Starting phenix.real_space_refine on Wed Apr 30 09:42:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ic0_35351/04_2025/8ic0_35351.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ic0_35351/04_2025/8ic0_35351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ic0_35351/04_2025/8ic0_35351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ic0_35351/04_2025/8ic0_35351.map" model { file = "/net/cci-nas-00/data/ceres_data/8ic0_35351/04_2025/8ic0_35351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ic0_35351/04_2025/8ic0_35351.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 71 5.16 5 C 6100 2.51 5 N 1638 2.21 5 O 1744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9553 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2420 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain: "B" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1805 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2579 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1750 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 564 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Time building chain proxies: 5.44, per 1000 atoms: 0.57 Number of scatterers: 9553 At special positions: 0 Unit cell: (91.216, 122.337, 149.165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 71 16.00 O 1744 8.00 N 1638 7.00 C 6100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 34 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 50 " 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: 2.12 Conformation dependent library (CDL) restraints added in 1.0 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 36.4% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 35 through 68 removed outlier: 3.521A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 68 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 102 removed outlier: 3.980A pdb=" N VAL A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix removed outlier: 3.858A pdb=" N SER A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 140 removed outlier: 3.585A pdb=" N LYS A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 128 " --> pdb=" O GLY A 124 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 removed outlier: 3.582A pdb=" N ASN A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.830A pdb=" N PHE A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 203 removed outlier: 3.892A pdb=" N VAL A 201 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.760A pdb=" N HIS A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 232 removed outlier: 3.594A pdb=" N PHE A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 225 " --> pdb=" O CYS A 221 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 226 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 270 removed outlier: 3.692A pdb=" N ILE A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE A 245 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Proline residue: A 257 - end of helix removed outlier: 3.645A pdb=" N THR A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.579A pdb=" N ASN A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 306 removed outlier: 4.476A pdb=" N ILE A 303 " --> pdb=" O CYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.674A pdb=" N HIS A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 33 removed outlier: 4.600A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.676A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 50' Processing helix chain 'B' and resid 207 through 212 removed outlier: 4.273A pdb=" N TRP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.957A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 275' Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.522A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.784A pdb=" N ALA B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 307 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 352 removed outlier: 4.236A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP B 350 " --> pdb=" O ASN B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 26 removed outlier: 4.070A pdb=" N ASN C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.883A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.526A pdb=" N ALA D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 45 removed outlier: 