliers : 3.02 % Allowed : 13.78 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.17), residues: 2634 helix: 0.98 (0.14), residues: 1395 sheet: -0.42 (0.29), residues: 315 loop : -0.63 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG d 134 TYR 0.017 0.002 TYR U 165 PHE 0.025 0.002 PHE O 265 TRP 0.016 0.002 TRP O 169 HIS 0.009 0.002 HIS O 256 Details of bonding type rmsd covalent geometry : bond 0.00467 (21411) covalent geometry : angle 0.78928 (28959) hydrogen bonds : bond 0.04403 ( 1217) hydrogen bonds : angle 5.42307 ( 3540) *********************** 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 247 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 176 time to evaluate : 0.922 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: M 321 MET cc_start: 0.6335 (ttt) cc_final: 0.5075 (mmp) REVERT: R 76 LYS cc_start: 0.9320 (pptt) cc_final: 0.9118 (pptt) REVERT: S 112 PHE cc_start: 0.6166 (OUTLIER) cc_final: 0.5497 (t80) REVERT: S 233 MET cc_start: 0.8000 (ptt) cc_final: 0.7048 (mtp) REVERT: U 184 MET cc_start: 0.8336 (mmm) cc_final: 0.8014 (mmm) REVERT: U 306 TYR cc_start: 0.2256 (OUTLIER) cc_final: -0.0109 (p90) REVERT: V 51 MET cc_start: 0.7361 (ptt) cc_final: 0.5535 (tmm) REVERT: V 99 ILE cc_start: 0.9020 (mm) cc_final: 0.8813 (mm) REVERT: W 51 MET cc_start: 0.3807 (ptt) cc_final: 0.3105 (ptt) REVERT: X 98 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8070 (t70) REVERT: Y 112 PHE cc_start: 0.5043 (OUTLIER) cc_final: 0.4568 (t80) REVERT: Z 532 MET cc_start: 0.3159 (mpp) cc_final: 0.2174 (mtm) REVERT: a 157 MET cc_start: 0.9203 (ttt) cc_final: 0.8941 (ppp) REVERT: a 306 TYR cc_start: 0.2535 (OUTLIER) cc_final: 0.1289 (p90) REVERT: b 51 MET cc_start: 0.2431 (ptt) cc_final: 0.2211 (ptm) REVERT: d 132 MET cc_start: 0.7920 (mpp) cc_final: 0.7627 (mpp) outliers start: 71 outliers final: 44 residues processed: 231 average time/residue: 0.1693 time to fit residues: 59.9036 Evaluate side-chains 205 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 555 MET Chi-restraints excluded: chain O residue 85 ARG Chi-restraints excluded: chain O residue 104 LEU 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 306 TYR Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 117 LYS Chi-restraints excluded: chain P residue 132 MET 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 110 LEU 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 155 ASN Chi-restraints excluded: chain U residue 162 LEU 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 V residue 77 GLU Chi-restraints excluded: chain V residue 80 ARG Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain V residue 106 ILE Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 77 GLU Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain X residue 98 ASP 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 112 PHE Chi-restraints excluded: chain Y residue 208 THR 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 225 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 chunk 222 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 58 ASN ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 102 ASN U 87 GLN ** U 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 534 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.059864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.049153 restraints weight = 292962.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.050034 restraints weight = 201806.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.050648 restraints weight = 152772.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.051123 restraints weight = 123452.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.051471 restraints weight = 104645.645| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.7105 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= 0.124 Angle : 0.661 13.234 28959 Z= 0.333 Chirality : 0.042 0.234 3468 Planarity : 0.004 0.053 3768 Dihedral : 4.944 51.397 2937 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.80 % Favored : 95.63 % Rotamer: Outliers : 2.34 % Allowed : 14.54 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.17), residues: 2634 helix: 1.39 (0.14), residues: 1395 sheet: 0.03 (0.36), residues: 207 loop : -0.58 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 66 TYR 0.010 0.001 TYR b 104 PHE 0.013 0.001 