Starting phenix.real_space_refine on Thu Feb 5 18:03:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uzp_64648/02_2026/9uzp_64648.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uzp_64648/02_2026/9uzp_64648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uzp_64648/02_2026/9uzp_64648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uzp_64648/02_2026/9uzp_64648.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uzp_64648/02_2026/9uzp_64648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uzp_64648/02_2026/9uzp_64648.map" } resolution = 3.05 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= 0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 12239 2.51 5 N 3214 2.21 5 O 3479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19067 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2881 Classifications: {'peptide': 356} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 337} Chain: "B" Number of atoms: 2698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2698 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 16, 'TRANS': 319} Chain: "C" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1141 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "D" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1309 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 157} Chain: "E" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 901 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "F" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 860 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "G" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1515 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 9, 'TRANS': 184} Chain: "I" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1049 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "J" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 958 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "K" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 297 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "c" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1141 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "d" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1309 Classifications: {'peptide': 162} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 157} Chain: "e" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 893 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 3, 'TRANS': 106} Chain: "f" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 860 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "j" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 958 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "k" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 297 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Time building chain proxies: 4.60, per 1000 atoms: 0.24 Number of scatterers: 19067 At special positions: 0 Unit cell: (119.893, 145.887, 178.778, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 3479 8.00 N 3214 7.00 C 12239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 70 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 147 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS A 204 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 245 " distance=2.03 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 88 " - pdb=" SG CYS B 117 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 145 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 223 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 243 " - pdb=" SG CYS B 267 " distance=2.03 Simple disulfide: pdb=" SG CYS B 272 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 75 " - pdb=" SG CYS C 112 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS D 102 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 75 " - pdb=" SG CYS F 107 " distance=2.03 Simple disulfide: pdb=" SG CYS G 33 " - pdb=" SG CYS G 55 " distance=2.03 Simple disulfide: pdb=" SG CYS G 47 " - pdb=" SG CYS G 127 " distance=2.03 Simple disulfide: pdb=" SG CYS G 107 " - pdb=" SG CYS G 149 " distance=2.04 Simple disulfide: pdb=" SG CYS I 10 " - pdb=" SG CYS I 19 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 46 " distance=2.03 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 64 " distance=2.03 Simple disulfide: pdb=" SG CYS I 69 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 45 " - pdb=" SG CYS J 75 " distance=2.03 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 106 " distance=2.03 Simple disulfide: pdb=" SG CYS c 75 " - pdb=" SG CYS c 112 " distance=2.03 Simple disulfide: pdb=" SG CYS c 129 " - pdb=" SG CYS c 139 " distance=2.03 Simple disulfide: pdb=" SG CYS d 102 " - pdb=" SG CYS d 148 " distance=2.03 Simple disulfide: pdb=" SG CYS d 162 " - pdb=" SG CYS d 182 " distance=2.03 Simple disulfide: pdb=" SG CYS j 45 " - pdb=" SG CYS j 75 " distance=2.03 Simple disulfide: pdb=" SG CYS j 92 " - pdb=" SG CYS j 106 " distance=2.03 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: 1.61 Conformation dependent library (CDL) restraints added in 809.2 milliseconds 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4556 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 23 sheets defined 52.9% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 removed outlier: 3.544A pdb=" N ASN A 34 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.711A pdb=" N HIS