3.842A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.709A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.703A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.895A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 69 removed outlier: 3.517A pdb=" N GLN F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG F 60 " --> pdb=" O ASN F 56 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL F 61 " --> pdb=" O TRP F 57 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU F 63 " --> pdb=" O GLN F 59 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS F 64 " --> pdb=" O ARG F 60 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 186 removed outlier: 3.906A pdb=" N VAL B 185 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.163A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.957A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 103 through 105 removed outlier: 6.378A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 149 through 153 removed outlier: 6.613A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.724A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 201 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 209 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.688A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.507A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.555A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.365A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.622A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.528A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR E 178 " --> pdb=" O ASN E 182 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASN E 182 " --> pdb=" O TYR E 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 146 Processing sheet with id=AB5, first strand: chain 'F' and resid 24 through 28 removed outlier: 4.475A pdb=" N GLU F 24 " --> pdb=" O LYS F 42 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS F 42 " --> pdb=" O GLU F 24 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU F 38 " --> pdb=" O ILE F 28 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 1014 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: 2.38 Time building geometry restraints manager: 2.56 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: 3081 1.34 - 1.46: 2281 1.46 - 1.58: 4289 1.58 - 1.70: 0 1.70 - 1.82: 101 Bond restraints: 9752 Sorted by residual: bond pdb=" CB PRO A 180 " pdb=" CG PRO A 180 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.46e+00 bond pdb=" CA PHE A 174 " pdb=" CB PHE A 174 " ideal model delta sigma weight residual 1.528 1.569 -0.040 2.61e-02 1.47e+03 2.38e+00 bond pdb=" C ASP C 333 " pdb=" N SER C 334 " ideal model delta sigma weight residual 1.332 1.312 0.020 1.40e-02 5.10e+03 2.08e+00 bond pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.41e-02 5.03e+03 1.35e+00 bond pdb=" CA ILE A 139 " pdb=" CB ILE A 139 " ideal model delta sigma weight residual 1.545 1.535 0.010 9.10e-03 1.21e+04 1.32e+00 ... (remaining 9747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 12835 1.35 - 2.70: 285 2.70 - 4.06: 57 4.06 - 5.41: 26 5.41 - 6.76: 6 Bond angle restraints: 13209 Sorted by residual: angle pdb=" N ILE C 270 " pdb=" CA ILE C 270 " pdb=" C ILE C 270 " ideal model delta sigma weight residual 113.71 107.78 5.93 9.50e-01 1.11e+00 3.89e+01 angle pdb=" N ILE C 33 " pdb=" CA ILE C 33 " pdb=" C ILE C 33 " ideal model delta sigma weight residual 113.42 108.77 4.65 1.17e+00 7.31e-01 1.58e+01 angle pdb=" N VAL A 272 " pdb=" CA VAL A 272 " pdb=" C VAL A 272 " ideal model delta sigma weight residual 111.56 108.59 2.97 8.60e-01 1.35e+00 1.19e+01 angle pdb=" C ASP C 118 " pdb=" N ASN C 119 " pdb=" CA ASN C 119 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" C ASP C 333 " pdb=" N SER C 334 " pdb=" CA SER C 334 " ideal model delta sigma weight residual 121.54 115.75 5.79 1.91e+00 2.74e-01 9.19e+00 ... (remaining 13204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 5225 17.54 - 35.08: 479 35.08 - 52.62: 87 52.62 - 70.16: 11 70.16 - 87.69: 7 Dihedral angle restraints: 5809 sinusoidal: 2247 harmonic: 3562 Sorted by residual: dihedral pdb=" CA TYR E 178 " pdb=" C TYR E 178 " pdb=" N ARG E 179 " pdb=" CA ARG E 179 " ideal model delta harmonic sigma weight residual -180.00 -144.01 -35.99 0 5.00e+00 4.00e-02 5.18e+01 dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 152.28 27.72 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual -86.00 -131.34 45.34 1 1.00e+01 1.00e-02 2.85e+01 ... (remaining 5806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 960 0.032 - 0.064: 392 0.064 - 0.096: 89 0.096 - 0.127: 66 0.127 - 0.159: 4 Chirality restraints: 1511 Sorted by residual: chirality pdb=" CA ASN C 119 " pdb=" N ASN C 119 " pdb=" C ASN C 119 " pdb=" CB ASN C 119 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CB THR E 160 " pdb=" CA THR E 160 " pdb=" OG1 THR E 160 " pdb=" CG2 THR E 160 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA TRP C 332 " pdb=" N TRP C 332 " pdb=" C TRP C 332 " pdb=" CB TRP C 332 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 1508 not shown) Planarity restraints: 1665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 179 " 0.070 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 180 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 332 " 0.018 2.00e-02 2.50e+03 1.43e-02 5.11e+00 pdb=" CG TRP C 332 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 332 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 332 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 332 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 332 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 332 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 332 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 332 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 193 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO C 194 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 194 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 194 " 0.027 5.00e-02 4.00e+02 ... (remaining 1662 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 288 2.71 - 3.26: 9590 3.26 - 3.81: 14494 3.81 - 4.35: 18741 4.35 - 4.90: 31644 Nonbonded interactions: 74757 Sorted by model distance: nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.163 3.040 nonbonded pdb=" OE1 GLN E 130 " pdb=" OG1 THR E 231 " model vdw 2.198 3.040 nonbonded pdb=" OG SER E 192 " pdb=" OG1 THR E 203 " model vdw 2.284 3.040 nonbonded pdb=" OH TYR E 101 " pdb=" NE2 HIS E 220 " model vdw 2.292 3.120 nonbonded pdb=" OH TYR C 289 " pdb=" NE1 TRP C 297 " model vdw 2.300 3.120 ... (remaining 74752 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.720 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.390 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 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 0.078 9758 Z= 0.131 Angle : 0.550 6.760 13221 Z= 0.296 Chirality : 0.041 0.159 1511 Planarity : 0.004 0.104 1665 Dihedral : 13.845 87.694 3491 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.24), residues: 1212 helix: 0.04 (0.27), residues: 373 sheet: -1.48 (0.34), residues: 258 loop : -1.49 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 332 HIS 0.006 0.001 HIS B 188 PHE 0.020 0.001 PHE A 174 TYR 0.025 0.001 TYR E 178 ARG 0.004 0.000 ARG C 214 Details of bonding type rmsd hydrogen bonds : bond 0.28947 ( 353) hydrogen bonds : angle 9.10456 ( 1014) SS BOND : bond 0.00145 ( 6) SS BOND : angle 0.96401 ( 12) covalent geometry : bond 0.00304 ( 9752) covalent geometry : angle 0.54995 (13209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: B 53 MET cc_start: 0.6706 (tpp) cc_final: 0.6252 (ttm) REVERT: C 61 MET cc_start: 0.7823 (ppp) cc_final: 0.7478 (ppp) REVERT: E 13 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7871 (mm110) REVERT: E 77 ASN cc_start: 0.7464 (t0) cc_final: 0.7260 (t0) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.2081 time to fit residues: 40.7164 Evaluate side-chains 110 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 271 GLN A 311 ASN B 244 HIS B 331 ASN C 220 GLN C 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.195250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127558 restraints weight = 11242.439| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.32 r_work: 0.3318 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9758 Z= 0.201 Angle : 0.627 6.900 13221 Z= 0.328 Chirality : 0.043 0.140 1511 Planarity : 0.005 0.063 1665 Dihedral : 4.495 33.989 1327 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.88 % Allowed : 9.74 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.24), residues: 1212 helix: 0.64 (0.26), residues: 380 sheet: -1.54 (0.33), residues: 263 loop : -1.36 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 332 