Starting phenix.real_space_refine on Wed Nov 15 17:18:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8at6_15635/11_2023/8at6_15635.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8at6_15635/11_2023/8at6_15635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8at6_15635/11_2023/8at6_15635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8at6_15635/11_2023/8at6_15635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8at6_15635/11_2023/8at6_15635.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8at6_15635/11_2023/8at6_15635.pdb" } resolution = 3.7 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= 0.000 sd= 0.002 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 49 5.16 5 C 8040 2.51 5 N 2112 2.21 5 O 2382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 391": "OD1" <-> "OD2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "F TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 256": "OE1" <-> "OE2" Residue "F TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 266": "OE1" <-> "OE2" Residue "F PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 12583 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2284 Classifications: {'peptide': 288} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 269} Chain breaks: 1 Chain: "B" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1842 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 9, 'TRANS': 217} Chain: "C" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2154 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "D" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2313 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 273} Chain breaks: 1 Chain: "E" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1848 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain: "F" Number of atoms: 2142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2142 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 259} Time building chain proxies: 7.26, per 1000 atoms: 0.58 Number of scatterers: 12583 At special positions: 0 Unit cell: (80.3, 115.5, 144.1, 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 49 16.00 O 2382 8.00 N 2112 7.00 C 8040 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 6.06 Conformation dependent library (CDL) restraints added in 2.4 seconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 34.4% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 removed outlier: 3.616A pdb=" N GLY A 98 " --> pdb=" O ASP A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 removed outlier: 3.714A pdb=" N LEU A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 removed outlier: 3.763A pdb=" N LEU A 164 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 303 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'B' and resid 7 through 17 removed outlier: 3.771A pdb=" N LEU B 11 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 79 through 90 removed outlier: 3.531A pdb=" N TYR B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 116 through 122 Processing helix chain 'B' and resid 156 through 165 Processing helix chain 'B' and resid 180 through 190 Processing helix chain 'C' and resid 19 through 23 removed outlier: 4.104A pdb=" N PHE C 22 " --> pdb=" O PRO C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 55 Processing helix chain 'C' and resid 85 through 95 removed outlier: 3.768A pdb=" N PHE C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 117 Processing helix chain 'C' and resid 121 through 140 removed outlier: 3.841A pdb=" N ALA C 136 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C 137 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 162 through 170 Processing helix chain 'C' and resid 170 through 177 removed outlier: 3.695A pdb=" N GLN C 177 " --> pdb=" O PRO C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 removed outlier: 4.127A pdb=" N ILE C 192 " --> pdb=" O ILE C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 removed outlier: 4.214A pdb=" N HIS C 200 " --> pdb=" O ASP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.731A pdb=" N GLN C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE C 207 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 97 Processing helix chain 'D' and resid 118 through 140 removed outlier: 4.000A pdb=" N LEU D 122 " --> pdb=" O PHE D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 163 removed outlier: 3.697A pdb=" N ALA D 161 " --> pdb=" O GLN D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 279 removed outlier: 3.559A pdb=" N ASN D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 302 Processing helix chain 'D' and resid 303 through 321 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 358 through 370 Processing helix chain 'E' and resid 7 through 17 Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 116 through 125 Processing helix chain 'E' and resid 156 through 165 Processing helix chain 'E' and resid 180 through 190 Processing helix chain 'F' and resid 20 through 25 removed outlier: 3.734A pdb=" N GLN F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 56 removed outlier: 3.606A pdb=" N ILE F 46 " --> pdb=" O PRO F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 94 Processing helix chain 'F' and resid 111 through 117 Processing helix chain 'F' and resid 121 through 139 removed outlier: 3.941A pdb=" N ASN