Starting phenix.real_space_refine on Sun Aug 4 11:30:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb8_23251/08_2024/7lb8_23251.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb8_23251/08_2024/7lb8_23251.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb8_23251/08_2024/7lb8_23251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb8_23251/08_2024/7lb8_23251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb8_23251/08_2024/7lb8_23251.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb8_23251/08_2024/7lb8_23251.cif" } resolution = 3.4 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= 0.003 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 64 5.16 5 C 6779 2.51 5 N 1785 2.21 5 O 1811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 521": "OD1" <-> "OD2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 61": "OD1" <-> "OD2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 126": "OD1" <-> "OD2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "D PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 241": "OD1" <-> "OD2" Residue "D ASP 247": "OD1" <-> "OD2" Residue "D PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 20": "NH1" <-> "NH2" Residue "U PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 119": "NH1" <-> "NH2" Residue "U GLU 130": "OE1" <-> "OE2" Residue "U ASP 165": "OD1" <-> "OD2" Residue "U ASP 179": "OD1" <-> "OD2" Residue "U TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ASP 165": "OD1" <-> "OD2" Residue "C ASP 179": "OD1" <-> "OD2" Residue "C ASP 185": "OD1" <-> "OD2" Residue "C ASP 207": "OD1" <-> "OD2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10439 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4610 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 30, 'TRANS': 599} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 57 Chain: "D" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2085 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 20, 'TRANS': 244} Chain: "U" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1896 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 17, 'TRANS': 237} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 17, 'TRANS': 237} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 1, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 66 Residues with excluded nonbonded symmetry interactions: 35 residue: pdb=" N ILE B 111 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 111 " occ=0.00 residue: pdb=" N PRO B 112 " occ=0.00 ... (3 atoms not shown) pdb=" CB PRO B 112 " occ=0.00 residue: pdb=" N GLY B 113 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 113 " occ=0.00 residue: pdb=" N VAL B 135 " occ=0.00 ... (3 atoms not shown) pdb=" CB VAL B 135 " occ=0.00 residue: pdb=" N ALA B 136 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA B 136 " occ=0.00 residue: pdb=" N TRP B 137 " occ=0.00 ... (3 atoms not shown) pdb=" CB TRP B 137 " occ=0.00 residue: pdb=" N GLY B 138 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY B 138 " occ=0.00 residue: pdb=" N LEU B 217 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 217 " occ=0.00 residue: pdb=" N ASP B 218 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASP B 218 " occ=0.00 residue: pdb=" N ASP B 219 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP B 219 " occ=0.00 residue: pdb=" N TRP B 449 " occ=0.00 ... (3 atoms not shown) pdb=" CB TRP B 449 " occ=0.00 residue: pdb=" N LEU B 450 " occ=0.00 ... (3 atoms not shown) pdb=" CB LEU B 450 " occ=0.00 ... (remaining 23 not shown) Time building chain proxies: 6.49, per 1000 atoms: 0.62 Number of scatterers: 10439 At special positions: 0 Unit cell: (81.498, 95.88, 140.624, 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 64 16.00 O 1811 8.00 N 1785 7.00 C 6779 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: 4.15 Conformation dependent library (CDL) restraints added in 2.1 seconds 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2556 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 8 sheets defined 61.3% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'B' and resid 6 through 32 Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 36 through 42 Processing helix chain 'B' and resid 49 through 54 removed outlier: 3.550A pdb=" N PHE B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 83 Proline residue: B 60 - end of helix removed outlier: 3.551A pdb=" N LEU B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 108 removed outlier: 3.813A pdb=" N LEU B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 134 removed outlier: 3.533A