Starting phenix.real_space_refine on Thu Feb 5 13:41:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uzo_64647/02_2026/9uzo_64647.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uzo_64647/02_2026/9uzo_64647.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9uzo_64647/02_2026/9uzo_64647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uzo_64647/02_2026/9uzo_64647.map" model { file = "/net/cci-nas-00/data/ceres_data/9uzo_64647/02_2026/9uzo_64647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uzo_64647/02_2026/9uzo_64647.cif" } 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= 0.039 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 125 5.16 5 C 11268 2.51 5 N 2964 2.21 5 O 3195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 17552 Number of models: 1 Model: "" Number of chains: 15 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: "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: 3.95, per 1000 atoms: 0.23 Number of scatterers: 17552 At special positions: 0 Unit cell: (120.423, 150.131, 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 125 16.00 O 3195 8.00 N 2964 7.00 C 11268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, 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=2.02 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=2.02 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 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 f 75 " - pdb=" SG CYS f 107 " 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: 1.54 Conformation dependent library (CDL) restraints added in 701.1 milliseconds 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4184 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 22 sheets defined 53.3% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 30 through 34 Processing helix chain 'A' and resid 66 through 74 removed outlier: 3.611A pdb=" N SER A 72 " --> pdb=" O HIS A 69 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A 73 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 74 " --> pdb=" O SER A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 108 through 115 Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 168 through 179 removed outlier: 4.049A pdb=" N GLY A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 191 removed outlier: 3.524A pdb=" N ALA A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 224 through 239 removed outlier: 4.383A pdb=" N GLY A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.634A pdb=" N TRP A 246 " --> pdb=" O ARG A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 267 removed outlier: 3.814A pdb=" N ARG A 263 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.516A pdb=" N LEU A 280 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 342 through 363 Processing helix chain 'B' and resid 26 through 29 Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.580A 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 127 through 135 Processing helix chain 'B' and resid 141 through 153 Processing helix chain 'B' and resid 159 through 180 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.568A 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 235 removed outlier: 3.708A pdb=" N LEU B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 245 removed outlier: 3.941A pdb=" N TRP B 244 " --> pdb=" O PRO B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 removed outlier: 3.705A pdb=" N ASN B 250 " --> pdb=" O GLU B 247 " (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 292 through 299 removed outlier: 3.503A pdb=" N ASN B 295 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ASP B 297 " --> pdb=" O SER B 294 " (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: 5.646A pdb=" N GLY C 31 " --> pdb=" O TYR C 27 " (cutoff:3.500A) removed outlier: 5.675A 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 68 through 72 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: 3.559A pdb=" N THR D 68 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N SER D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU D 75 " --> pdb=" O ASP D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 155 removed outlier: 3.543A 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 184 through 189 Processing helix chain 'E' and resid 2 through 23 Processing helix chain 'E' and resid 26 through 49 removed outlier: 4.093A 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 47 through 53 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 'I' and resid 2 through 13 Processing helix chain 'I' and resid 17 through 21 removed outlier: 