F 139 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 158 Processing helix chain 'F' and resid 162 through 170 Processing helix chain 'F' and resid 170 through 177 removed outlier: 3.522A pdb=" N GLN F 177 " --> pdb=" O PRO F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 214 removed outlier: 4.106A pdb=" N PHE F 207 " --> pdb=" O ASN F 203 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR F 208 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 259 removed outlier: 3.892A pdb=" N SER A 290 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A 108 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE A 331 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL A 110 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ILE A 352 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 109 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU A 354 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL A 351 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 384 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 379 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TRP A 402 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N ILE A 383 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N SER A 400 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N LYS A 385 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N LEU A 398 " --> pdb=" O LYS A 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 74 removed outlier: 6.345A pdb=" N VAL B 56 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B 104 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR B 134 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE B 106 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N HIS B 136 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE B 24 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL B 169 " --> pdb=" O PHE B 24 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU B 26 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE B 171 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU B 28 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N VAL B 173 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP B 172 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ARG B 210 " --> pdb=" O ARG B 214 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ARG B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 103 through 107 removed outlier: 3.955A pdb=" N SER C 81 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N HIS C 76 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE C 147 " --> pdb=" O HIS C 76 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL C 78 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N GLU C 149 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA C 80 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL C 180 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C 31 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LEU C 219 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE C 33 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N LEU C 221 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR C 35 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 264 Processing sheet with id=AA6, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AA7, first strand: chain 'D' and resid 256 through 259 removed outlier: 6.498A pdb=" N VAL D 326 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL D 287 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE D 328 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N SER D 330 " --> pdb=" O PRO D 289 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER D 332 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE D 331 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU D 109 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU D 354 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N GLU D 111 " --> pdb=" O LEU D 354 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL D 351 " --> pdb=" O LEU D 384 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 384 " --> pdb=" O VAL D 351 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY D 379 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TRP D 402 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 165 through 167 removed outlier: 3.550A pdb=" N GLY D 166 " --> pdb=" O ASP D 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 71 through 74 removed outlier: 3.551A pdb=" N GLN E 71 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL E 56 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N HIS E 102 " --> pdb=" O THR E 130 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL E 132 " --> pdb=" O HIS E 102 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL E 104 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N THR E 134 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE E 106 " --> pdb=" O THR E 134 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N HIS E 136 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE E 25 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR E 135 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N CYS E 27 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR E 167 " --> pdb=" O PHE E 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 103 through 107 removed outlier: 