pdb=" N GLN B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 168 Processing helix chain 'B' and resid 172 through 179 Processing helix chain 'B' and resid 188 through 207 Proline residue: B 196 - end of helix Processing helix chain 'B' and resid 208 through 217 removed outlier: 3.555A pdb=" N LEU B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 228 through 251 Processing helix chain 'B' and resid 256 through 259 Processing helix chain 'B' and resid 260 through 269 Processing helix chain 'B' and resid 272 through 302 removed outlier: 3.697A pdb=" N ARG B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 323 Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 349 through 370 Processing helix chain 'B' and resid 380 through 387 removed outlier: 3.753A pdb=" N ASP B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 416 Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 426 through 442 Processing helix chain 'B' and resid 454 through 473 removed outlier: 3.511A pdb=" N GLY B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 500 removed outlier: 3.528A pdb=" N SER B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 513 Processing helix chain 'B' and resid 520 through 538 Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.593A pdb=" N ARG B 556 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 584 removed outlier: 3.760A pdb=" N ALA B 568 " --> pdb=" O PRO B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 602 Proline residue: B 595 - end of helix removed outlier: 3.759A pdb=" N GLY B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 631 Processing helix chain 'B' and resid 638 through 658 removed outlier: 3.697A pdb=" N LEU B 642 " --> pdb=" O PRO B 638 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) Proline residue: B 649 - end of helix Processing helix chain 'D' and resid 34 through 36 No H-bonds generated for 'chain 'D' and resid 34 through 36' Processing helix chain 'D' and resid 42 through 53 Processing helix chain 'D' and resid 61 through 69 removed outlier: 3.623A pdb=" N TYR D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 95 Processing helix chain 'D' and resid 109 through 115 Processing helix chain 'D' and resid 129 through 146 removed outlier: 3.702A pdb=" N MET D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.518A pdb=" N MET D 165 " --> pdb=" O PHE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.780A pdb=" N VAL D 170 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 204 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.513A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 293 Processing helix chain 'U' and resid 49 through 58 removed outlier: 3.947A pdb=" N LEU U 53 " --> pdb=" O GLY U 49 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU U 54 " --> pdb=" O LYS U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 86 Processing helix chain 'U' and resid 101 through 109 Processing helix chain 'U' and resid 110 through 115 removed outlier: 4.136A pdb=" N HIS U 114 " --> pdb=" O ARG U 110 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 135 removed outlier: 3.725A pdb=" N VAL U 128 " --> pdb=" O ASP U 124 " (cutoff:3.500A) Processing helix chain 'U' and resid 149 through 164 Processing helix chain 'U' and resid 179 through 198 Processing helix chain 'U' and resid 207 through 214 Processing helix chain 'U' and resid 236 through 246 removed outlier: 4.196A pdb=" N GLU U 242 " --> pdb=" O GLY U 238 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET U 243 " --> pdb=" O GLU U 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 49 through 58 Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.508A pdb=" N GLU C 129 " --> pdb=" O ARG C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 165 removed outlier: 3.758A pdb=" N ARG C 155 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET C 160 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 161 " --> pdb=" O TRP C 157 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 197 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 237 through 246 Processing sheet with id=AA1, first strand: chain 'D' and resid 79 through 80 removed outlier: 3.746A pdb=" N GLY D 58 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE D 122 " --> pdb=" O MET D 100 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TRP D 102 " --> pdb=" O PHE D 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 220 through 223 removed outlier: 6.710A pdb=" N HIS D 187 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE D 183 " --> pdb=" O HIS D 187 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU D 178 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE D 238 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N THR D 180 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL D 235 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL D 269 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N CYS D 237 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'U' and resid 30 through 33 removed outlier: 4.344A pdb=" N ALA U 13 " --> pdb=" O LEU U 69 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU U 69 " --> pdb=" O ALA U 13 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'U' and resid 87 through 89 removed outlier: 6.271A pdb=" N ALA U 88 " --> pdb=" O LEU U 170 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL U 39 " --> pdb=" O TYR U 217 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL U 219 " --> pdb=" O VAL U 39 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLY U 41 " --> pdb=" O VAL U 219 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA U 228 " --> pdb=" O ALA U 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'U' and resid 250 through 252 Processing sheet with id=AA6, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 90 removed outlier: 5.935A pdb=" N ALA C 88 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASP C 172 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU C 90 " --> pdb=" O ASP C 172 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 169 " --> pdb=" O ILE C 202 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL C 204 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU C 171 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL C 219 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLY C 41 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LEU C 221 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE C 43 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 249 through 252 598 hydrogen bonds defined for protein. 1749 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: 3.08 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3367 1.34 - 1.46: 2164 1.46 - 1.58: 5023 1.58 - 1.69: 0 1.69 - 1.81: 117 Bond restraints: 10671 Sorted by residual: bond pdb=" CA LEU B 550 " pdb=" C LEU B 550 " ideal model delta sigma weight residual 1.525 1.571 -0.045 1.40e-02 5.10e+03 1.04e+01 bond pdb=" N PRO B 549 " pdb=" CD PRO B 549 " ideal model delta sigma weight residual 1.473 1.506 -0.033 1.40e-02 5.10e+03 5.47e+00 bond pdb=" N PRO B 549 " pdb=" CA PRO B 549 " ideal model delta sigma weight residual 1.467 1.483 -0.016 1.21e-02 6.83e+03 1.70e+00 bond pdb=" N LEU B 550 " pdb=" CA LEU B 550 " ideal model delta sigma weight residual 1.461 1.480 -0.018 1.49e-02 4.50e+03 1.49e+00 bond pdb=" CA ALA U 72 " pdb=" C ALA U 72 " ideal model delta sigma weight residual 1.530 1.515 0.015 1.30e-02 5.92e+03 1.32e+00 ... (remaining 10666 not shown) Histogram of bond angle deviations from ideal: 99.86 - 106.72: 421 106.72 - 113.58: 5989 113.58 - 120.44: 4119 120.44 - 127.30: 3873 127.30 - 134.16: 159 Bond angle restraints: 14561 Sorted by residual: angle pdb=" C PRO B 549 " pdb=" CA PRO B 549 " pdb=" CB PRO B 549 " ideal model delta sigma weight residual 111.21 100.99 10.22 1.33e+00 5.65e-01 5.91e+01 angle pdb=" N LEU B 550 " pdb=" CA LEU B 550 " pdb=" CB LEU B 550 " ideal model delta sigma weight residual 112.30 103.05 9.25 1.52e+00 4.33e-01 3.70e+01 angle pdb=" N LEU B 550 " pdb=" CA LEU B 550 " pdb=" C LEU B 550 " ideal model delta sigma weight residual 112.24 118.73 -6.49 1.28e+00 6.10e-01 2.57e+01 angle pdb=" N LEU B 548 " pdb=" CA LEU B 548 " pdb=" C LEU B 548 " ideal model delta sigma weight residual 113.16 106.36 6.80 1.42e+00 4.96e-01 2.29e+01 angle pdb=" N GLY B 551 " pdb=" CA GLY B 551 " pdb=" C GLY B 551 " ideal model delta sigma weight residual 113.18 121.39 -8.21 2.37e+00 1.78e-01 1.20e+01 ... (remaining 14556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5621 17.97 - 35.95: 531 35.95 - 53.92: 124 53.92 - 71.90: 15 71.90 - 89.87: 8 Dihedral angle restraints: 6299 sinusoidal: 2319 harmonic: 3980 Sorted by residual: dihedral pdb=" C PRO B 549 " pdb=" N PRO B 549 " pdb=" CA PRO B 549 " pdb=" CB PRO B 549 " ideal model delta harmonic sigma weight residual -120.70 -107.88 -12.82 0 2.50e+00 1.60e-01 2.63e+01 dihedral pdb=" CB GLU U 65 " pdb=" CG GLU U 65 " pdb=" CD GLU U 65 " pdb=" OE1 GLU U 65 " ideal model delta sinusoidal sigma weight residual 0.00 89.87 -89.87 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASN U 16 " pdb=" CB ASN U 16 " pdb=" CG ASN U 16 " pdb=" OD1 ASN U 16 " ideal model delta