4.233A pdb=" N CYS I 21 " --> pdb=" O ARG I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 36 Processing helix chain 'I' and resid 38 through 43 removed outlier: 3.889A pdb=" N TRP I 42 " --> pdb=" O PRO I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 48 Processing helix chain 'I' and resid 54 through 62 Processing helix chain 'I' and resid 116 through 127 removed outlier: 4.646A pdb=" N ILE I 120 " --> pdb=" O LYS I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 132 removed outlier: 3.906A pdb=" N ALA I 131 " --> pdb=" O ILE I 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 39 removed outlier: 5.131A pdb=" N VAL J 19 " --> pdb=" O PHE J 15 " (cutoff:3.500A) Proline residue: J 20 - end of helix removed outlier: 3.554A pdb=" N LEU J 39 " --> pdb=" O ASN J 35 " (cutoff:3.500A) 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 removed outlier: 3.530A pdb=" N ASN J 84 " --> pdb=" O GLU J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 112 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 41 Processing helix chain 'c' and resid 42 through 45 removed outlier: 4.201A pdb=" N TYR c 45 " --> pdb=" O ALA c 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 42 through 45' Processing helix chain 'c' and resid 61 through 66 removed outlier: 4.371A pdb=" N THR c 65 " --> pdb=" O ASP c 61 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE c 66 " --> pdb=" O VAL c 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 61 through 66' Processing helix chain 'c' and resid 68 through 72 Processing helix chain 'c' and resid 108 through 117 Processing helix chain 'c' and resid 136 through 146 removed outlier: 3.536A 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: 4.680A pdb=" N LYS d 73 " --> pdb=" O VAL d 69 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER d 74 " --> pdb=" O ASN d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 99 Processing helix chain 'd' and resid 141 through 154 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 49 removed outlier: 3.763A 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 46 Processing helix chain 'f' and resid 47 through 55 removed outlier: 3.532A pdb=" N LEU f 51 " --> pdb=" O PHE f 47 " (cutoff:3.500A) Processing helix chain 'f' and resid 63 through 69 removed outlier: 3.515A pdb=" N ARG f 67 " --> pdb=" O ASP f 63 " (cutoff:3.500A) Processing helix chain 'f' and resid 106 through 115 Processing helix chain 'f' and resid 121 through 128 removed outlier: 3.908A pdb=" N VAL f 125 " --> pdb=" O SER f 121 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 17 Processing helix chain 'j' and resid 17 through 40 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 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 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 294 removed outlier: 6.759A 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: 6.482A pdb=" N ILE A 298 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ASN B 277 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N VAL A 300 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU B 279 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N SER A 302 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 10.038A pdb=" N MET B 281 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N ALA A 304 " --> pdb=" O MET B 281 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 301 " --> pdb=" O LEU I 73 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN I 75 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU A 303 " --> pdb=" O ASN I 75 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER I 77 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 305 " --> pdb=" O SER I 77 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR I 79 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.709A pdb=" N GLN A 309 " --> pdb=" O LEU I 83 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N VAL I 85 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU A 311 " --> pdb=" O VAL I 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 44 Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AA9, first strand: chain 'C' and resid 74 through 78 removed outlier: 15.629A pdb=" N PHE C 83 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N GLU C 94 " --> pdb=" O PHE C 83 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N SER C 85 " --> pdb=" O GLN C 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 101 through 103 removed outlier: 5.727A pdb=" N SER C 85 " --> pdb=" O GLN C 92 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N