PHE U 221 TRP 0.014 0.001 TRP O 246 HIS 0.004 0.001 HIS O 319 Details of bonding type rmsd covalent geometry : bond 0.00260 (21411) covalent geometry : angle 0.66089 (28959) hydrogen bonds : bond 0.03442 ( 1217) hydrogen bonds : angle 4.84494 ( 3540) *********************** 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 231 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 176 time to evaluate : 0.843 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 193 MET cc_start: 0.7336 (ttt) cc_final: 0.5817 (pmm) REVERT: M 233 MET cc_start: 0.7930 (mmt) cc_final: 0.7725 (mmm) REVERT: M 321 MET cc_start: 0.6723 (ttt) cc_final: 0.5351 (mmp) REVERT: O 157 MET cc_start: 0.8582 (mmm) cc_final: 0.7972 (mtm) REVERT: S 112 PHE cc_start: 0.5820 (OUTLIER) cc_final: 0.5289 (t80) REVERT: S 124 ASP cc_start: 0.8216 (m-30) cc_final: 0.7442 (p0) REVERT: S 233 MET cc_start: 0.8020 (ptt) cc_final: 0.7096 (mtp) REVERT: U 306 TYR cc_start: 0.1522 (OUTLIER) cc_final: -0.0569 (p90) REVERT: V 51 MET cc_start: 0.7075 (ptt) cc_final: 0.5882 (ttm) REVERT: W 51 MET cc_start: 0.4242 (ptt) cc_final: 0.3645 (ptt) REVERT: X 58 MET cc_start: 0.5067 (mmm) cc_final: 0.4854 (mmm) REVERT: X 98 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8057 (t0) REVERT: Y 112 PHE cc_start: 0.5135 (OUTLIER) cc_final: 0.4798 (t80) REVERT: Z 532 MET cc_start: 0.2943 (mpp) cc_final: 0.2156 (mtm) REVERT: a 157 MET cc_start: 0.9170 (ttt) cc_final: 0.8789 (tmm) REVERT: a 306 TYR cc_start: 0.2328 (OUTLIER) cc_final: 0.0961 (p90) REVERT: c 118 TYR cc_start: 0.8940 (m-10) cc_final: 0.8605 (m-10) REVERT: c 132 MET cc_start: 0.9222 (mpp) cc_final: 0.8885 (mpp) REVERT: d 132 MET cc_start: 0.7867 (mpp) cc_final: 0.7604 (mpp) outliers start: 55 outliers final: 37 residues processed: 225 average time/residue: 0.1594 time to fit residues: 55.3106 Evaluate side-chains 203 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 275 ILE Chi-restraints excluded: chain O residue 306 TYR Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 86 VAL 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 110 LEU Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 298 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 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 X residue 98 ASP 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 112 PHE Chi-restraints excluded: chain Y residue 214 VAL 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 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 105 LEU Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 188 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 239 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 245 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 70 ASN ** U 129 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 = 0.4019 r_free = 0.4019 target = 0.059875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.049179 restraints weight = 298745.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.050068 restraints weight = 204773.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.050703 restraints weight = 154510.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.051166 restraints weight = 124464.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.051487 restraints weight = 105095.237| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.7245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21411 Z= 0.118 Angle : 0.663 12.326 28959 Z= 0.330 Chirality : 0.043 0.259 3468 Planarity : 0.004 0.046 3768 Dihedral : 4.806 52.544 2937 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.25 % Favored : 95.18 % Rotamer: Outliers : 2.42 % Allowed : 15.18 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.17), residues: 2634 helix: 1.49 (0.14), residues: 1395 sheet: -0.22 (0.34), residues: 237 loop : -0.41 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 537 TYR 0.008 0.001 TYR U 165 PHE 0.010 0.001 PHE U 221 TRP 0.015 0.001 TRP O 246 HIS 0.004 0.001 HIS O 319 Details of bonding type rmsd covalent geometry : bond 0.00246 (21411) covalent geometry : angle 0.66278 (28959) hydrogen bonds : bond 0.03328 ( 1217) hydrogen bonds : angle 4.70333 ( 3540) *********************** 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 233 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 176 time to evaluate : 0.883 