4.028A pdb=" N SER F 81 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N HIS F 76 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ILE F 147 " --> pdb=" O HIS F 76 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL F 78 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLU F 149 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ALA F 80 " --> pdb=" O GLU F 149 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR F 144 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ILE F 182 " --> pdb=" O THR F 144 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL F 146 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL F 184 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE F 148 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N ASN F 186 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN F 30 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE F 183 " --> pdb=" O ASN F 30 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE F 32 " --> pdb=" O ILE F 183 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N SER F 185 " --> pdb=" O PHE F 32 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE F 34 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE F 217 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE F 33 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER F 267 " --> pdb=" O GLU F 264 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 6.45 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: 4074 1.34 - 1.46: 2820 1.46 - 1.58: 5872 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 12850 Sorted by residual: bond pdb=" CA SER F 65 " pdb=" C SER F 65 " ideal model delta sigma weight residual 1.523 1.501 0.022 1.41e-02 5.03e+03 2.44e+00 bond pdb=" N SER D 114 " pdb=" CA SER D 114 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.80e+00 bond pdb=" CA THR D 115 " pdb=" C THR D 115 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.34e-02 5.57e+03 1.66e+00 bond pdb=" CA ASN E 110 " pdb=" C ASN E 110 " ideal model delta sigma weight residual 1.523 1.505 0.018 1.41e-02 5.03e+03 1.60e+00 bond pdb=" CB GLN A 274 " pdb=" CG GLN A 274 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.43e+00 ... (remaining 12845 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.91: 290 105.91 - 112.94: 7197 112.94 - 119.96: 4149 119.96 - 126.99: 5669 126.99 - 134.02: 137 Bond angle restraints: 17442 Sorted by residual: angle pdb=" CA ARG F 74 " pdb=" CB ARG F 74 " pdb=" CG ARG F 74 " ideal model delta sigma weight residual 114.10 122.86 -8.76 2.00e+00 2.50e-01 1.92e+01 angle pdb=" N SER D 114 " pdb=" CA SER D 114 " pdb=" C SER D 114 " ideal model delta sigma weight residual 110.80 120.13 -9.33 2.13e+00 2.20e-01 1.92e+01 angle pdb=" CB MET C 45 " pdb=" CG MET C 45 " pdb=" SD MET C 45 " ideal model delta sigma weight residual 112.70 124.96 -12.26 3.00e+00 1.11e-01 1.67e+01 angle pdb=" N THR D 115 " pdb=" CA THR D 115 " pdb=" C THR D 115 " ideal model delta sigma weight residual 110.80 117.98 -7.18 2.13e+00 2.20e-01 1.14e+01 angle pdb=" CA LEU E 18 " pdb=" CB LEU E 18 " pdb=" CG LEU E 18 " ideal model delta sigma weight residual 116.30 128.05 -11.75 3.50e+00 8.16e-02 1.13e+01 ... (remaining 17437 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6800 17.81 - 35.63: 802 35.63 - 53.44: 158 53.44 - 71.25: 37 71.25 - 89.07: 17 Dihedral angle restraints: 7814 sinusoidal: 3142 harmonic: 4672 Sorted by residual: dihedral pdb=" CA ASP E 149 " pdb=" C ASP E 149 " pdb=" N TRP E 150 " pdb=" CA TRP E 150 " ideal model delta harmonic sigma weight residual 180.00 -156.00 -24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA PRO A 387 " pdb=" C PRO A 387 " pdb=" N VAL A 388 " pdb=" CA VAL A 388 " ideal model delta harmonic sigma weight residual 180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA HIS F 84 " pdb=" C HIS F 84 " pdb=" N GLU F 85 " pdb=" CA GLU F 85 " ideal model delta harmonic sigma weight residual -180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 7811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1430 0.038 - 0.077: 426 0.077 - 0.115: 152 0.115 - 0.154: 25 0.154 - 0.192: 5 Chirality restraints: 2038 Sorted by residual: chirality pdb=" CG LEU F 157 " pdb=" CB LEU F 157 " pdb=" CD1 LEU F 157 " pdb=" CD2 LEU F 157 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.23e-01 chirality pdb=" CA ILE A 352 " pdb=" N ILE A 352 " pdb=" C ILE A 352 " pdb=" CB ILE A 352 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CG LEU E 161 " pdb=" CB LEU E 161 " pdb=" CD1 LEU E 161 " pdb=" CD2 LEU E 161 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 2035 not shown) Planarity restraints: 2221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 386 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.83e+00 pdb=" N PRO A 387 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 147 " 0.033 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 148 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 148 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 148 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 386 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO D 387 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 387 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 387 " -0.028 5.00e-02 4.00e+02 ... (remaining 2218 