A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 80 removed outlier: 3.640A pdb=" N LYS A 80 " --> pdb=" O GLU A 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 77 through 80' Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.807A pdb=" N GLY A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 225 through 239 removed outlier: 3.753A pdb=" N THR A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.824A pdb=" N TRP A 246 " --> pdb=" O ARG A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 267 removed outlier: 3.733A pdb=" N ARG A 263 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 267 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 340 through 363 removed outlier: 4.288A pdb=" N GLY A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 25 removed outlier: 3.558A pdb=" N LEU B 25 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 29 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.563A pdb=" N ALA B 35 " --> pdb=" O HIS B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 120 through 125 removed outlier: 3.547A pdb=" N GLY B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 135 removed outlier: 4.487A pdb=" N ASP B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP B 133 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.504A pdb=" N ASN B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 211 Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 240 through 245 removed outlier: 4.118A pdb=" N TRP B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 293 through 299 removed outlier: 5.977A pdb=" N ASP B 297 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 298 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 316 Processing helix chain 'B' and resid 321 through 338 Processing helix chain 'C' and resid 3 through 40 removed outlier: 5.676A pdb=" N GLY C 31 " --> pdb=" O TYR C 27 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASN C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 44 Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.608A pdb=" N ASP C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'D' and resid 29 through 51 Processing helix chain 'D' and resid 53 through 91 removed outlier: 3.804A pdb=" N ASN D 67 " --> pdb=" O MET D 63 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N SER D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU D 75 " --> pdb=" O ASP D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 removed outlier: 4.266A pdb=" N PHE D 98 " --> pdb=" O ASP D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 154 Processing helix chain 'D' and resid 163 through 171 Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.541A pdb=" N ASN D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 23 Processing helix chain 'E' and resid 26 through 49 removed outlier: 4.151A pdb=" N ILE E 49 " --> pdb=" O ARG E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 Proline residue: E 105 - end of helix Processing helix chain 'F' and resid 26 through 47 Processing helix chain 'F' and resid 48 through 56 Processing helix chain 'F' and resid 65 through 69 Processing helix chain 'F' and resid 106 through 115 Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'G' and resid 9 through 25 Processing helix chain 'G' and resid 58 through 74 Processing helix chain 'G' and resid 78 through 90 Processing helix chain 'G' and resid 101 through 108 Processing helix chain 'G' and resid 109 through 111 No H-bonds generated for 'chain 'G' and resid 109 through 111' Processing helix chain 'G' and resid 144 through 160 Processing helix chain 'G' and resid 176 through 195 removed outlier: 4.107A pdb=" N VAL G 180 " --> pdb=" O PRO G 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'I' and resid 25 through 35 Processing helix chain 'I' and resid 38 through 42 Processing helix chain 'I' and resid 43 through 48 removed outlier: 3.530A pdb=" N LYS I 47 " --> pdb=" O TYR I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 62 Processing helix chain 'I' and resid 116 through 127 removed outlier: 4.544A pdb=" N ILE I 120 " --> pdb=" O LYS I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 132 Processing helix chain 'J' and resid 2 through 38 removed outlier: 5.171A pdb=" N VAL J 19 " --> pdb=" O PHE J 15 " (cutoff:3.500A) Proline residue: J 20 - end of helix Processing helix chain 'J' and resid 74 through 76 No H-bonds generated for 'chain 'J' and resid 74 through 76' Processing helix chain 'J' and resid 77 through 83 removed outlier: 3.807A pdb=" N ASN J 83 " --> pdb=" O ASN J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 114 removed outlier: 3.631A pdb=" N LEU J 113 " --> pdb=" O ALA J 109 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE J 114 " --> pdb=" O TYR J 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 27 Proline residue: K 24 - end of helix Processing helix chain 'K' and resid 28 through 34 Processing helix chain 'c' and resid 3 through 29 Processing helix chain 'c' and resid 29 through 40 Processing helix chain 'c' and resid 41 through 45 removed outlier: 3.995A pdb=" N TYR c 45 " --> pdb=" O ALA c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 66 removed outlier: 4.077A pdb=" N THR c 65 " --> pdb=" O ASP c 61 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 118 Processing helix chain 'c' and resid 136 through 146 removed outlier: 3.502A pdb=" N GLN c 140 " --> pdb=" O ASN c 136 