HIS 0.006 0.001 HIS B 188 PHE 0.019 0.002 PHE A 174 TYR 0.030 0.002 TYR E 178 ARG 0.004 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.06012 ( 353) hydrogen bonds : angle 5.92089 ( 1014) SS BOND : bond 0.00464 ( 6) SS BOND : angle 1.55463 ( 12) covalent geometry : bond 0.00468 ( 9752) covalent geometry : angle 0.62512 (13209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 268 MET cc_start: 0.7396 (mtm) cc_final: 0.6902 (mtm) REVERT: B 53 MET cc_start: 0.6436 (tpp) cc_final: 0.6234 (ttm) REVERT: C 61 MET cc_start: 0.8550 (ppp) cc_final: 0.8274 (ppp) REVERT: D 42 GLU cc_start: 0.8390 (pp20) cc_final: 0.7944 (mm-30) REVERT: E 13 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7808 (mm110) REVERT: E 221 LEU cc_start: 0.8464 (tt) cc_final: 0.8260 (tt) outliers start: 9 outliers final: 6 residues processed: 128 average time/residue: 0.2150 time to fit residues: 38.7793 Evaluate side-chains 119 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 39 optimal weight: 0.0470 chunk 70 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 104 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN C 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.199516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.134269 restraints weight = 11325.020| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 3.15 r_work: 0.3384 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9758 Z= 0.109 Angle : 0.532 6.343 13221 Z= 0.274 Chirality : 0.040 0.136 1511 Planarity : 0.004 0.052 1665 Dihedral : 4.204 33.207 1327 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.88 % Allowed : 13.15 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.24), residues: 1212 helix: 1.00 (0.27), residues: 380 sheet: -1.45 (0.33), residues: 253 loop : -1.36 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 332 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE A 174 TYR 0.026 0.001 TYR E 178 ARG 0.003 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.04499 ( 353) hydrogen bonds : angle 5.16261 ( 1014) SS BOND : bond 0.00090 ( 6) SS BOND : angle 1.10663 ( 12) covalent geometry : bond 0.00233 ( 9752) covalent geometry : angle 0.53078 (13209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8847 (mp10) cc_final: 0.8575 (mp10) REVERT: C 61 MET cc_start: 0.8423 (ppp) cc_final: 0.8209 (ppp) REVERT: D 42 GLU cc_start: 0.8298 (pp20) cc_final: 0.7913 (mm-30) REVERT: E 13 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7729 (mm110) REVERT: E 18 ARG cc_start: 0.6054 (mtp85) cc_final: 0.5526 (mtp180) REVERT: E 77 ASN cc_start: 0.6753 (t0) cc_final: 0.6325 (t0) outliers start: 9 outliers final: 4 residues processed: 131 average time/residue: 0.2129 time to fit residues: 39.3353 Evaluate side-chains 123 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 0 optimal weight: 70.0000 chunk 45 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.196267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.132154 restraints weight = 11234.950| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.26 r_work: 0.3349 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9758 Z= 0.162 Angle : 0.569 7.818 13221 Z= 0.290 Chirality : 0.042 0.136 1511 Planarity : 0.004 0.052 1665 Dihedral : 4.281 33.063 1327 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.56 % Allowed : 14.51 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.24), residues: 1212 helix: 1.06 (0.27), residues: 380 sheet: -1.36 (0.32), residues: 264 loop : -1.38 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.011 0.001 HIS C 266 PHE 0.013 0.001 PHE A 174 TYR 0.027 0.001 TYR E 178 ARG 0.006 0.000 ARG D 62 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 353) hydrogen bonds : angle 5.01221 ( 1014) SS BOND : bond 0.00110 ( 6) SS BOND : angle 1.23782 ( 12) covalent geometry : bond 0.00378 ( 9752) covalent geometry : angle 0.56778 (13209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 1.061 Fit side-chains REVERT: C 75 GLN cc_start: 0.7909 (pt0) cc_final: 0.7708 (tt0) REVERT: C 220 GLN cc_start: 0.8523 (mt0) cc_final: 0.8094 (mt0) REVERT: C 234 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.6573 (t80) REVERT: D 42 GLU cc_start: 0.8290 (pp20) cc_final: 0.7906 (mm-30) REVERT: E 77 ASN cc_start: 0.6800 (t0) cc_final: 0.6297 (t0) REVERT: E 93 MET cc_start: 0.7801 (ptt) cc_final: 0.7507 (ppp) REVERT: E 160 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7336 (t) outliers start: 16 outliers final: 10 residues processed: 124 average time/residue: 0.2133 time to fit residues: 38.9292 Evaluate side-chains 122 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 25 optimal weight: 30.0000 chunk 114 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 104 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.193684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128481 restraints weight = 11474.055| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 3.50 r_work: 0.3300 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9758 Z= 0.116 Angle : 0.536 7.516 13221 Z= 0.273 Chirality : 0.041 0.145 1511 Planarity : 0.003 0.051 1665 Dihedral : 4.166 32.471 1327 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.85 % Allowed : 15.48 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.24), residues: 1212 helix: 1.17 (0.27), residues: 380 sheet: -1.32 (0.32), residues: 269 loop : -1.35 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 103 HIS 0.003 0.001 HIS B 188 PHE 0.010 0.001 PHE A 174 TYR 0.024 0.001 TYR E 178 ARG 0.005 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 353) hydrogen bonds : angle 4.82308 ( 1014) SS BOND : bond 0.00078 ( 6) SS BOND : angle 1.00965 ( 12) covalent geometry : bond 0.00261 ( 9752) covalent geometry : angle 0.53567 (13209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.997 Fit side-chains REVERT: A 165 MET cc_start: 0.5150 (mmt) cc_final: 0.3814 (mtp) REVERT: A 241 MET cc_start: 0.7755 (ttt) cc_final: 0.7546 (ttt) REVERT: C 220 GLN cc_start: 0.8612 (mt0) cc_final: 0.8180 (mt0) REVERT: C 234 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.6656 (t80) REVERT: D 42 GLU cc_start: 0.8326 (pp20) cc_final: 0.7929 (mm-30) REVERT: E 160 THR cc_start: 0.7667 (OUTLIER) cc_final: 0.7428 (t) outliers start: 19 outliers final: 9 residues processed: 129 average time/residue: 0.2508 time to fit residues: 46.5295 Evaluate side-chains 120 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 38 optimal weight: 0.0470 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 16 optimal weight: 0.2980 overall best weight: 2.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS B 213 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.190918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117933 restraints weight = 11666.102| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 3.28 r_work: 0.3256 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9758 Z= 0.183 Angle : 0.588 7.680 13221 Z= 0.300 Chirality : 0.042 0.138 1511 Planarity : 0.004 0.052 1665 Dihedral : 4.348 32.920 1327 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.14 % Allowed : 16.36 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.24), residues: 1212 helix: 1.06 (0.26), residues: 383 sheet: -1.43 (0.32), residues: 268 loop : -1.43 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.005 0.001 HIS B 188 PHE 0.015 0.001 PHE E 27 TYR 0.026 0.002 TYR E 178 ARG 0.004 0.000 ARG D 62 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 353) hydrogen bonds : angle 4.88743 ( 1014) SS BOND : bond 0.00246 ( 6) SS BOND : angle 1.35867 ( 12) covalent geometry : bond 0.00434 ( 9752) covalent geometry : angle 0.58685 (13209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.086 Fit side-chains REVERT: A 109 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8567 (tp) REVERT: A 165 MET cc_start: 0.4957 (mmt) cc_final: 0.3648 (mtp) REVERT: C 61 MET cc_start: 0.8478 (ppp) cc_final: 0.8254 (ppp) REVERT: C 220 GLN cc_start: 0.8585 (mt0) cc_final: 0.8123 (mt0) REVERT: C 234 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.6547 (t80) REVERT: D 42 GLU cc_start: 0.8365 (pp20) cc_final: 0.7937 (mm-30) REVERT: E 160 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7383 (t) outliers start: 22 outliers final: 13 residues processed: 127 average time/residue: 0.1871 time to fit residues: 34.9907 Evaluate side-chains 126 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 47 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.190618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.123618 restraints weight = 11528.572| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.63 r_work: 0.3261 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9758 Z= 0.161 Angle : 0.579 8.141 13221 Z= 0.295 Chirality : 0.042 0.141 1511 