Starting phenix.real_space_refine on Thu Feb 15 14:47:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8at6_15635/02_2024/8at6_15635.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8at6_15635/02_2024/8at6_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_15635/02_2024/8at6_15635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8at6_15635/02_2024/8at6_15635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8at6_15635/02_2024/8at6_15635.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8at6_15635/02_2024/8at6_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 6.79, per 1000 atoms: 0.54 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: 4.87 Conformation dependent library (CDL) restraints added in 2.3 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: 1.24 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: 3.40 Time building geometry restraints manager: 5.27 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: 1.720 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: 7.130 Check model and map are aligned: 0.210 Set scattering table: 0.100 Process input model: 34.670 Find NCS groups from input model: 0.760 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.450 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 44 HIS 0.003 0.001 HIS A 312 PHE 0.012 0.001 PHE C 32 TYR 0.023 0.001 TYR F 103 ARG 0.004 0.000 ARG F 74 *********************** 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 : 1.630 Fit side-chains revert: symmetry clash REVERT: B 86 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7849 (tm-30) REVERT: C 1 MET cc_start: 0.6978 (tpp) cc_final: 0.6716 (tpt) REVERT: E 214 ARG cc_start: 0.8152 (tpp80) cc_final: 0.7926 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2571 time to fit residues: 37.5579 Evaluate side-chains 96 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12850 Z= 0.178 Angle : 0.513 10.392 17442 Z= 0.270 Chirality : 0.042 0.167 2038 Planarity : 0.004 0.055 2221 Dihedral : 4.362 45.352 1678 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.75 % Favored : 94.12 % Rotamer: Outliers : 2.05 % Allowed : 19.44 % 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: 0.68 (0.23), residues: 1564 helix: 1.63 (0.25), residues: 494 sheet: 1.48 (0.30), residues: 349 loop : -0.94 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 402 HIS 0.003 0.001 HIS A 312 PHE 0.009 0.001 PHE C 228 TYR 0.021 0.001 TYR C 88 ARG 0.005 0.000 ARG F 74 *********************** 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: 30 poor density : 100 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.6944 (tpp) cc_final: 0.6571 (tpt) REVERT: E 78 MET cc_start: 0.8135 (ppp) cc_final: 0.7802 (ppp) outliers start: 30 outliers final: 17 residues processed: 124 average time/residue: 0.2344 time to fit residues: 43.6484 Evaluate side-chains 110 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 255 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 0.0170 chunk 43 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 141 optimal weight: 0.0370 chunk 152 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 48 optimal weight: 0.0370 chunk 113 optimal weight: 3.9990 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN F 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12850 Z= 0.120 Angle : 0.484 12.155 17442 Z= 0.251 Chirality : 0.042 0.180 2038 Planarity : 0.004 0.055 2221 Dihedral : 4.118 43.768 1678 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.31 % Favored : 94.57 % Rotamer: Outliers : 1.64 % Allowed : 19.78 % Favored : 78.58 % 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: 0.86 (0.23), residues: 1564 helix: 1.79 (0.25), residues: 495 sheet: 1.73 (0.30), residues: 348 loop : -0.95 (0.25), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 402 HIS 0.003 0.000 HIS F 36 PHE 0.009 0.001 PHE D 348 TYR 0.017 0.001 TYR C 88 ARG 0.003 0.000 ARG C 74 *********************** 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 129 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 1.510 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.6804 (tpp) cc_final: 0.6443 (tpt) REVERT: D 276 ILE cc_start: 0.9073 (mm) cc_final: 0.8870 (mm) REVERT: E 78 MET cc_start: 0.8292 (ppp) cc_final: 0.7755 (ppp) REVERT: E 230 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7059 (tm-30) outliers start: 24 outliers final: 13 residues processed: 125 average time/residue: 0.2393 time to fit residues: 44.4265 Evaluate side-chains 105 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 133 HIS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 199 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 0.0010 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 141 optimal weight: 0.0970 chunk 149 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1153 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= 0.124 Angle : 0.467 11.376 17442 Z= 0.243 Chirality : 0.041 0.160 2038 Planarity : 0.004 0.055 2221 Dihedral : 4.052 43.463 1678 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.18 % Favored : 94.69 % Rotamer: Outliers : 2.12 % Allowed : 19.71 % 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: 0.92 (0.23), residues: 1564 helix: 1.79 (0.25), residues: 497 sheet: 1.78 (0.31), residues: 349 loop : -0.89 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 44 HIS 0.003 0.000 HIS F 36 PHE 0.017 0.001 PHE E 72 TYR 0.017 0.001 TYR C 88 ARG 0.002 0.000 ARG E 214 *********************** 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 