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 51 Processing helix chain 'd' and resid 53 through 91 removed outlier: 4.522A pdb=" N LYS d 73 " --> pdb=" O VAL d 69 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER d 74 " --> pdb=" O ASN d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 95 through 99 removed outlier: 3.555A pdb=" N GLU d 99 " --> pdb=" O ASP d 96 " (cutoff:3.500A) Processing helix chain 'd' and resid 141 through 154 removed outlier: 3.522A pdb=" N GLN d 145 " --> pdb=" O ASP d 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 171 Processing helix chain 'd' and resid 180 through 189 Processing helix chain 'e' and resid 3 through 23 Processing helix chain 'e' and resid 26 through 47 Processing helix chain 'e' and resid 96 through 109 Proline residue: e 105 - end of helix Processing helix chain 'f' and resid 26 through 47 Processing helix chain 'f' and resid 47 through 56 Processing helix chain 'f' and resid 63 through 69 Processing helix chain 'f' and resid 106 through 113 Processing helix chain 'f' and resid 121 through 128 Processing helix chain 'j' and resid 2 through 17 Processing helix chain 'j' and resid 17 through 38 Processing helix chain 'j' and resid 74 through 76 No H-bonds generated for 'chain 'j' and resid 74 through 76' Processing helix chain 'j' and resid 77 through 84 Processing helix chain 'j' and resid 101 through 117 Processing helix chain 'k' and resid 2 through 27 Proline residue: k 24 - end of helix Processing helix chain 'k' and resid 27 through 34 removed outlier: 3.758A pdb=" N LEU k 31 " --> pdb=" O SER k 27 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA4, first strand: chain 'A' and resid 292 through 293 removed outlier: 6.961A pdb=" N LYS A 292 " --> pdb=" O ILE B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 274 through 281 removed outlier: 6.722A pdb=" N SER A 302 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 279 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA A 304 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET B 281 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LYS A 306 " --> pdb=" O MET B 281 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN I 75 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 303 " --> pdb=" O ASN I 75 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER I 77 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU A 305 " --> pdb=" O SER I 77 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR I 79 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N CYS G 33 " --> pdb=" O THR I 70 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N SER I 72 " --> pdb=" O CYS G 33 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE G 35 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLY I 74 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILE G 37 " --> pdb=" O GLY I 74 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL I 76 " --> pdb=" O ILE G 37 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N GLU G 39 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 10.106A pdb=" N ILE I 78 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ILE G 41 " --> pdb=" O ILE I 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 274 through 281 removed outlier: 6.722A pdb=" N SER A 302 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 279 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA A 304 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET B 281 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LYS A 306 " --> pdb=" O MET B 281 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN I 75 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 303 " --> pdb=" O ASN I 75 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER I 77 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU A 305 " --> pdb=" O SER I 77 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR I 79 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N CYS G 33 " --> pdb=" O THR I 70 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N SER I 72 " --> pdb=" O CYS G 33 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE G 35 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLY I 74 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILE G 37 " --> pdb=" O GLY I 74 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL I 76 " --> pdb=" O ILE G 37 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N GLU G 39 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 10.106A pdb=" N ILE I 78 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ILE G 41 " --> pdb=" O ILE I 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 286 through 291 removed outlier: 3.775A pdb=" N LEU I 83 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS I 82 " --> pdb=" O CYS G 47 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS G 5 " --> pdb=" O HIS G 134 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU G 136 " --> pdb=" O LYS G 5 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 46 removed outlier: 5.948A pdb=" N SER B 74 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU B 73 " --> pdb=" O THR B 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AB1, first strand: chain 'C' and resid 74 through 77 Processing sheet with id=AB2, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AB3, first strand: chain 'D' and resid 101 through 104 Processing sheet with