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: M 15 MET cc_start: 0.7671 (mmp) cc_final: 0.7445 (mmp) REVERT: M 193 MET cc_start: 0.7699 (ttt) cc_final: 0.5945 (pmm) REVERT: M 321 MET cc_start: 0.6885 (ttt) cc_final: 0.5689 (mmp) REVERT: R 73 MET cc_start: 0.8890 (mpp) cc_final: 0.8545 (mpp) REVERT: R 76 LYS cc_start: 0.9093 (pptt) cc_final: 0.8853 (tppt) REVERT: S 112 PHE cc_start: 0.5635 (OUTLIER) cc_final: 0.5167 (t80) REVERT: S 124 ASP cc_start: 0.8204 (m-30) cc_final: 0.7453 (p0) REVERT: S 233 MET cc_start: 0.8088 (ptt) cc_final: 0.7826 (ptp) REVERT: S 321 MET cc_start: 0.4579 (OUTLIER) cc_final: 0.3954 (tpp) REVERT: U 169 TRP cc_start: 0.7914 (OUTLIER) cc_final: 0.7642 (t60) REVERT: U 306 TYR cc_start: 0.1328 (OUTLIER) cc_final: -0.0620 (p90) REVERT: V 51 MET cc_start: 0.6174 (ptt) cc_final: 0.4740 (tmm) REVERT: W 51 MET cc_start: 0.4248 (ptt) cc_final: 0.3853 (ptt) REVERT: X 98 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7989 (t70) REVERT: Y 60 GLU cc_start: 0.6573 (mt-10) cc_final: 0.6120 (tp30) REVERT: Y 112 PHE cc_start: 0.5231 (OUTLIER) cc_final: 0.4866 (t80) REVERT: Z 532 MET cc_start: 0.2678 (mpp) cc_final: 0.1988 (mtm) REVERT: a 157 MET cc_start: 0.9143 (ttt) cc_final: 0.8781 (tmm) REVERT: a 306 TYR cc_start: 0.2425 (OUTLIER) cc_final: 0.0995 (p90) REVERT: c 118 TYR cc_start: 0.9028 (m-10) cc_final: 0.8737 (m-10) REVERT: c 132 MET cc_start: 0.9222 (mpp) cc_final: 0.8910 (mpp) outliers start: 57 outliers final: 39 residues processed: 220 average time/residue: 0.1700 time to fit residues: 57.5062 Evaluate side-chains 206 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 532 MET 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 275 ILE Chi-restraints excluded: chain O residue 306 TYR Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 59 ASP 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 110 LEU Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain S residue 321 MET 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 169 TRP 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 73 MET Chi-restraints excluded: chain W residue 111 VAL Chi-restraints excluded: chain X residue 98 ASP 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 Y residue 208 THR 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 a residue 306 TYR Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 105 LEU Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 192 optimal weight: 0.2980 chunk 107 optimal weight: 0.9980 chunk 229 optimal weight: 0.0270 chunk 111 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 217 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 238 ASN ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN ** c 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.059476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.048884 restraints weight = 299715.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.049753 restraints weight = 205730.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.050358 restraints weight = 155490.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.050819 restraints weight = 125611.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.051133 restraints weight = 106376.095| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.7622 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= 0.131 Angle : 0.681 13.738 28959 Z= 0.342 Chirality : 0.043 0.256 3468 Planarity : 0.004 0.044 3768 Dihedral : 4.817 52.129 2937 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.25 % Favored : 95.18 % Rotamer: Outliers : 2.34 % Allowed : 15.39 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.17), residues: 2634 helix: 1.41 (0.14), residues: 1398 sheet: 0.10 (0.36), residues: 207 loop : -0.54 (0.21), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG V 133 TYR 0.009 0.001 TYR U 165 PHE 0.012 0.001 PHE Y 26 TRP 0.016 0.002 TRP Z 554 HIS 0.004 0.001 HIS O 241 Details of bonding type rmsd covalent geometry : bond 0.00278 (21411) covalent geometry : angle 0.68138 (28959) hydrogen bonds : bond 0.03452 ( 1217) hydrogen bonds : angle 4.77836 ( 3540) *********************** 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 221 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 166 time to evaluate : 0.895 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: M 158 MET cc_start: 0.8681 (ppp) cc_final: 0.8013 (pmm) REVERT: M 321 MET cc_start: 0.6964 (ttt) cc_final: 0.6020 (mmp) REVERT: O 157 MET cc_start: 0.8441 (mmm) cc_final: 0.7886 (mtm) REVERT: R 73 MET cc_start: 0.8880 (mpp) cc_final: 0.8516 (mpp) REVERT: R 76 LYS cc_start: 0.9151 (pptt) cc_final: 0.8764 (tppt) REVERT: R 80 ARG cc_start: 0.9173 (mtt180) cc_final: 0.8620 (mtm110) REVERT: S 15 MET cc_start: 0.4873 (mpp) cc_final: 0.4628 (pmm) REVERT: S 112 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.5416 (t80) REVERT: S 124 ASP cc_start: 0.8199 (m-30) cc_final: 0.7453 (p0) REVERT: S 233 MET cc_start: 0.8078 (ptt) cc_final: 0.7803 (ptp) REVERT: S 278 MET cc_start: 0.5428 (mmm) cc_final: 0.4853 (mmt) REVERT: U 306 TYR cc_start: 0.1364 (OUTLIER) cc_final: -0.0536 (p90) REVERT: X 98 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.7984 (t70) REVERT: Y 60 GLU cc_start: 0.6649 (mt-10) cc_final: 0.6236 (tp30) REVERT: Y 112 PHE cc_start: 0.5280 (OUTLIER) cc_final: 0.4878 (t80) REVERT: Z 532 MET cc_start: 0.2958 (mpp) cc_final: 0.2410 (mtm) REVERT: a 157 MET cc_start: 0.9145 (ttt) cc_final: 0.8814 (tmm) REVERT: a 306 TYR cc_start: 0.2760 (OUTLIER) cc_final: 0.1259 (p90) REVERT: c 118 TYR cc_start: 0.9051 (m-10) cc_final: 0.8784 (m-10) REVERT: c 132 MET cc_start: 0.9222 (mpp) cc_final: 0.8987 (mpp) outliers start: 55 outliers final: 42 residues processed: 209 average time/residue: 0.1661 time to fit residues: 53.0198 Evaluate side-chains 204 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 157 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 251 VAL Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 306 TYR Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 59 ASP 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 110 LEU Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 298 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 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 80 ARG 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 X residue 98 ASP 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 211 LEU Chi-restraints excluded: chain a residue 290 ASP Chi-restraints excluded: chain a residue 306 TYR Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 105 LEU Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 220 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 232 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 89 optimal weight: 0.0370 chunk 78 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 216 optimal weight: 8.9990 overall best weight: 1.3662 ------------------------------------------------------------------------------- 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** ** U 129 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.059399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.048817 restraints weight = 300188.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.049691 restraints weight = 204309.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.050288 restraints weight = 153581.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.050759 restraints weight = 123764.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.051094 restraints weight = 104486.300| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.7916 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= 0.129 Angle : 0.698 13.674 28959 Z= 0.347 Chirality : 0.043 0.258 3468 Planarity : 0.004 0.046 3768 Dihedral : 4.846 51.005 2937 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.37 % Favored : 95.06 % Rotamer: Outliers : 2.13 % Allowed : 15.94 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.17), residues: 2634 helix: 1.44 (0.14), residues: 1392 sheet: 0.03 (0.29), residues: 315 loop : -0.55 (0.23), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Z 537 TYR 0.008 0.001 TYR U 165 PHE 0.033 0.001 PHE Y 26 TRP 0.017 0.002 TRP T 554 HIS 0.003 0.001 HIS O 319 Details of bonding type rmsd covalent geometry : bond 0.00273 (21411) covalent geometry : angle 0.69801 (28959) hydrogen bonds : bond 0.03420 ( 1217) hydrogen bonds : angle 4.80225 ( 3540) *********************** 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 224 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 174 time to evaluate : 0.942 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 193 MET cc_start: 0.7967 (ttt) cc_final: 0.6122 (pmm) REVERT: M 206 MET cc_start: 0.8157 (ppp) cc_final: 0.7925 (ppp) REVERT: M 321 MET cc_start: 0.6962 (ttt) cc_final: 0.6114 (mmp) REVERT: O 157 MET cc_start: 0.8444 (mmm) cc_final: 0.7887 (mtm) REVERT: R 73 MET cc_start: 0.8836 (mpp) cc_final: 0.8461 (mpp) REVERT: R 76 LYS cc_start: 0.9166 (pptt) cc_final: 0.8763 (pttm) REVERT: R 80 ARG cc_start: 0.9162 (mtt180) cc_final: 0.8616 (mtm110) REVERT: S 124 ASP cc_start: 0.8283 (m-30) cc_final: 0.7518 (p0) REVERT: S 233 MET cc_start: 0.8112 (ptt) cc_final: 0.7849 (ptp) REVERT: S 278 MET cc_start: 0.5459 (mmm) cc_final: 0.4791 (mmt) REVERT: U 169 TRP cc_start: 0.7877 (OUTLIER) cc_final: 0.7656 (t60) REVERT: U 306 TYR cc_start: 0.1400 (OUTLIER) cc_final: -0.0489 (p90) REVERT: W 51 MET cc_start: 0.3342 (ptt) cc_final: 0.2920 (ppp) REVERT: X 98 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8004 (t70) REVERT: Y 112 PHE cc_start: 0.5246 (OUTLIER) cc_final: 0.4845 (t80) REVERT: Z 532 MET cc_start: 0.3367 (mpp) cc_final: 0.2874 (mtm) REVERT: a 157 MET cc_start: 0.9144 (ttt) cc_final: 0.8809 (tmm) REVERT: a 306 TYR cc_start: 0.2964 (OUTLIER) cc_final: 0.1477 (p90) REVERT: c 118 TYR cc_start: 0.9029 (m-10) cc_final: 0.8753 (m-10) REVERT: c 132 MET cc_start: 0.9225 (mpp) cc_final: 0.8989 (mpp) outliers start: 50 outliers final: 42 residues processed: 214 average time/residue: 0.1654 time to fit residues: 54.0744 Evaluate side-chains 207 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 251 VAL Chi-restraints excluded: chain O residue 254 VAL Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 306 TYR Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 59 ASP 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 110 LEU Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 298 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 169 TRP Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 306 TYR 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 X residue 98 ASP 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 211 LEU Chi-restraints excluded: chain a residue 223 MET Chi-restraints excluded: chain a residue 290 ASP Chi-restraints excluded: chain a residue 306 TYR Chi-restraints excluded: chain b residue 74 THR Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 74 THR Chi-restraints excluded: chain c residue 105 LEU Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 157 optimal weight: 2.9990 chunk 242 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 193 optimal weight: 8.9990 chunk 204 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 65 GLN M 227 GLN ** N 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 58 ASN O 190 ASN ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 49 ASN S 70 ASN U 101 ASN ** 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** a 173 ASN a 216 ASN ** a 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 310 ASN c 52 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.056495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.046213 restraints weight = 311206.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.047026 restraints weight = 211514.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.047603 restraints weight = 159155.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.048032 restraints weight = 128050.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.048362 restraints weight = 108379.915| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.9130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21411 Z= 0.254 Angle : 0.900 15.002 28959 Z= 0.464 Chirality : 0.049 0.229 3468 Planarity : 0.006 0.069 3768 Dihedral : 5.989 50.453 2937 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.69 % Favored : 93.74 % Rotamer: Outliers : 2.34 % Allowed : 16.33 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.16), residues: 2634 helix: 0.41 (0.13), residues: 1404 sheet: -0.76 (0.29), residues: 327 loop : -1.03 (0.22), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 537 TYR 0.019 0.002 TYR U 89 PHE 0.025 0.003 PHE M 112 TRP 0.016 0.003 TRP T 554 HIS 0.006 0.002 HIS a 148 Details of bonding type rmsd covalent geometry : bond 0.00539 (21411) covalent geometry : angle 0.90030 (28959) hydrogen bonds : bond 0.04803 ( 1217) hydrogen bonds : angle 5.72727 ( 3540) ********************** 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 