GLU C 94 " --> pdb=" O PHE C 83 " (cutoff:3.500A) removed outlier: 15.629A pdb=" N PHE C 83 " --> pdb=" O GLU C 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 101 through 104 Processing sheet with id=AB3, first strand: chain 'D' and resid 101 through 104 removed outlier: 5.674A pdb=" N ALA D 111 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 54 through 58 Processing sheet with id=AB5, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.929A pdb=" N THR F 92 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 44 through 46 removed outlier: 5.349A pdb=" N LEU J 50 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP J 88 " --> pdb=" O VAL J 66 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 74 through 77 Processing sheet with id=AB8, first strand: chain 'c' and resid 101 through 103 Processing sheet with id=AB9, first strand: chain 'd' and resid 101 through 104 Processing sheet with id=AC1, first strand: chain 'd' and resid 101 through 104 removed outlier: 5.992A pdb=" N ALA d 111 " --> pdb=" O ILE d 124 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'e' and resid 54 through 58 Processing sheet with id=AC3, first strand: chain 'f' and resid 72 through 76 Processing sheet with id=AC4, first strand: chain 'j' and resid 44 through 46 removed outlier: 5.341A pdb=" N LEU j 50 " --> pdb=" O ALA j 65 " (cutoff:3.500A) 913 hydrogen bonds defined for protein. 2535 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 2.10 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: 5585 1.34 - 1.47: 4376 1.47 - 1.59: 7813 1.59 - 1.71: 0 1.71 - 1.83: 172 Bond restraints: 17946 Sorted by residual: bond pdb=" N GLN A 126 " pdb=" CA GLN A 126 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.27e-02 6.20e+03 4.71e+00 bond pdb=" CB CYS D 148 " pdb=" SG CYS D 148 " ideal model delta sigma weight residual 1.808 1.750 0.058 3.30e-02 9.18e+02 3.07e+00 bond pdb=" CG ARG A 190 " pdb=" CD ARG A 190 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.54e+00 bond pdb=" CG LEU D 39 " pdb=" CD1 LEU D 39 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.49e+00 bond pdb=" CB CYS A 185 " pdb=" SG CYS A 185 " ideal model delta sigma weight residual 1.808 1.757 0.051 3.30e-02 9.18e+02 2.37e+00 ... (remaining 17941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 23645 1.50 - 3.00: 526 3.00 - 4.50: 92 4.50 - 6.00: 22 6.00 - 7.50: 6 Bond angle restraints: 24291 Sorted by residual: angle pdb=" N TRP d 132 " pdb=" CA TRP d 132 " pdb=" C TRP d 132 " ideal model delta sigma weight residual 110.50 106.45 4.05 1.41e+00 5.03e-01 8.26e+00 angle pdb=" C SER J 111 " pdb=" N ASP J 112 " pdb=" CA ASP J 112 " ideal model delta sigma weight residual 121.94 116.72 5.22 2.00e+00 2.50e-01 6.80e+00 angle pdb=" N ASN B 154 " pdb=" CA ASN B 154 " pdb=" C ASN B 154 " ideal model delta sigma weight residual 110.44 107.46 2.98 1.20e+00 6.94e-01 6.15e+00 angle pdb=" N GLU A 215 " pdb=" CA GLU A 215 " pdb=" CB GLU A 215 " ideal model delta sigma weight residual 110.12 113.65 -3.53 1.47e+00 4.63e-01 5.76e+00 angle pdb=" C ALA I 126 " pdb=" N ILE I 127 " pdb=" CA ILE I 127 " ideal model delta sigma weight residual 121.19 117.54 3.65 1.59e+00 3.96e-01 5.26e+00 ... (remaining 24286 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 10060 17.91 - 35.82: 746 35.82 - 53.73: 84 53.73 - 71.64: 23 71.64 - 89.55: 6 Dihedral angle restraints: 10919 sinusoidal: 4468 harmonic: 6451 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 93.00 -179.54 -87.46 1 1.00e+01 1.00e-02 9.17e+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 93.00 158.57 -65.57 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CB CYS F 75 " pdb=" SG CYS F 75 " pdb=" SG CYS F 107 " pdb=" CB CYS F 107 " ideal model delta sinusoidal sigma weight residual 93.00 139.93 -46.93 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 10916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1677 0.036 - 0.072: 755 0.072 - 0.109: 220 0.109 - 0.145: 54 0.145 - 0.181: 3 Chirality restraints: 2709 Sorted by residual: chirality pdb=" CG LEU D 75 " pdb=" CB LEU D 75 " pdb=" CD1 LEU D 75 " pdb=" CD2 LEU D 75 " both_signs ideal model delta sigma weight residual False -2.59 -2.77 0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CA VAL J 46 " pdb=" N VAL J 46 " pdb=" C VAL J 46 " pdb=" CB VAL J 46 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CB VAL J 46 " pdb=" CA VAL J 46 " pdb=" CG1 VAL J 46 " pdb=" CG2 VAL J 46 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 2706 not shown) Planarity restraints: 3077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP d 132 " -0.019 2.00e-02 2.50e+03 2.44e-02 1.49e+01 pdb=" CG TRP d 132 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP d 132 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP d 132 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP d 132 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP d 132 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP d 132 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP d 132 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP d 132 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP d 132 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 47 " -0.020 2.00e-02 2.50e+03 1.63e-02 6.66e+00 pdb=" CG TRP D 47 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP D 47 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP D 47 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 47 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 47 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 47 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 47 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 47 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 47 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE J 14 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C ILE J 14 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE J 14 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE J 15 " -0.015 2.00e-02 2.50e+03 ... (remaining 3074 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.95: 7888 2.95 - 3.44: 17731 3.44 - 3.93: 29036 3.93 - 4.41: 33872 4.41 - 4.90: 55827 Nonbonded interactions: 144354 Sorted by model distance: nonbonded pdb=" O ARG A 211 " pdb=" OE1 GLU A 215 " model vdw 2.465 3.040 nonbonded pdb=" O ILE C 49 " pdb=" OG1 THR E 35 " model vdw 2.511 3.040 nonbonded pdb=" OH TYR J 36 " pdb=" O ASN J 42 " model vdw 2.565 3.040 nonbonded pdb=" O ALA E 31 " pdb=" OG1 THR E 35 " model vdw 2.565 3.040 nonbonded pdb=" O SER J 58 " pdb=" OG SER J 58 " model vdw 2.588 3.040 ... (remaining 144349 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: 26.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.950 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.005 0.077 17981 Z= 0.214 Angle : 0.584 7.500 24361 Z= 0.308 Chirality : 0.044 0.181 2709 Planarity : 0.004 0.054 3077 Dihedral : 12.172 89.546 6630 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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: 0.51 (0.18), residues: 2141 helix: 1.20 (0.16), residues: 1010 sheet: -0.61 (0.34), residues: 215 loop : -0.30 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 190 TYR 0.021 0.002 TYR J 107 PHE 0.023 0.002 PHE d 100 TRP 0.064 0.002 TRP d 132 HIS 0.006 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00521 (17946) covalent geometry : angle 0.57885 (24291) SS BOND : bond 0.00318 ( 35) SS BOND : angle 1.51051 ( 70) hydrogen bonds : bond 0.13108 ( 902) hydrogen bonds : angle 5.78124 ( 2535) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: D 58 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7683 (mm-30) REVERT: D 184 ASP cc_start: 0.7296 (m-30) cc_final: 0.7028 (m-30) REVERT: E 61 ASP cc_start: 0.8817 (t70) cc_final: 0.8490 (t0) REVERT: d 135 LYS cc_start: 0.8379 (mptt) cc_final: 0.7660 (ttpt) REVERT: e 33 MET cc_start: 0.6408 (ttp) cc_final: 0.6196 (ttm) REVERT: e 83 MET cc_start: 0.5512 (ppp) cc_final: 0.5093 (tpt) REVERT: f 42 LEU cc_start: 0.8266 (mt) cc_final: 0.7919 (tp) REVERT: f 81 MET cc_start: 0.2251 (tpt) cc_final: 0.1756 (ptm) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1366 time to fit residues: 49.5892 Evaluate side-chains 196 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS C 81 ASN C 92 GLN E 75 ASN c 63 ASN d 168 ASN f 115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.191257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.146061 restraints weight = 18623.897| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.48 r_work: 0.3179 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17981 Z= 0.157 Angle : 0.509 5.992 24361 Z= 0.267 Chirality : 0.042 0.170 2709 Planarity : 0.004 0.045 3077 Dihedral : 3.890 19.454 2383 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.25 % Allowed : 4.73 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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: 0.79 (0.18), residues: 2141 helix: 1.47 (0.16), residues: 1018 sheet: -0.55 (0.35), residues: 207 loop : -0.20 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 190 TYR 0.017 0.001 TYR k 21 PHE 0.020 0.001 PHE k 7 TRP 