id=AB4, first strand: chain 'D' and resid 101 through 104 removed outlier: 5.709A pdb=" N ALA D 111 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 54 through 59 Processing sheet with id=AB6, first strand: chain 'F' and resid 72 through 73 removed outlier: 3.991A pdb=" N THR F 92 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 44 through 46 removed outlier: 5.345A pdb=" N LEU J 50 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP J 88 " --> pdb=" O VAL J 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 76 through 77 Processing sheet with id=AB9, first strand: chain 'c' and resid 101 through 103 removed outlier: 3.618A pdb=" N SER c 102 " --> pdb=" O GLU c 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 101 through 104 Processing sheet with id=AC2, first strand: chain 'd' and resid 101 through 104 removed outlier: 6.008A pdb=" N ALA d 111 " --> pdb=" O ILE d 124 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'e' and resid 54 through 58 Processing sheet with id=AC4, first strand: chain 'f' and resid 72 through 76 Processing sheet with id=AC5, first strand: chain 'j' and resid 44 through 46 removed outlier: 5.224A pdb=" N LEU j 50 " --> pdb=" O ALA j 65 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP j 88 " --> pdb=" O VAL j 66 " (cutoff:3.500A) 995 hydrogen bonds defined for protein. 2814 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: 3.11 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6077 1.34 - 1.46: 4650 1.46 - 1.59: 8575 1.59 - 1.71: 0 1.71 - 1.83: 185 Bond restraints: 19487 Sorted by residual: bond pdb=" C ASN A 315 " pdb=" N CYS A 316 " ideal model delta sigma weight residual 1.332 1.315 0.017 1.40e-02 5.10e+03 1.52e+00 bond pdb=" CG ARG e 43 " pdb=" CD ARG e 43 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CB CYS D 148 " pdb=" SG CYS D 148 " ideal model delta sigma weight residual 1.808 1.768 0.040 3.30e-02 9.18e+02 1.45e+00 bond pdb=" CB ARG e 43 " pdb=" CG ARG e 43 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" CA CYS I 19 " pdb=" CB CYS I 19 " ideal model delta sigma weight residual 1.528 1.555 -0.027 2.61e-02 1.47e+03 1.06e+00 ... (remaining 19482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 26057 1.86 - 3.72: 292 3.72 - 5.59: 31 5.59 - 7.45: 3 7.45 - 9.31: 1 Bond angle restraints: 26384 Sorted by residual: angle pdb=" N GLU G 87 " pdb=" CA GLU G 87 " pdb=" CB GLU G 87 " ideal model delta sigma weight residual 110.28 114.76 -4.48 1.55e+00 4.16e-01 8.34e+00 angle pdb=" N GLU C 35 " pdb=" CA GLU C 35 " pdb=" CB GLU C 35 " ideal model delta sigma weight residual 110.28 114.50 -4.22 1.55e+00 4.16e-01 7.40e+00 angle pdb=" CA LEU B 40 " pdb=" CB LEU B 40 " pdb=" CG LEU B 40 " ideal model delta sigma weight residual 116.30 125.61 -9.31 3.50e+00 8.16e-02 7.08e+00 angle pdb=" N GLN G 152 " pdb=" CA GLN G 152 " pdb=" CB GLN G 152 " ideal model delta sigma weight residual 110.28 114.22 -3.94 1.55e+00 4.16e-01 6.47e+00 angle pdb=" C ILE A 10 " pdb=" N LYS A 11 " pdb=" CA LYS A 11 " ideal model delta sigma weight residual 121.75 117.62 4.13 1.73e+00 3.34e-01 5.71e+00 ... (remaining 26379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 10890 17.59 - 35.18: 817 35.18 - 52.78: 124 52.78 - 70.37: 29 70.37 - 87.96: 11 Dihedral angle restraints: 11871 sinusoidal: 4849 harmonic: 7022 Sorted by residual: dihedral pdb=" CB CYS A 70 " pdb=" SG CYS A 70 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual -86.00 -173.96 87.96 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS B 88 " pdb=" SG CYS B 88 " pdb=" SG CYS B 117 " pdb=" CB CYS B 117 " ideal model delta sinusoidal sigma weight residual 93.00 151.02 -58.02 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CB CYS j 45 " pdb=" SG CYS j 45 " pdb=" SG CYS j 75 " pdb=" CB CYS j 75 " ideal model delta sinusoidal sigma weight residual -86.00 -142.29 56.29 1 1.00e+01 1.00e-02 4.27e+01 ... (remaining 11868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1761 0.031 - 0.062: 813 0.062 - 0.094: 265 0.094 - 0.125: 106 0.125 - 0.156: 16 Chirality restraints: 2961 Sorted by residual: chirality pdb=" CA ILE A 10 " pdb=" N ILE A 10 " pdb=" C ILE A 10 " pdb=" CB ILE A 10 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE B 104 " pdb=" N ILE B 104 " pdb=" C ILE B 104 " pdb=" CB ILE B 104 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE G 139 " pdb=" N ILE G 139 " pdb=" C ILE G 139 " pdb=" CB ILE G 139 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 2958 not shown) Planarity restraints: 3343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE J 14 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C ILE J 14 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE J 14 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE J 15 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG e 43 " 0.201 9.50e-02 1.11e+02 9.02e-02 4.99e+00 pdb=" NE ARG e 43 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG e 43 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG e 43 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG e 43 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP d 132 " -0.013 2.00e-02 2.50e+03 1.40e-02 4.89e+00 pdb=" CG TRP d 132 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP d 132 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP d 132 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP d 132 