216 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 0.905 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: M 193 MET cc_start: 0.7817 (ttt) cc_final: 0.5943 (pmm) REVERT: M 321 MET cc_start: 0.6705 (ttt) cc_final: 0.6281 (mmp) REVERT: O 157 MET cc_start: 0.8409 (mmm) cc_final: 0.7823 (mtm) REVERT: R 58 MET cc_start: 0.4128 (tpt) cc_final: 0.3917 (tpt) REVERT: R 76 LYS cc_start: 0.9230 (pptt) cc_final: 0.8952 (pttm) REVERT: R 80 ARG cc_start: 0.9257 (mtt180) cc_final: 0.8877 (mtp85) REVERT: R 137 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8334 (mtt180) REVERT: S 112 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.5975 (t80) REVERT: S 177 GLU cc_start: 0.9389 (tp30) cc_final: 0.9027 (mp0) REVERT: S 233 MET cc_start: 0.8142 (ptt) cc_final: 0.7884 (ptp) REVERT: U 306 TYR cc_start: 0.1457 (OUTLIER) cc_final: -0.0223 (p90) REVERT: X 98 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8079 (t70) REVERT: Y 112 PHE cc_start: 0.5326 (OUTLIER) cc_final: 0.4915 (t80) REVERT: Z 532 MET cc_start: 0.3269 (mpp) cc_final: 0.2973 (mtm) REVERT: a 67 MET cc_start: 0.9504 (mmm) cc_final: 0.9287 (mmm) REVERT: a 157 MET cc_start: 0.9151 (ttt) cc_final: 0.8950 (ppp) REVERT: a 169 TRP cc_start: 0.9119 (OUTLIER) cc_final: 0.8509 (t60) REVERT: a 306 TYR cc_start: 0.3805 (OUTLIER) cc_final: 0.2239 (p90) REVERT: b 51 MET cc_start: -0.0003 (ptt) cc_final: -0.0204 (ptm) outliers start: 55 outliers final: 35 residues processed: 208 average time/residue: 0.1673 time to fit residues: 53.4895 Evaluate side-chains 195 residues out of total 2352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 187 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 254 VAL Chi-restraints excluded: chain O residue 275 ILE Chi-restraints excluded: chain O residue 306 TYR Chi-restraints excluded: chain P residue 74 THR 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 R residue 137 ARG Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain S residue 179 LEU Chi-restraints excluded: chain S residue 298 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 80 ARG 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 X residue 98 ASP 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 306 TYR Chi-restraints excluded: chain b residue 74 THR 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 105 LEU Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain c residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 235 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 123 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 206 optimal weight: 0.5980 chunk 234 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 168 GLN N 534 GLN O 58 ASN ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 101 ASN ** U 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 186 GLN a 310 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.057866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.047337 restraints weight = 302166.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.048174 restraints weight = 204193.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.048778 restraints weight = 153391.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.049238 restraints weight = 123582.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.049546 restraints weight = 104220.347| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.9030 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= 0.138 Angle : 0.770 13.462 28959 Z= 0.384 Chirality : 0.044 0.251 3468 Planarity : 0.004 0.054 3768 Dihedral : 5.324 49.831 2937 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.40 % Favored : 95.03 % Rotamer: Outliers : 1.66 % Allowed : 17.64 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.17), residues: 2634 helix: 0.98 (0.14), residues: 1380 sheet: -0.41 (0.27), residues: 357 loop : -0.87 (0.23), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG T 545 TYR 0.009 0.001 TYR M 76 PHE 0.011 0.001 PHE U 221 TRP 0.022 0.002 TRP T 554 HIS 0.005 0.001 HIS O 319 Details of bonding type rmsd covalent geometry : bond 0.00292 (21411) covalent geometry : angle 0.77019 (28959) hydrogen bonds : bond 0.03765 ( 1217) hydrogen bonds : angle 5.15497 ( 3540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5263.05 seconds wall clock time: 91 minutes 11.40 seconds (5471.40 seconds total)