0.022 0.001 TRP d 132 HIS 0.005 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00375 (17946) covalent geometry : angle 0.50703 (24291) SS BOND : bond 0.00250 ( 35) SS BOND : angle 1.03265 ( 70) hydrogen bonds : bond 0.04394 ( 902) hydrogen bonds : angle 4.75686 ( 2535) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 208 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 24 MET cc_start: 0.6018 (ttm) cc_final: 0.4784 (tpt) REVERT: D 184 ASP cc_start: 0.7531 (m-30) cc_final: 0.7238 (m-30) REVERT: E 61 ASP cc_start: 0.8818 (t70) cc_final: 0.8587 (t0) REVERT: d 77 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7788 (m-30) REVERT: e 33 MET cc_start: 0.6206 (ttp) cc_final: 0.5988 (ttm) REVERT: e 83 MET cc_start: 0.5428 (ppp) cc_final: 0.4914 (tpt) REVERT: f 81 MET cc_start: 0.2032 (tpt) cc_final: 0.1616 (ttm) outliers start: 5 outliers final: 4 residues processed: 211 average time/residue: 0.1456 time to fit residues: 46.0167 Evaluate side-chains 199 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 194 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain d residue 75 LEU Chi-restraints excluded: chain d residue 77 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 2 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN E 75 ASN d 168 ASN j 70 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.188593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.151123 restraints weight = 18994.677| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.38 r_work: 0.3162 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 17981 Z= 0.219 Angle : 0.548 6.777 24361 Z= 0.284 Chirality : 0.044 0.158 2709 Planarity : 0.004 0.050 3077 Dihedral : 3.999 19.710 2383 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.92 % Allowed : 7.47 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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: 0.65 (0.18), residues: 2141 helix: 1.38 (0.16), residues: 1012 sheet: -0.58 (0.34), residues: 217 loop : -0.30 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 190 TYR 0.015 0.001 TYR I 110 PHE 0.025 0.002 PHE d 100 TRP 0.026 0.002 TRP d 132 HIS 0.006 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00541 (17946) covalent geometry : angle 0.54540 (24291) SS BOND : bond 0.00301 ( 35) SS BOND : angle 1.06258 ( 70) hydrogen bonds : bond 0.04633 ( 902) hydrogen bonds : angle 4.72826 ( 2535) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.6055 (ttm) cc_final: 0.4779 (tpt) REVERT: D 184 ASP cc_start: 0.7544 (m-30) cc_final: 0.7199 (m-30) REVERT: d 58 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7648 (mm-30) REVERT: d 77 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7850 (m-30) outliers start: 18 outliers final: 13 residues processed: 223 average time/residue: 0.1481 time to fit residues: 49.9493 Evaluate side-chains 221 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain d residue 75 LEU Chi-restraints excluded: chain d residue 77 ASP Chi-restraints excluded: chain d residue 188 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 195 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 204 optimal weight: 0.0170 chunk 147 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS D 168 ASN E 75 ASN J 35 ASN d 168 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.222778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.183690 restraints weight = 18417.684| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 1.50 r_work: 0.3631 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17981 Z= 0.119 Angle : 0.463 7.628 24361 Z= 0.243 Chirality : 0.041 0.167 2709 Planarity : 0.003 0.044 3077 Dihedral : 3.773 19.191 2383 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.76 % Allowed : 9.00 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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: 2141 helix: 1.69 (0.16), residues: 1014 sheet: -0.59 (0.34), residues: 217 loop : -0.21 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.018 0.001 TYR B 207 PHE 0.017 0.001 PHE k 7 TRP 0.010 0.001 TRP d 181 HIS 0.004 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00280 (17946) covalent geometry : angle 0.46198 (24291) SS BOND : bond 0.00185 ( 35) SS BOND : angle 0.78911 ( 70) hydrogen bonds : bond 0.03776 ( 902) hydrogen bonds : angle 4.49281 ( 2535) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.6072 (ttm) cc_final: 0.5267 (tpt) REVERT: A 162 ASN cc_start: 0.8009 (t0) cc_final: 0.7692 (m-40) REVERT: D 184 ASP cc_start: 0.7639 (m-30) cc_final: 0.7318 (m-30) outliers start: 15 outliers final: 12 