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP d 132 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP d 132 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP d 132 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP d 132 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP d 132 " -0.001 2.00e-02 2.50e+03 ... (remaining 3340 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 7284 2.90 - 3.40: 18943 3.40 - 3.90: 31990 3.90 - 4.40: 36540 4.40 - 4.90: 62245 Nonbonded interactions: 157002 Sorted by model distance: nonbonded pdb=" O GLY C 31 " pdb=" OE1 GLU C 35 " model vdw 2.401 3.040 nonbonded pdb=" O ARG G 83 " pdb=" OE1 GLU G 87 " model vdw 2.407 3.040 nonbonded pdb=" O ASN G 148 " pdb=" OE1 GLN G 152 " model vdw 2.412 3.040 nonbonded pdb=" OG1 THR E 35 " pdb=" OH TYR J 107 " model vdw 2.565 3.040 nonbonded pdb=" N ASP A 134 " pdb=" O ASP A 134 " model vdw 2.583 2.496 ... (remaining 156997 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = (chain 'E' and resid 2 through 111) selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.030 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.003 0.040 19524 Z= 0.132 Angle : 0.506 9.311 26458 Z= 0.273 Chirality : 0.042 0.156 2961 Planarity : 0.004 0.090 3343 Dihedral : 12.295 84.165 7204 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2333 helix: 1.45 (0.16), residues: 1099 sheet: -0.36 (0.33), residues: 231 loop : -0.33 (0.19), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.026 0.001 TYR I 43 PHE 0.014 0.001 PHE A 216 TRP 0.037 0.001 TRP d 132 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00298 (19487) covalent geometry : angle 0.50188 (26384) SS BOND : bond 0.00227 ( 37) SS BOND : angle 1.26484 ( 74) hydrogen bonds : bond 0.12191 ( 981) hydrogen bonds : angle 5.63149 ( 2814) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 ARG cc_start: 0.7733 (ptm-80) cc_final: 0.6577 (ptp-170) REVERT: C 81 ASN cc_start: 0.7822 (m110) cc_final: 0.7426 (m110) REVERT: D 99 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7950 (mt-10) REVERT: D 157 ASN cc_start: 0.7686 (m-40) cc_final: 0.7339 (p0) REVERT: G 152 GLN cc_start: 0.7792 (mp10) cc_final: 0.7474 (mp10) REVERT: J 85 LYS cc_start: 0.8564 (mttt) cc_final: 0.7806 (mmtt) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.1772 time to fit residues: 64.8535 Evaluate side-chains 201 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS A 249 ASN A 287 GLN B 79 GLN B 211 GLN D 67 ASN D 168 ASN G 12 ASN J 35 ASN J 40 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.220449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.176218 restraints weight = 20754.617| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.65 r_work: 0.3514 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19524 Z= 0.153 Angle : 0.497 8.644 26458 Z= 0.261 Chirality : 0.042 0.149 2961 Planarity : 0.004 0.045 3343 Dihedral : 3.919 25.025 2588 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.42 % Allowed : 4.95 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.17), residues: 2333 helix: 1.53 (0.16), residues: 1118 sheet: -0.34 (0.33), residues: 238 loop : -0.30 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 102 TYR 0.024 0.001 TYR I 43 PHE 0.014 0.001 PHE A 216 TRP 0.016 0.001 TRP d 132 HIS 0.005 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00365 (19487) covalent geometry : angle 0.49344 (26384) SS BOND : bond 0.00278 ( 37) SS BOND : angle 1.18425 ( 74) hydrogen bonds : bond 0.04052 ( 981) hydrogen bonds : angle 4.54254 ( 2814) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 211 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 290 ARG cc_start: 0.7788 (ptm-80) cc_final: 0.6977 (ptp-170) REVERT: E 61 ASP cc_start: 0.8792 (t70) cc_final: 0.8590 (t0) REVERT: G 56 MET cc_start: 0.6082 (ttp) cc_final: 0.5743 (ttm) REVERT: G 106 ASN cc_start: 0.8372 (m-40) cc_final: 0.7803 (t0) REVERT: J 85 LYS cc_start: 0.8671 (mttt) cc_final: 0.8188 (mmtt) REVERT: f 50 GLU cc_start: 0.7230 (mp0) cc_final: 0.7024 (mp0) REVERT: j 1 MET cc_start: 0.5915 (mmp) cc_final: 0.5524 (mmt) REVERT: j 61 LYS cc_start: 0.8198 (mttt) cc_final: 0.7718 (mmtt) outliers start: 9 outliers final: 5 residues processed: 215 average time/residue: 0.1576 time to fit residues: 51.2735 Evaluate side-chains 206 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 201 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain f residue 88 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 83 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 201 optimal weight: 50.0000 chunk 140 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 36 optimal weight: 0.0470 chunk 170 optimal weight: 0.0770 overall best weight: 1.2240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS B 79 GLN B 211 GLN D 168 ASN J 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.213663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.175331 restraints weight = 20495.782| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.44 r_work: 0.3580 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 19524 Z= 0.170 Angle : 0.500 9.612 26458 Z= 0.260 Chirality : 0.043 0.147 2961 Planarity : 0.004 0.045 3343 Dihedral : 3.900 20.658 2588 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.70 % Allowed : 7.43 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.18), residues: 2333 helix: 1.52 (0.16), residues: 1126 sheet: -0.28 (0.33), residues: 246 loop : -0.33 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG e 43 TYR 0.021 0.001 TYR I 43 PHE 0.015 0.001 PHE D 35 TRP 0.022 0.001 TRP d 132 HIS 0.006 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00412 (19487) covalent geometry : angle 0.49691 (26384) SS BOND : bond 0.00299 ( 37) SS BOND : angle 1.17021 ( 74) hydrogen bonds : bond 0.03998 ( 981) hydrogen bonds : angle 4.40249 ( 2814) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 186 LEU cc_start: 0.7310 (tt) cc_final: 0.6671 (tt) REVERT: j 1 MET cc_start: 0.6073 (mmp) cc_final: 0.5796 (mmt) outliers start: 15 outliers final: 9 residues processed: 221 average time/residue: 0.1482 time to fit residues: 49.4895 Evaluate side-chains 211 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 202 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain d residue 173 SER Chi-restraints excluded: chain f residue 88 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 15 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 211 optimal weight: 40.0000 chunk 16 optimal weight: 0.7980 chunk 94 optimal weight: 0.0570 chunk 208 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 194 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS B 79 GLN D 168 ASN J 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.212600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.173390 restraints weight = 20438.201| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.49 r_work: 0.3518 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19524 Z= 0.151 Angle : 0.479 8.341 26458 Z= 0.252 Chirality : 0.042 0.200 2961 Planarity : 0.003 0.045 3343 Dihedral : 3.886 24.933 2588 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.84 % Allowed : 8.64 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.18), residues: 2333 helix: 1.58 (0.15), residues: 1130 sheet: -0.32 (0.33), residues: 246 loop : -0.34 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 43 TYR 0.016 0.001 TYR I 43 PHE 0.013 0.001 PHE A 216 TRP 0.017 0.001 TRP d 132 HIS 0.005 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00363 (19487) covalent geometry : angle 0.47467 (26384) SS BOND : bond 0.00293 ( 37) SS BOND : angle 1.28497 ( 74) hydrogen bonds : bond 0.03763 ( 981) hydrogen bonds : angle 4.31217 ( 2814) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 186 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6807 (tt) REVERT: e 83 MET cc_start: 0.2523 (tmm) cc_final: 0.2137 (mmm) REVERT: f 50 GLU cc_start: 0.7202 (mp0) cc_final: 0.6911 (mp0) REVERT: f 81 MET cc_start: 0.5203 (tpt) cc_final: 0.4837 (tpt) outliers start: 18 outliers final: 13 residues processed: 216 average time/residue: 0.1574 time to fit residues: 50.8773 Evaluate side-chains 216 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain c residue 134 ILE Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain f residue 88 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 147 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS B 79 GLN D 168 ASN J 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.210228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.175552 restraints weight = 20581.770| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 1.34 r_work: 0.3572 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19524 Z= 0.137 Angle : 0.465 8.228 26458 Z= 0.244 Chirality : 0.042 0.146 2961 Planarity : 0.003 0.044 3343 Dihedral : 3.810 27.269 2588 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.84 % Allowed : 10.28 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.18), residues: 2333 helix: 1.66 (0.15), residues: 1130 sheet: -0.33 (0.33), residues: 246 loop : -0.32 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 86 TYR 0.014 0.001 TYR f 44 PHE 0.012 0.001 PHE D 48 TRP 0.017 0.001 TRP d 132 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00328 (19487) covalent geometry : angle 0.46094 (26384) SS BOND : bond 0.00279 ( 37) SS BOND : angle 1.24900 ( 74) hydrogen bonds : bond 0.03614 ( 981) hydrogen bonds : angle 4.22311 ( 2814) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: G 186 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6565 (tt) REVERT: I 132 PHE cc_start: 0.8071 (m-80) cc_final: 0.7767 (m-80) REVERT: J 35 ASN cc_start: 0.8392 (m-40) cc_final: 0.8133 (m-40) REVERT: f 50 GLU cc_start: 0.7109 (mp0) cc_final: 0.6889 (mp0) REVERT: f 81 MET cc_start: 0.4592 (tpt) cc_final: 0.4204 (tpt) outliers start: 18 outliers final: 13 residues processed: 219 average time/residue: 0.1435 time to fit residues: 47.1525 Evaluate side-chains 217 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LYS Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain c residue 134 ILE Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain f residue 88 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 165 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 219 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS B 79 GLN D 168 ASN I 86 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.208772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.169522 restraints weight = 20561.899| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.51 r_work: 0.3548 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 19524 Z= 0.174 Angle : 0.494 7.884 26458 Z= 0.258 Chirality : 0.043 0.145 2961 Planarity : 0.004 0.046 3343 Dihedral : 3.871 27.244 2588 