sinusoidal sigma weight residual -90.00 -158.21 68.21 2 2.00e+01 2.50e-03 1.03e+01 ... (remaining 6296 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1327 0.043 - 0.086: 330 0.086 - 0.128: 81 0.128 - 0.171: 4 0.171 - 0.214: 1 Chirality restraints: 1743 Sorted by residual: chirality pdb=" CA PRO B 549 " pdb=" N PRO B 549 " pdb=" C PRO B 549 " pdb=" CB PRO B 549 " both_signs ideal model delta sigma weight residual False 2.72 2.93 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE U 247 " pdb=" CA ILE U 247 " pdb=" CG1 ILE U 247 " pdb=" CG2 ILE U 247 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA ILE C 251 " pdb=" N ILE C 251 " pdb=" C ILE C 251 " pdb=" CB ILE C 251 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 1740 not shown) Planarity restraints: 1827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 548 " -0.043 5.00e-02 4.00e+02 6.30e-02 6.34e+00 pdb=" N PRO B 549 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 549 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 549 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 550 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" C LEU B 550 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU B 550 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY B 551 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 44 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO D 45 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 45 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 45 " 0.024 5.00e-02 4.00e+02 ... (remaining 1824 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 118 2.65 - 3.22: 9889 3.22 - 3.78: 16347 3.78 - 4.34: 21405 4.34 - 4.90: 35357 Nonbonded interactions: 83116 Sorted by model distance: nonbonded pdb=" O PRO B 549 " pdb=" CG LEU B 550 " model vdw 2.093 3.470 nonbonded pdb=" O ILE B 103 " pdb=" OG1 THR B 107 " model vdw 2.193 3.040 nonbonded pdb=" OG1 THR C 231 " pdb=" OE2 GLU C 234 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR U 217 " pdb=" OE1 GLN U 229 " model vdw 2.215 3.040 nonbonded pdb=" O THR B 546 " pdb=" CG PRO B 549 " model vdw 2.235 3.440 ... (remaining 83111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 11 through 72 or (resid 73 through 75 and (name N or name \ CA or name C or name O or name CB )) or resid 76 through 137 or (resid 138 and ( \ name N or name CA or name C or name O or name CB )) or resid 139 or (resid 140 t \ hrough 141 and (name N or name CA or name C or name O or name CB )) or resid 142 \ through 265)) selection = (chain 'U' and (resid 11 through 19 or (resid 20 and (name N or name CA or name \ C or name O or name CB )) or resid 21 or (resid 22 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 23 through 25 and (name N or name CA or na \ me C or name O or name CB )) or resid 26 or (resid 27 through 28 and (name N or \ name CA or name C or name O or name CB )) or resid 29 through 37 or (resid 38 an \ d (name N or name CA or name C or name O or name CB )) or resid 39 through 59 or \ (resid 60 and (name N or name CA or name C or name O or name CB )) or resid 61 \ through 93 or (resid 94 and (name N or name CA or name C or name O or name CB )) \ or resid 95 through 118 or (resid 119 through 120 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 121 through 125 and (name N or name CA or \ name C or name O or name CB )) or resid 126 through 195 or (resid 196 and (name \ N or name CA or name C or name O or name CB )) or resid 197 through 247 or (resi \ d 248 and (name N or name CA or name C or name O or name CB )) or resid 249 thro \ ugh 259 or (resid 260 and (name N or name CA or name C or name O or name CB )) o \ r resid 261 through 265)) } 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=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 31.860 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 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 : 0.002 0.045 10671 Z= 0.157 Angle : 0.620 10.221 14561 Z= 0.328 Chirality : 0.039 0.214 1743 Planarity : 0.004 0.063 1827 Dihedral : 14.950 89.874 3743 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.73 % Favored : 94.98 % Rotamer: Outliers : 2.66 % Allowed : 23.36 % Favored : 73.98 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: -1.98 (0.20), residues: 1395 helix: -0.21 (0.17), residues: 796 sheet: -2.06 (0.41), residues: 97 loop : -2.96 (0.22), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 195 HIS 0.004 0.001 HIS C 114 PHE 0.024 0.001 PHE B 589 TYR 0.014 0.001 TYR U 245 ARG 0.011 0.001 ARG C 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 221 time to