residues processed: 217 average time/residue: 0.1497 time to fit residues: 48.5923 Evaluate side-chains 217 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain c residue 52 THR Chi-restraints excluded: chain d residue 75 LEU Chi-restraints excluded: chain d residue 188 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 206 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 67 optimal weight: 0.9990 chunk 108 optimal weight: 0.2980 chunk 143 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN E 75 ASN d 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.220635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.175945 restraints weight = 18285.384| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.58 r_work: 0.3535 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 17981 Z= 0.180 Angle : 0.508 6.561 24361 Z= 0.264 Chirality : 0.042 0.180 2709 Planarity : 0.004 0.047 3077 Dihedral : 3.872 19.366 2383 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.12 % Allowed : 9.81 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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 (0.18), residues: 2141 helix: 1.58 (0.16), residues: 1011 sheet: -0.62 (0.33), residues: 217 loop : -0.24 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.018 0.001 TYR B 207 PHE 0.016 0.001 PHE d 100 TRP 0.011 0.001 TRP d 181 HIS 0.005 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00441 (17946) covalent geometry : angle 0.50637 (24291) SS BOND : bond 0.00256 ( 35) SS BOND : angle 0.89231 ( 70) hydrogen bonds : bond 0.04242 ( 902) hydrogen bonds : angle 4.59482 ( 2535) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 CYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6779 (t) REVERT: D 168 ASN cc_start: 0.8369 (m110) cc_final: 0.8047 (m110) REVERT: D 184 ASP cc_start: 0.7647 (m-30) cc_final: 0.7308 (m-30) REVERT: F 77 ASP cc_start: 0.8205 (t70) cc_final: 0.8002 (t70) REVERT: F 78 ASP cc_start: 0.8365 (p0) cc_final: 0.8071 (p0) outliers start: 22 outliers final: 17 residues processed: 222 average time/residue: 0.1487 time to fit residues: 50.1025 Evaluate side-chains 225 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 207 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain c residue 52 THR Chi-restraints excluded: chain d residue 75 LEU Chi-restraints excluded: chain d residue 188 MET Chi-restraints excluded: chain e residue 33 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 59 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 75 ASN d 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.220848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.178877 restraints weight = 18293.821| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.58 r_work: 0.3559 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17981 Z= 0.169 Angle : 0.495 6.310 24361 Z= 0.258 Chirality : 0.042 0.183 2709 Planarity : 0.004 0.047 3077 Dihedral : 3.843 19.181 2383 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.32 % Allowed : 10.37 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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 (0.18), residues: 2141 helix: 1.59 (0.16), residues: 1015 sheet: -0.59 (0.33), residues: 221 loop : -0.25 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.019 0.001 TYR B 207 PHE 0.015 0.001 PHE k 7 TRP 0.011 0.001 TRP d 181 HIS 0.005 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00413 (17946) covalent geometry : angle 0.49343 (24291) SS BOND : bond 0.00243 ( 35) SS BOND : angle 0.84807 ( 70) hydrogen bonds : bond 0.04103 ( 902) hydrogen bonds : angle 4.55464 ( 2535) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 CYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6778 (t) REVERT: D 168 ASN cc_start: 0.8267 (m110) cc_final: 0.7958 (m110) REVERT: D 184 ASP cc_start: 0.7737 (m-30) cc_final: 0.7403 (m-30) REVERT: F 77 ASP cc_start: 0.8273 (t70) cc_final: 0.8054 (t70) REVERT: F 78 ASP cc_start: 0.8389 (p0) cc_final: 0.8068 (p0) REVERT: d 77 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7963 (m-30) outliers start: 26 outliers final: 19 residues processed: 222 average time/residue: 0.1540 time to fit residues: 51.4198 Evaluate side-chains 226 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain c residue 52 THR Chi-restraints excluded: chain d residue 75 LEU Chi-restraints excluded: chain d residue 77 ASP Chi-restraints excluded: chain j residue 60 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 25 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN d 