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.03 % Allowed : 11.26 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2333 helix: 1.57 (0.15), residues: 1131 sheet: -0.29 (0.33), residues: 244 loop : -0.38 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 102 TYR 0.018 0.001 TYR B 207 PHE 0.015 0.001 PHE A 216 TRP 0.017 0.001 TRP d 132 HIS 0.006 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00423 (19487) covalent geometry : angle 0.48899 (26384) SS BOND : bond 0.00303 ( 37) SS BOND : angle 1.36297 ( 74) hydrogen bonds : bond 0.03882 ( 981) hydrogen bonds : angle 4.27589 ( 2814) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: G 186 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6968 (tt) REVERT: J 35 ASN cc_start: 0.8300 (m-40) cc_final: 0.8025 (m-40) REVERT: f 50 GLU cc_start: 0.7357 (mp0) cc_final: 0.7079 (mp0) REVERT: f 81 MET cc_start: 0.5390 (tpt) cc_final: 0.4984 (tpt) outliers start: 22 outliers final: 15 residues processed: 221 average time/residue: 0.1573 time to fit residues: 52.4514 Evaluate side-chains 215 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 34 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain c residue 134 ILE Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain f residue 88 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 12 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 105 optimal weight: 0.0980 chunk 214 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 144 optimal weight: 0.0870 chunk 131 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS B 79 GLN D 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.210858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.169365 restraints weight = 20482.364| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.70 r_work: 0.3507 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19524 Z= 0.163 Angle : 0.484 7.559 26458 Z= 0.254 Chirality : 0.042 0.145 2961 Planarity : 0.003 0.046 3343 Dihedral : 3.884 26.457 2588 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.89 % Allowed : 11.96 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2333 helix: 1.58 (0.15), residues: 1130 sheet: -0.19 (0.34), residues: 233 loop : -0.42 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 102 TYR 0.014 0.001 TYR B 207 PHE 0.014 0.001 PHE A 216 TRP 0.012 0.001 TRP d 132 HIS 0.005 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00395 (19487) covalent geometry : angle 0.47815 (26384) SS BOND : bond 0.00325 ( 37) SS BOND : angle 1.49335 ( 74) hydrogen bonds : bond 0.03789 ( 981) hydrogen bonds : angle 4.26051 ( 2814) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: G 152 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7239 (mt0) REVERT: G 186 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6947 (tt) REVERT: f 81 MET cc_start: 0.5377 (tpt) cc_final: 0.4989 (tpt) outliers start: 19 outliers final: 13 residues processed: 219 average time/residue: 0.1365 time to fit residues: 45.4211 Evaluate side-chains 219 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 152 GLN Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain f residue 88 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 48 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS B 79 GLN D 168 ASN G 106 ASN J 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.207474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.172260 restraints weight = 20617.902| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.39 r_work: 0.3521 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 19524 Z= 0.199 Angle : 0.514 7.740 26458 Z= 0.269 Chirality : 0.043 0.145 2961 Planarity : 0.004 0.047 3343 Dihedral : 3.955 25.876 2588 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.21 % Allowed : 12.06 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2333 helix: 1.47 (0.15), residues: 1133 sheet: -0.30 (0.34), residues: 237 loop : -0.45 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 57 TYR 0.014 0.001 TYR B 207 PHE 0.017 0.001 PHE A 216 TRP 0.013 0.001 TRP d 132 HIS 0.007 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00488 (19487) covalent geometry : angle 0.50882 (26384) SS BOND : bond 0.00364 ( 37) SS BOND : angle 1.50091 ( 74) hydrogen bonds : bond 0.04060 ( 981) hydrogen bonds : angle 4.33518 ( 2814) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: G 152 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7071 (mt0) REVERT: G 186 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6644 (tt) REVERT: f 50 GLU cc_start: 0.7089 (mp0) cc_final: 0.6754 (mp0) REVERT: f 81 MET cc_start: 0.4614 (tpt) cc_final: 0.4082 (tpt) outliers start: 26 outliers final: 15 residues processed: 226 average time/residue: 0.1419 time to fit residues: 48.1883 Evaluate side-chains 224 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain C residue 34 LYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 152 GLN Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 173 SER Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain j residue 18 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 150 optimal weight: 0.7980 chunk 218 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 217 optimal weight: 0.0370 chunk 124 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 0 optimal weight: 40.0000 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS B 79 GLN D 67 ASN D 168 ASN G 106 ASN I 