evaluate : 1.087 Fit side-chains REVERT: B 147 ILE cc_start: 0.7801 (mt) cc_final: 0.7523 (mt) REVERT: B 288 LEU cc_start: 0.6779 (OUTLIER) cc_final: 0.5957 (tt) REVERT: B 493 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6721 (mt) REVERT: B 495 MET cc_start: 0.7495 (mmm) cc_final: 0.6510 (mtt) REVERT: B 593 MET cc_start: 0.5923 (mmt) cc_final: 0.5702 (mmt) REVERT: B 607 MET cc_start: 0.8129 (tpp) cc_final: 0.7844 (tpp) REVERT: B 657 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6862 (mtmt) REVERT: D 288 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7889 (mp) REVERT: U 53 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7240 (tm) REVERT: U 57 LEU cc_start: 0.6060 (tp) cc_final: 0.5724 (tp) REVERT: U 100 MET cc_start: 0.3827 (tpt) cc_final: 0.3530 (mmp) REVERT: U 129 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7378 (tp30) REVERT: U 226 MET cc_start: 0.3298 (tpt) cc_final: 0.2278 (tmm) REVERT: C 65 GLU cc_start: 0.6397 (mt-10) cc_final: 0.5050 (tp30) REVERT: C 167 ARG cc_start: 0.6878 (mmp80) cc_final: 0.5178 (ttp80) outliers start: 28 outliers final: 10 residues processed: 247 average time/residue: 0.2390 time to fit residues: 80.4298 Evaluate side-chains 191 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 176 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 180 ILE Chi-restraints excluded: chain U residue 216 ASP Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN B 171 GLN U 16 ASN C 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10671 Z= 0.194 Angle : 0.607 10.973 14561 Z= 0.289 Chirality : 0.042 0.258 1743 Planarity : 0.005 0.048 1827 Dihedral : 5.461 59.389 1521 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.58 % Favored : 96.27 % Rotamer: Outliers : 3.04 % Allowed : 22.41 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.22), residues: 1395 helix: 0.84 (0.19), residues: 786 sheet: -1.50 (0.45), residues: 102 loop : -2.50 (0.23), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 113 HIS 0.007 0.001 HIS C 114 PHE 0.031 0.002 PHE U 120 TYR 0.012 0.001 TYR C 214 ARG 0.005 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 1.059 Fit side-chains REVERT: B 288 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6337 (tt) REVERT: B 495 MET cc_start: 0.7695 (mmm) cc_final: 0.6713 (mtt) REVERT: B 607 MET cc_start: 0.8204 (tpp) cc_final: 0.7999 (tpp) REVERT: D 288 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7864 (mp) REVERT: U 53 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7073 (tm) REVERT: U 57 LEU cc_start: 0.6153 (tp) cc_final: 0.5826 (tp) REVERT: U 129 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7350 (tp30) REVERT: U 226 MET cc_start: 0.3878 (tpt) cc_final: 0.2869 (tmm) REVERT: C 65 GLU cc_start: 0.6417 (mt-10) cc_final: 0.5064 (tp30) REVERT: C 167 ARG cc_start: 0.7023 (mmp80) cc_final: 0.5259 (ttp80) outliers start: 32 outliers final: 22 residues processed: 226 average time/residue: 0.2044 time to fit residues: 66.3068 Evaluate side-chains 202 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 0.0770 chunk 39 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10671 Z= 0.228 Angle : 0.623 10.528 14561 Z= 0.299 Chirality : 0.043 0.308 1743 Planarity : 0.005 0.047 1827 Dihedral : 5.344 56.108 1508 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.80 % Favored : 95.13 % Rotamer: Outliers : 4.56 % Allowed : 22.79 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1395 helix: 1.14 (0.19), residues: 784 sheet: -1.57 (0.47), residues: 96 loop : -2.17 (0.24), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 389 HIS 0.008 0.001 HIS C 114 PHE 0.019 0.002 PHE B 54 TYR 0.023 0.002 TYR C 214 ARG 0.008 0.001 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 189 time to evaluate : 1.073 Fit side-chains REVERT: B 288 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6557 (tt) REVERT: B 384 ASP cc_start: 0.7620 (m-30) cc_final: 0.7103 (m-30) REVERT: B 395 MET cc_start: 0.7822 (tpp) cc_final: 0.7520 (mmt) REVERT: B 480 LEU cc_start: 0.8551 (tt) cc_final: 0.8257 (tt) REVERT: B 493 LEU cc_start: 0.7494 (mp) cc_final: 0.7135 (mp) REVERT: B 495 MET cc_start: 0.7775 (mmm) cc_final: 0.6914 (mtt) REVERT: B 525 TRP cc_start: 0.6433 (m100) cc_final: 0.6050 (m100) REVERT: B 593 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5841 (mmt) REVERT: B 600 MET cc_start: 0.7038 (mtm) cc_final: 0.6741 (ptp) REVERT: B 607 MET cc_start: 0.8332 (tpp) cc_final: 0.8068 (tpp) REVERT: U 30 LEU cc_start: 0.6955 (pt) cc_final: 0.6705 (pt) REVERT: U 53 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7187 (tm) REVERT: U 57 