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.222082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.178238 restraints weight = 18316.938| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.58 r_work: 0.3561 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17981 Z= 0.129 Angle : 0.469 8.833 24361 Z= 0.245 Chirality : 0.041 0.181 2709 Planarity : 0.003 0.045 3077 Dihedral : 3.731 19.009 2383 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.97 % Allowed : 11.13 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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: 0.99 (0.18), residues: 2141 helix: 1.73 (0.16), residues: 1016 sheet: -0.66 (0.32), residues: 228 loop : -0.16 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.019 0.001 TYR B 207 PHE 0.015 0.001 PHE k 7 TRP 0.011 0.001 TRP d 181 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00307 (17946) covalent geometry : angle 0.46770 (24291) SS BOND : bond 0.00193 ( 35) SS BOND : angle 0.76709 ( 70) hydrogen bonds : bond 0.03798 ( 902) hydrogen bonds : angle 4.46090 ( 2535) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 CYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6758 (t) REVERT: D 168 ASN cc_start: 0.8260 (m110) cc_final: 0.7956 (m110) REVERT: D 184 ASP cc_start: 0.7703 (m-30) cc_final: 0.7362 (m-30) outliers start: 19 outliers final: 17 residues processed: 227 average time/residue: 0.1495 time to fit residues: 50.8743 Evaluate side-chains 226 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain c residue 52 THR Chi-restraints excluded: chain d residue 75 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 88 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 206 optimal weight: 0.1980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN J 35 ASN d 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.220022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.175392 restraints weight = 18179.645| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 1.52 r_work: 0.3544 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 17981 Z= 0.194 Angle : 0.522 8.215 24361 Z= 0.271 Chirality : 0.043 0.188 2709 Planarity : 0.004 0.057 3077 Dihedral : 3.882 19.302 2383 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.27 % Allowed : 11.29 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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 (0.18), residues: 2141 helix: 1.58 (0.16), residues: 1009 sheet: -0.58 (0.33), residues: 221 loop : -0.23 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 275 TYR 0.019 0.001 TYR B 207 PHE 0.017 0.002 PHE D 35 TRP 0.012 0.001 TRP d 181 HIS 0.005 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00479 (17946) covalent geometry : angle 0.52090 (24291) SS BOND : bond 0.00271 ( 35) SS BOND : angle 0.88354 ( 70) hydrogen bonds : bond 0.04297 ( 902) hydrogen bonds : angle 4.57422 ( 2535) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 291 CYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6763 (t) REVERT: D 168 ASN cc_start: 0.8280 (m110) cc_final: 0.7951 (m110) REVERT: D 184 ASP cc_start: 0.7719 (m-30) cc_final: 0.7380 (m-30) REVERT: F 77 ASP cc_start: 0.8258 (t70) cc_final: 0.8049 (t70) REVERT: d 77 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7932 (m-30) outliers start: 25 outliers final: 21 residues processed: 224 average time/residue: 0.1525 time to fit residues: 51.4297 Evaluate side-chains 230 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 65 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain c residue 52 THR Chi-restraints excluded: chain d residue 75 LEU Chi-restraints excluded: chain d residue 77 ASP Chi-restraints excluded: chain j residue 60 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 172 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 152 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN E 75 ASN J 35 ASN d 168 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.222306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.182072 restraints weight = 18435.284| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 1.48 r_work: 0.3613 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17981 Z= 0.121 Angle : 0.466 7.290 24361 Z= 0.244 Chirality : 0.041 0.187 2709 Planarity : 0.003 0.045 3077 Dihedral : 3.721 19.026 2383 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.12 % Allowed : 11.79 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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: 1.00 (0.18), residues: 2141 helix: 1.75 (0.16), residues: 1016 sheet: -0.68 (0.32), residues: 228 loop : -0.15 