125 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.6860 (tpp) cc_final: 0.6481 (tpt) REVERT: D 276 ILE cc_start: 0.9082 (mm) cc_final: 0.8881 (mm) REVERT: E 78 MET cc_start: 0.8262 (ppp) cc_final: 0.7836 (ppp) REVERT: E 230 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6977 (tm-30) outliers start: 31 outliers final: 22 residues processed: 119 average time/residue: 0.2287 time to fit residues: 41.3715 Evaluate side-chains 115 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 255 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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: 0.8482 moved from start: 0.1036 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 : 0.530 10.181 17442 Z= 0.278 Chirality : 0.042 0.165 2038 Planarity : 0.004 0.055 2221 Dihedral : 4.395 43.882 1678 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.14 % Favored : 93.61 % Rotamer: Outliers : 2.87 % Allowed : 19.64 % Favored : 77.48 % 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: 1.64 (0.25), residues: 494 sheet: 1.68 (0.30), residues: 347 loop : -0.90 (0.25), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 44 HIS 0.004 0.001 HIS A 312 PHE 0.015 0.001 PHE E 72 TYR 0.021 0.001 TYR C 88 ARG 0.002 0.000 ARG E 210 *********************** 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 126 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 84 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6976 (tpp) cc_final: 0.6557 (tpt) REVERT: C 216 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.7657 (ppp) REVERT: E 78 MET cc_start: 0.8167 (ppp) cc_final: 0.7697 (ppp) outliers start: 42 outliers final: 31 residues processed: 117 average time/residue: 0.2225 time to fit residues: 39.6591 Evaluate side-chains 114 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 82 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 133 HIS Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 255 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 0.0670 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- 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: 0.8474 moved from start: 0.1116 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= 0.212 Angle : 0.513 11.509 17442 Z= 0.268 Chirality : 0.042 0.156 2038 Planarity : 0.004 0.055 2221 Dihedral : 4.398 46.050 1678 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.69 % Favored : 94.05 % Rotamer: Outliers : 3.01 % Allowed : 20.26 % Favored : 76.73 % 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: 1.69 (0.25), residues: 492 sheet: 1.67 (0.31), residues: 350 loop : -0.90 (0.25), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 416 HIS 0.004 0.001 HIS A 312 PHE 0.014 0.001 PHE E 72 TYR 0.020 0.001 TYR C 88 ARG 0.003 0.000 ARG E 214 *********************** 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 131 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 87 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7018 (tpp) cc_final: 0.6590 (tpt) REVERT: C 216 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7647 (ppp) REVERT: D 276 ILE cc_start: 0.9084 (mm) cc_final: 0.8879 (mm) REVERT: E 78 MET cc_start: 0.8210 (ppp) cc_final: 0.7885 (ppp) outliers start: 44 outliers final: 34 residues processed: 120 average time/residue: 0.2445 time to fit residues: 44.6667 Evaluate side-chains 119 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 84 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 133 HIS Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 255 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 93 optimal weight: 0.0000 chunk 91 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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: 0.8449 moved from start: 0.1208 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= 0.147 Angle : 0.498 12.646 17442 Z= 0.258 Chirality : 0.041 0.155 2038 Planarity : 0.004 0.054 2221 Dihedral : 4.271 44.972 1678 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.69 % Favored : 94.18 % Rotamer: Outliers : 2.33 % Allowed : 20.88 % 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: 0.84 (0.23), residues: 1564 helix: 1.68 (0.25), residues: 498 sheet: 1.75 (0.31), residues: 350 loop : -0.91 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 44 HIS 0.003 0.001 HIS F 36 PHE 0.013 0.001 PHE E 72 TYR 0.017 0.001 TYR C 88 ARG 0.002 0.000 ARG E 214 *********************** 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 122 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 88 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7000 (tpp) cc_final: 0.6547 (tpt) REVERT: C 216 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7651 (ppp) REVERT: E 78 MET cc_start: 0.8237 (ppp) cc_final: 0.7861 (ppp) outliers start: 34 outliers final: 29 residues processed: 113 average time/residue: 0.2525 time to fit residues: 43.4651 Evaluate side-chains 116 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 86 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 133 HIS Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 255 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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: 0.8483 moved from start: 0.1212 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= 0.245 Angle : 0.541 12.484 17442 Z= 0.280 Chirality : 0.042 0.155 2038 Planarity : 0.004 0.055 2221 Dihedral : 4.451 44.086 1678 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.27 % Favored : 93.48 % Rotamer: Outliers : 3.01 % Allowed : 20.67 % 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: 0.78 (0.23), residues: 1564 helix: 1.64 (0.25), residues: 494 sheet: 1.58 (0.30), residues: 362 loop : -0.91 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.004 0.001 HIS A 312 PHE 0.013 0.001 PHE E 72 TYR 0.021 0.001 TYR C 88 ARG 0.008 0.000 ARG E 214 *********************** 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 129 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 85 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.7121 (tpp) cc_final: 0.6671 (tpt) REVERT: C 216 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7659 (ppp) REVERT: D 83 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8138 (pt0) REVERT: E 78 MET cc_start: 0.8233 (ppp) cc_final: 0.7813 (ppp) outliers start: 44 outliers final: 33 residues processed: 120 average time/residue: 0.2247 time to fit residues: 41.1151 Evaluate side-chains 123 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 229 TYR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 133 HIS Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain F residue 255 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 0.0270 chunk 125 optimal weight: 3.9990 chunk 131 optimal weight: 0.0040 chunk 138 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 0.5250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 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: 0.8440 moved from start: 0.1335 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= 0.136 Angle : 0.501 13.089 17442 Z= 0.258 Chirality : 0.041 0.155 2038 Planarity : 0.004 0.055 2221 Dihedral : 4.233 44.176 1678 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.31 % Favored : 94.63 % Rotamer: Outliers : 1.92 % Allowed : 22.04 % Favored : 76.04 % 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: 0.83 (0.23), residues: 1564 helix: 1.68 (0.25), residues: 500 sheet: 1.68 (0.31), residues: 354 loop : -0.91 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 44 HIS 0.003 0.001 HIS F 36 PHE 0.013 0.001 PHE E 72 TYR 0.016 0.001 TYR C 88 ARG 0.006 0.000 ARG E 214 *********************** 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 123 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.6977 (tpp) cc_final: 0.6581 (tpt) REVERT: C 216 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7644 (ppp) REVERT: E 78 MET cc_start: 0.8276 (ppp) cc_final: 0.7857 (ppp) outliers start: 28 outliers final: 24 residues processed: 114 average time/residue: 0.2236 time to fit residues: 39.2564 Evaluate side-chains 115 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 133 HIS Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 255 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 12 optimal weight: 0.3980 chunk 94 optimal weight: 0.3980 chunk 75 optimal weight: 0.0060 chunk 97 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1391 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= 0.138 Angle : 0.513 13.225 17442 Z= 0.260 Chirality : 0.041 0.184 2038 Planarity : 0.004 0.054 2221 Dihedral : 4.165 42.015 1678 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.50 % Favored : 94.37 % Rotamer: Outliers : 1.98 % Allowed : 21.83 % Favored : 76.18 % 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: 0.88 (0.23), residues: 1564 helix: 1.68 (0.25), residues: 500 sheet: 1.93 (0.31), residues: 342 loop : -0.94 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 44 HIS 0.003 0.001 HIS F 36 PHE 0.013 0.001 PHE E 72 TYR 0.017 0.001 TYR C 88 ARG 0.007 0.000 ARG E 214 ********************** 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 123 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 216 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7648 (ppp) REVERT: E 78 MET cc_start: 0.8291 (ppp) cc_final: 0.7892 (ppp) outliers start: 29 outliers final: 26 residues processed: 115 average time/residue: 0.2403 time to fit residues: 42.2856 Evaluate side-chains 117 residues out of total 1461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 69 CYS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 216 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 133 HIS Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 211 SER Chi-restraints excluded: chain F residue 255 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 123 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 126 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.068877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.055151 restraints weight = 47310.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.056848 restraints weight = 26607.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.057971 restraints weight = 18479.137| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1347 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= 0.195 Angle : 0.531 12.886 17442 Z= 0.271 Chirality : 0.042 0.191 2038 Planarity : 0.004 0.055 2221 Dihedral : 4.280 43.264 1678 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.69 % Favored : 94.18 % Rotamer: Outliers : 2.19 % Allowed : 21.42 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.23), residues: 1564 helix: 1.70 (0.25), residues: 494 sheet: 1.62 (0.30), residues: 364 loop : -0.88 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 44 HIS 0.004 0.001 HIS D 119 PHE 0.013 0.001 PHE E 72 TYR 0.024 0.001 TYR F 103 ARG 0.007 0.000 ARG E 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2263.04 seconds wall clock time: 42 minutes 24.35 seconds (2544.35 seconds total)