60 ASN J 35 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.209907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.170194 restraints weight = 20603.295| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 1.50 r_work: 0.3562 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19524 Z= 0.112 Angle : 0.459 7.668 26458 Z= 0.242 Chirality : 0.041 0.175 2961 Planarity : 0.003 0.044 3343 Dihedral : 3.822 27.187 2588 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.75 % Allowed : 12.66 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.18), residues: 2333 helix: 1.72 (0.15), residues: 1128 sheet: -0.31 (0.34), residues: 242 loop : -0.38 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 43 TYR 0.016 0.001 TYR B 207 PHE 0.010 0.001 PHE d 147 TRP 0.012 0.001 TRP d 181 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00258 (19487) covalent geometry : angle 0.45537 (26384) SS BOND : bond 0.00244 ( 37) SS BOND : angle 1.20134 ( 74) hydrogen bonds : bond 0.03488 ( 981) hydrogen bonds : angle 4.18968 ( 2814) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 170 ASP cc_start: 0.8241 (t70) cc_final: 0.7851 (m-30) REVERT: G 152 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7160 (mt0) REVERT: G 186 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6916 (tt) REVERT: f 50 GLU cc_start: 0.7284 (mp0) cc_final: 0.7049 (mp0) REVERT: f 81 MET cc_start: 0.5298 (tpt) cc_final: 0.4825 (tpt) outliers start: 16 outliers final: 13 residues processed: 222 average time/residue: 0.1390 time to fit residues: 46.7070 Evaluate side-chains 225 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 152 GLN Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain c residue 134 ILE Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain f residue 88 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 131 optimal weight: 0.0060 chunk 132 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 162 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS B 79 GLN D 168 ASN I 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.212037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.173946 restraints weight = 20458.970| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.49 r_work: 0.3533 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19524 Z= 0.117 Angle : 0.458 7.694 26458 Z= 0.241 Chirality : 0.041 0.147 2961 Planarity : 0.003 0.043 3343 Dihedral : 3.783 26.674 2588 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.89 % Allowed : 12.62 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2333 helix: 1.75 (0.15), residues: 1129 sheet: -0.31 (0.34), residues: 242 loop : -0.37 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 102 TYR 0.017 0.001 TYR B 207 PHE 0.010 0.001 PHE D 48 TRP 0.011 0.001 TRP d 181 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00273 (19487) covalent geometry : angle 0.45471 (26384) SS BOND : bond 0.00238 ( 37) SS BOND : angle 1.19253 ( 74) hydrogen bonds : bond 0.03465 ( 981) hydrogen bonds : angle 4.17747 ( 2814) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4666 Ramachandran restraints generated. 2333 Oldfield, 0 Emsley, 2333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.5061 (tpt) cc_final: 0.4773 (tpt) REVERT: A 170 ASP cc_start: 0.8297 (t70) cc_final: 0.7899 (m-30) REVERT: G 152 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7177 (mt0) REVERT: G 186 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6898 (tt) REVERT: f 50 GLU cc_start: 0.7330 (mp0) cc_final: 0.7094 (mp0) REVERT: f 81 MET cc_start: 0.5238 (tpt) cc_final: 0.4748 (tpt) outliers start: 19 outliers final: 15 residues processed: 221 average time/residue: 0.1551 time to fit residues: 51.5465 Evaluate side-chains 225 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 135 LYS Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 152 GLN Chi-restraints excluded: chain G residue 186 LEU Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain c residue 134 ILE Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain f residue 88 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 198 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 42 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 HIS B 79 GLN D 168 ASN ** I 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.209497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.170541 restraints weight = 20615.620| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.53 r_work: 0.3516 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19524 Z= 0.159 Angle : 0.655 59.189 26458 Z= 0.368 Chirality : 0.042 0.226 2961 Planarity : 0.003 0.044 3343 Dihedral : 3.804 26.538 2588 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.89 % Allowed : 12.52 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2333 helix: 1.72 (0.15), residues: 1128 sheet: -0.30 (0.34), residues: 242 loop : -0.37 (0.20), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 102 TYR 0.016 0.001 TYR B 207 PHE 0.012 0.001 PHE A 216 TRP 0.011 0.001 TRP d 181 HIS 0.004 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00380 (19487) covalent geometry : angle 0.65299 (26384) SS BOND : bond 0.00262 ( 37) SS BOND : angle 1.18780 ( 74) hydrogen bonds : bond 0.03562 ( 981) hydrogen bonds : angle 4.18372 ( 2814) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6003.22 seconds wall clock time: 103 minutes 27.56 seconds (6207.56 seconds total)