Planarity : 0.004 0.052 1665 Dihedral : 4.337 32.436 1327 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.53 % Allowed : 17.04 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.24), residues: 1212 helix: 1.11 (0.26), residues: 383 sheet: -1.40 (0.32), residues: 266 loop : -1.45 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.005 0.001 HIS B 188 PHE 0.014 0.001 PHE E 27 TYR 0.024 0.001 TYR E 178 ARG 0.003 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 353) hydrogen bonds : angle 4.80725 ( 1014) SS BOND : bond 0.00134 ( 6) SS BOND : angle 1.24776 ( 12) covalent geometry : bond 0.00384 ( 9752) covalent geometry : angle 0.57807 (13209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.098 Fit side-chains REVERT: A 165 MET cc_start: 0.5073 (mmt) cc_final: 0.3764 (mtp) REVERT: C 220 GLN cc_start: 0.8696 (mt0) cc_final: 0.8277 (mt0) REVERT: C 234 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.6533 (t80) REVERT: D 42 GLU cc_start: 0.8371 (pp20) cc_final: 0.7952 (mm-30) REVERT: E 160 THR cc_start: 0.7729 (OUTLIER) cc_final: 0.7525 (t) outliers start: 26 outliers final: 17 residues processed: 129 average time/residue: 0.2604 time to fit residues: 49.8398 Evaluate side-chains 134 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 22 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 119 optimal weight: 50.0000 chunk 52 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.191441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126826 restraints weight = 11400.811| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.14 r_work: 0.3319 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9758 Z= 0.115 Angle : 0.551 8.163 13221 Z= 0.280 Chirality : 0.041 0.160 1511 Planarity : 0.003 0.052 1665 Dihedral : 4.243 32.498 1327 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.04 % Allowed : 17.82 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.24), residues: 1212 helix: 1.23 (0.27), residues: 383 sheet: -1.30 (0.32), residues: 264 loop : -1.45 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 103 HIS 0.004 0.001 HIS B 188 PHE 0.011 0.001 PHE E 29 TYR 0.022 0.001 TYR E 178 ARG 0.003 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 353) hydrogen bonds : angle 4.72236 ( 1014) SS BOND : bond 0.00065 ( 6) SS BOND : angle 1.04455 ( 12) covalent geometry : bond 0.00261 ( 9752) covalent geometry : angle 0.55001 (13209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 1.153 Fit side-chains REVERT: A 165 MET cc_start: 0.5049 (mmt) cc_final: 0.3706 (mtp) REVERT: A 271 GLN cc_start: 0.8866 (mp10) cc_final: 0.8627 (mp10) REVERT: C 75 GLN cc_start: 0.7788 (mt0) cc_final: 0.7312 (mm-40) REVERT: C 188 MET cc_start: 0.7231 (mtt) cc_final: 0.6970 (mtt) REVERT: C 191 SER cc_start: 0.7988 (t) cc_final: 0.7747 (p) REVERT: C 220 GLN cc_start: 0.8666 (mt0) cc_final: 0.8219 (mt0) REVERT: C 234 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.6672 (t80) REVERT: D 42 GLU cc_start: 0.8356 (pp20) cc_final: 0.7933 (mm-30) REVERT: E 218 MET cc_start: 0.7706 (ttt) cc_final: 0.7501 (ttt) outliers start: 21 outliers final: 17 residues processed: 128 average time/residue: 0.2272 time to fit residues: 42.2166 Evaluate side-chains 131 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 45 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 57 optimal weight: 0.1980 chunk 29 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 84 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 183 HIS ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.188678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117228 restraints weight = 11661.597| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.15 r_work: 0.3259 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9758 Z= 0.204 Angle : 0.623 8.315 13221 Z= 0.316 Chirality : 0.043 0.154 1511 Planarity : 0.004 0.052 1665 Dihedral : 4.461 32.901 1327 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.24 % Allowed : 18.21 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.24), residues: 1212 helix: 1.10 (0.27), residues: 383 sheet: -1.62 (0.31), residues: 277 loop : -1.45 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.006 0.001 HIS B 188 PHE 0.017 0.002 PHE E 27 TYR 0.027 0.002 TYR E 178 ARG 0.003 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 353) hydrogen bonds : angle 4.89983 ( 1014) SS BOND : bond 0.00146 ( 