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 275 TYR 0.019 0.001 TYR B 207 PHE 0.014 0.001 PHE k 7 TRP 0.010 0.001 TRP d 181 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00285 (17946) covalent geometry : angle 0.46469 (24291) SS BOND : bond 0.00180 ( 35) SS BOND : angle 0.75370 ( 70) hydrogen bonds : bond 0.03728 ( 902) hydrogen bonds : angle 4.45293 ( 2535) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 291 CYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6616 (t) REVERT: D 168 ASN cc_start: 0.8234 (m110) cc_final: 0.7915 (m110) REVERT: D 184 ASP cc_start: 0.7631 (m-30) cc_final: 0.7287 (m-30) outliers start: 22 outliers final: 20 residues processed: 223 average time/residue: 0.1400 time to fit residues: 47.5162 Evaluate side-chains 229 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain c residue 52 THR Chi-restraints excluded: chain d residue 75 LEU Chi-restraints excluded: chain j residue 60 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 44 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.0010 chunk 99 optimal weight: 0.5980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN C 92 GLN E 75 ASN d 168 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.222331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.182366 restraints weight = 18229.440| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 1.46 r_work: 0.3625 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17981 Z= 0.125 Angle : 0.472 7.361 24361 Z= 0.246 Chirality : 0.041 0.193 2709 Planarity : 0.003 0.044 3077 Dihedral : 3.691 18.986 2383 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.12 % Allowed : 11.74 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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: 1.05 (0.18), residues: 2141 helix: 1.79 (0.16), residues: 1016 sheet: -0.58 (0.33), residues: 221 loop : -0.14 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 275 TYR 0.024 0.001 TYR B 108 PHE 0.014 0.001 PHE k 7 TRP 0.011 0.001 TRP d 181 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00296 (17946) covalent geometry : angle 0.47059 (24291) SS BOND : bond 0.00191 ( 35) SS BOND : angle 0.77613 ( 70) hydrogen bonds : bond 0.03735 ( 902) hydrogen bonds : angle 4.42862 ( 2535) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4282 Ramachandran restraints generated. 2141 Oldfield, 0 Emsley, 2141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 291 CYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6551 (t) REVERT: D 168 ASN cc_start: 0.8214 (m110) cc_final: 0.7895 (m110) REVERT: D 184 ASP cc_start: 0.7619 (m-30) cc_final: 0.7263 (m-30) REVERT: d 133 MET cc_start: 0.8996 (mtt) cc_final: 0.8519 (mtp) outliers start: 22 outliers final: 20 residues processed: 224 average time/residue: 0.1435 time to fit residues: 48.5176 Evaluate side-chains 230 residues out of total 1967 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 87 ASN Chi-restraints excluded: chain c residue 52 THR Chi-restraints excluded: chain d residue 75 LEU Chi-restraints excluded: chain j residue 60 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 211 random chunks: chunk 119 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 209 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 80 optimal weight: 0.0270 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN E 75 ASN d 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.223239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.184028 restraints weight = 18411.161| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 1.42 r_work: 0.3653 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17981 Z= 0.111 Angle : 0.460 8.276 24361 Z= 0.240 Chirality : 0.041 0.187 2709 Planarity : 0.003 0.044 3077 Dihedral : 3.619 18.915 2383 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 1.02 % Allowed : 12.05 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.49 % 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: 1.11 (0.18), residues: 2141 helix: 1.86 (0.16), residues: 1018 sheet: -0.63 (0.32), residues: 230 loop : -0.13 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 275 TYR 0.019 0.001 TYR B 207 PHE 0.013 0.001 PHE k 7 TRP 0.011 0.001 TRP d 181 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00260 (17946) covalent geometry : angle 0.45945 (24291) SS BOND : bond 0.00166 ( 35) SS BOND : angle 0.73101 ( 70) hydrogen bonds : bond 0.03569 ( 902) hydrogen bonds : angle 4.37211 ( 2535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7437.80 seconds wall clock time: 127 minutes 35.17 seconds (7655.17 seconds total)