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2039 2.76 - 3.29: 12461 3.29 - 3.83: 20324 3.83 - 4.36: 23167 4.36 - 4.90: 40328 Nonbonded interactions: 98319 Sorted by model distance: nonbonded pdb=" OE2 GLU A 112 " pdb=" OG1 THR A 116 " model vdw 2.222 2.440 nonbonded pdb=" N GLU F 85 " pdb=" OE1 GLU F 85 " model vdw 2.223 2.520 nonbonded pdb=" NH2 ARG C 74 " pdb=" O THR C 142 " model vdw 2.234 2.520 nonbonded pdb=" O GLY A 374 " pdb=" NZ LYS A 405 " model vdw 2.241 2.520 nonbonded pdb=" O PRO C 223 " pdb=" NH2 ARG E 192 " model vdw 2.244 2.520 ... (remaining 98314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'D' and (resid 66 through 169 or resid 233 through 416)) } ncs_group { reference = chain 'B' selection = (chain 'E' and resid 6 through 232) } ncs_group { reference = (chain 'C' and resid 3 through 273) selection = chain 'F' } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 7.160 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 37.090 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 0.037 12850 Z= 0.222 Angle : 0.641 12.260 17442 Z= 0.356 Chirality : 0.043 0.192 2038 Planarity : 0.004 0.055 2221 Dihedral : 16.248 89.068 4764 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.88 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 20.74 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1564 helix: 1.45 (0.25), residues: 483 sheet: 1.25 (0.30), residues: 350 loop : -0.95 (0.24), residues: 731 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.582 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2579 time to fit residues: 37.6937 Evaluate side-chains 96 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12850 Z= 0.179 Angle : 0.514 10.505 17442 Z= 0.270 Chirality : 0.042 0.183 2038 Planarity : 0.004 0.055 2221 Dihedral : 4.332 41.564 1678 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.69 % Favored : 94.18 % Rotamer: Outliers : 2.12 % Allowed : 19.37 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.23), residues: 1564 helix: 1.61 (0.25), residues: 494 sheet: 1.47 (0.30), residues: 349 loop : -0.94 (0.25), residues: 721 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 1.656 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 19 residues processed: 123 average time/residue: 0.2387 time to fit residues: 44.3746 Evaluate side-chains 113 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 1.592 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1176 time to fit residues: 6.0605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 141 optimal weight: 0.4980 chunk 152 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 113 optimal weight: 0.0670 overall best weight: 0.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12850 Z= 0.153 Angle : 0.496 11.549 17442 Z= 0.259 Chirality : 0.041 0.181 2038 Planarity : 0.004 0.054 2221 Dihedral : 4.247 40.866 1678 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.63 % Favored : 94.25 % Rotamer: Outliers : 1.30 % Allowed : 19.58 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.23), residues: 1564 helix: 1.69 (0.25), residues: 494 sheet: 1.61 (0.30), residues: 349 loop : -0.90 (0.25), residues: 721 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 1.522 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 113 average time/residue: 0.2521 time to fit residues: 42.7603 Evaluate side-chains 94 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 1.570 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1241 time to fit residues: 3.9821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 0.0670 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12850 Z= 0.175 Angle : 0.500 11.408 17442 Z= 0.260 Chirality : 0.042 0.183 2038 Planarity : 0.004 0.055 2221 Dihedral : 4.291 42.230 1678 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.88 % Favored : 94.05 % Rotamer: Outliers : 1.51 % Allowed : 19.85 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1564 helix: 1.68 (0.25), residues: 494 sheet: 1.70 (0.31), residues: 346 loop : -0.89 (0.25), residues: 724 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 1.544 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 108 average time/residue: 0.2373 time to fit residues: 38.7388 Evaluate side-chains 103 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 1.507 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1172 time to fit residues: 5.2694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 0.0030 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12850 Z= 0.274 Angle : 0.551 10.007 17442 Z= 0.288 Chirality : 0.043 0.206 2038 Planarity : 0.004 0.055 2221 Dihedral : 4.566 43.654 1678 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.65 % Favored : 93.09 % Rotamer: Outliers : 1.23 % Allowed : 20.60 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1564 helix: 1.56 (0.25), residues: 494 sheet: 1.52 (0.30), residues: 353 loop : -0.98 (0.24), residues: 717 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 1.576 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 102 average time/residue: 0.2452 time to fit residues: 38.1529 Evaluate side-chains 88 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 1.680 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1291 time to fit residues: 3.8631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 0.4980 chunk 149 optimal