6) SS BOND : angle 1.26410 ( 12) covalent geometry : bond 0.00491 ( 9752) covalent geometry : angle 0.62170 (13209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.981 Fit side-chains REVERT: A 165 MET cc_start: 0.4992 (mmt) cc_final: 0.3676 (mtp) REVERT: A 271 GLN cc_start: 0.8805 (mp10) cc_final: 0.8602 (mp10) REVERT: C 117 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8075 (tp) REVERT: C 188 MET cc_start: 0.7315 (mtt) cc_final: 0.6531 (mtt) REVERT: C 220 GLN cc_start: 0.8672 (mt0) cc_final: 0.8366 (mt0) REVERT: C 234 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.6489 (t80) REVERT: D 42 GLU cc_start: 0.8395 (pp20) cc_final: 0.7930 (mm-30) REVERT: E 160 THR cc_start: 0.7711 (OUTLIER) cc_final: 0.7479 (t) REVERT: E 218 MET cc_start: 0.7989 (ttt) cc_final: 0.7737 (ttt) outliers start: 23 outliers final: 17 residues processed: 127 average time/residue: 0.1908 time to fit residues: 35.3209 Evaluate side-chains 130 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 95 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 118 optimal weight: 30.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.190800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123605 restraints weight = 11627.958| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.45 r_work: 0.3256 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9758 Z= 0.169 Angle : 0.606 8.991 13221 Z= 0.307 Chirality : 0.042 0.151 1511 Planarity : 0.004 0.052 1665 Dihedral : 4.417 32.764 1327 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.04 % Allowed : 18.79 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.24), residues: 1212 helix: 1.14 (0.27), residues: 383 sheet: -1.65 (0.31), residues: 272 loop : -1.50 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.005 0.001 HIS B 188 PHE 0.014 0.001 PHE A 121 TYR 0.025 0.001 TYR E 178 ARG 0.003 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 353) hydrogen bonds : angle 4.85199 ( 1014) SS BOND : bond 0.00119 ( 6) SS BOND : angle 1.17819 ( 12) covalent geometry : bond 0.00402 ( 9752) covalent geometry : angle 0.60559 (13209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.021 Fit side-chains REVERT: A 165 MET cc_start: 0.5101 (mmt) cc_final: 0.3787 (mtp) REVERT: B 247 MET cc_start: 0.7859 (mmm) cc_final: 0.7572 (mmm) REVERT: C 188 MET cc_start: 0.7350 (mtt) cc_final: 0.6570 (mtt) REVERT: C 191 SER cc_start: 0.8030 (t) cc_final: 0.7776 (p) REVERT: C 220 GLN cc_start: 0.8692 (mt0) cc_final: 0.8401 (mt0) REVERT: C 234 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.6651 (t80) REVERT: D 42 GLU cc_start: 0.8375 (pp20) cc_final: 0.7907 (mm-30) REVERT: E 160 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7543 (t) outliers start: 21 outliers final: 17 residues processed: 127 average time/residue: 0.1905 time to fit residues: 35.2416 Evaluate side-chains 133 residues out of total 1059 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain F residue 41 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 2 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 50 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.0270 chunk 118 optimal weight: 40.0000 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 183 HIS ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.191835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124910 restraints weight = 11561.308| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.32 r_work: 0.3284 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9758 Z= 0.127 Angle : 0.583 9.328 13221 Z= 0.296 Chirality : 0.041 0.149 1511 Planarity : 0.003 0.052 1665 Dihedral : 4.285 32.787 1327 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.85 % Allowed : 18.79 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.24), residues: 1212 helix: 1.24 (0.27), residues: 383 sheet: -1.63 (0.31), residues: 277 loop : -1.49 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 47 HIS 0.004 0.001 HIS B 188 PHE 0.011 0.001 PHE E 29 TYR 0.023 0.001 TYR E 178 ARG 0.002 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 353) hydrogen bonds : angle 4.73988 ( 1014) SS BOND : bond 0.00100 ( 6) SS BOND : angle 1.01084 ( 12) covalent geometry : bond 0.00296 ( 9752) covalent geometry : angle 0.58230 (13209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5179.11 seconds wall clock time: 90 minutes 47.61 seconds (5447.61 seconds total)