weight: 0.6980 chunk 124 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12850 Z= 0.146 Angle : 0.507 12.398 17442 Z= 0.262 Chirality : 0.042 0.207 2038 Planarity : 0.004 0.055 2221 Dihedral : 4.370 43.066 1678 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.43 % Favored : 94.37 % Rotamer: Outliers : 1.03 % Allowed : 21.70 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.23), residues: 1564 helix: 1.70 (0.25), residues: 492 sheet: 1.63 (0.31), residues: 352 loop : -0.90 (0.25), residues: 720 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 102 average time/residue: 0.2526 time to fit residues: 38.8985 Evaluate side-chains 90 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1138 time to fit residues: 3.1586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 109 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 0.1980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12850 Z= 0.204 Angle : 0.528 12.049 17442 Z= 0.274 Chirality : 0.042 0.186 2038 Planarity : 0.004 0.055 2221 Dihedral : 4.424 43.442 1678 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.93 % Rotamer: Outliers : 0.75 % Allowed : 22.45 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.23), residues: 1564 helix: 1.61 (0.25), residues: 494 sheet: 1.60 (0.31), residues: 352 loop : -0.92 (0.25), residues: 718 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 96 average time/residue: 0.2613 time to fit residues: 37.7376 Evaluate side-chains 90 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 1.675 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1188 time to fit residues: 2.9196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12850 Z= 0.253 Angle : 0.560 12.257 17442 Z= 0.290 Chirality : 0.043 0.173 2038 Planarity : 0.004 0.056 2221 Dihedral : 4.598 45.608 1678 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.33 % Favored : 93.41 % Rotamer: Outliers : 1.10 % Allowed : 22.45 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.23), residues: 1564 helix: 1.55 (0.25), residues: 494 sheet: 1.46 (0.30), residues: 364 loop : -0.99 (0.25), residues: 706 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 98 average time/residue: 0.2442 time to fit residues: 36.0957 Evaluate side-chains 90 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.514 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1120 time to fit residues: 3.6938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 139 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 ASN D 83 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12850 Z= 0.159 Angle : 0.531 13.163 17442 Z= 0.272 Chirality : 0.042 0.198 2038 Planarity : 0.004 0.055 2221 Dihedral : 4.439 48.937 1678 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.69 % Favored : 94.05 % Rotamer: Outliers : 0.34 % Allowed : 23.27 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.23), residues: 1564 helix: 1.65 (0.25), residues: 493 sheet: 1.55 (0.31), residues: 354 loop : -0.93 (0.25), residues: 717 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 93 average time/residue: 0.2520 time to fit residues: 35.7467 Evaluate side-chains 89 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 1.645 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1203 time to fit residues: 2.6358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.0570 chunk 89 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 94 optimal weight: 0.9980 chunk 75 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN A 359 GLN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12850 Z= 0.128 Angle : 0.521 13.349 17442 Z= 0.263 Chirality : 0.042 0.168 2038 Planarity : 0.004 0.054 2221 Dihedral : 4.176 45.521 1678 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.43 % Favored : 94.50 % Rotamer: Outliers : 0.21 % Allowed : 23.48 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.23), residues: 1564 helix: 1.67 (0.25), residues: 499 sheet: 1.85 (0.31), residues: 343 loop : -1.00 (0.24), residues: 722 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 100 average time/residue: 0.2352 time to fit residues: 36.4399 Evaluate side-chains 94 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.458 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1249 time to fit residues: 2.4131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 113 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 123 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.070135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.056310 restraints weight = 47106.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.058039 restraints weight = 26494.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.058983 restraints weight = 18406.766| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12850 Z= 0.146 Angle : 0.518 12.650 17442 Z= 0.262 Chirality : 0.041 0.187 2038 Planarity : 0.004 0.054 2221 Dihedral : 4.164 44.118 1678 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.43 % Favored : 94.44 % Rotamer: Outliers : 0.07 % Allowed : 23.68 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1564 helix: 1.76 (0.25), residues: 493 sheet: 1.90 (0.31), residues: 342 loop : -0.90 (0.24), residues: 729 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2169.94 seconds wall clock time: 40 minutes 50.40 seconds (2450.40 seconds total)