LEU cc_start: 0.6116 (tp) cc_final: 0.5661 (tp) REVERT: U 129 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7330 (tp30) REVERT: U 210 MET cc_start: 0.7259 (mmt) cc_final: 0.7001 (mmt) REVERT: U 226 MET cc_start: 0.4153 (tpt) cc_final: 0.3722 (tmm) REVERT: U 229 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.7088 (mt0) REVERT: C 65 GLU cc_start: 0.6197 (mt-10) cc_final: 0.4932 (tp30) outliers start: 48 outliers final: 28 residues processed: 225 average time/residue: 0.1948 time to fit residues: 65.1307 Evaluate side-chains 212 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain U residue 186 VAL Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain U residue 229 GLN Chi-restraints excluded: chain U residue 249 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 184 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.5980 chunk 95 optimal weight: 0.0770 chunk 65 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 187 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10671 Z= 0.176 Angle : 0.601 15.290 14561 Z= 0.282 Chirality : 0.041 0.215 1743 Planarity : 0.004 0.051 1827 Dihedral : 5.170 56.166 1506 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.23 % Favored : 95.70 % Rotamer: Outliers : 3.80 % Allowed : 24.79 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.09 (0.23), residues: 1395 helix: 1.34 (0.19), residues: 787 sheet: -1.56 (0.45), residues: 112 loop : -2.03 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 389 HIS 0.007 0.001 HIS C 114 PHE 0.032 0.001 PHE U 120 TYR 0.012 0.001 TYR C 214 ARG 0.006 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 182 time to evaluate : 1.097 Fit side-chains REVERT: B 384 ASP cc_start: 0.7606 (m-30) cc_final: 0.7074 (m-30) REVERT: B 480 LEU cc_start: 0.8464 (tt) cc_final: 0.8221 (tt) REVERT: B 495 MET cc_start: 0.7781 (mmm) cc_final: 0.6834 (mtt) REVERT: B 525 TRP cc_start: 0.6399 (m100) cc_final: 0.6050 (m100) REVERT: B 593 MET cc_start: 0.6186 (OUTLIER) cc_final: 0.5910 (mmt) REVERT: U 30 LEU cc_start: 0.7248 (pt) cc_final: 0.7003 (pt) REVERT: U 53 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7104 (tm) REVERT: U 57 LEU cc_start: 0.6117 (tp) cc_final: 0.5771 (tp) REVERT: U 129 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7322 (tp30) REVERT: U 210 MET cc_start: 0.7167 (mmt) cc_final: 0.6732 (mmt) REVERT: U 226 MET cc_start: 0.4225 (tpt) cc_final: 0.3767 (tmm) REVERT: U 229 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6976 (mt0) REVERT: C 65 GLU cc_start: 0.6072 (mt-10) cc_final: 0.4910 (tp30) outliers start: 40 outliers final: 26 residues processed: 216 average time/residue: 0.1833 time to fit residues: 59.7481 Evaluate side-chains 207 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain U residue 229 GLN Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 120 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10671 Z= 0.297 Angle : 0.662 14.667 14561 Z= 0.320 Chirality : 0.044 0.188 1743 Planarity : 0.005 0.051 1827 Dihedral : 5.609 58.307 1506 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 5.60 % Allowed : 24.41 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.32 (0.22), residues: 1395 helix: 1.08 (0.19), residues: 789 sheet: -1.26 (0.43), residues: 120 loop : -2.12 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 375 HIS 0.008 0.001 HIS C 114 PHE 0.023 0.002 PHE B 433 TYR 0.014 0.002 TYR C 214 ARG 0.005 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 174 time to evaluate : 1.283 Fit side-chains REVERT: B 153 VAL cc_start: 0.7066 (t) cc_final: 0.6756 (p) REVERT: B 192 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6889 (mm-30) REVERT: B 376 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8513 (t) REVERT: B 384 ASP cc_start: 0.7743 (m-30) cc_final: 0.7267 (m-30) REVERT: B 462 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6498 (tp) REVERT: B 480 LEU cc_start: 0.8449 (tt) cc_final: 0.8219 (tt) REVERT: B 495 MET cc_start: 0.7840 (mmm) cc_final: 0.7079 (mtt) REVERT: B 525 TRP cc_start: 0.6620 (m100) cc_final: 0.6222 (m100) REVERT: B 593 MET cc_start: 0.6285 (OUTLIER) cc_final: 0.6061 (mmt) REVERT: U 53 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7203 (tm) REVERT: U 57 LEU cc_start: 0.6233 (tp) cc_final: 0.5955 (tp) REVERT: U 185 ASP cc_start: 0.6780 (t0) cc_final: 0.6058 (m-30) REVERT: U 229 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7089 (mt0) REVERT: C 65 GLU cc_start: 0.6022 (mt-10) cc_final: 0.4863 (tp30) outliers start: 59 outliers final: 41 residues processed: 220 average time/residue: 0.1929 time to fit residues: 64.0548 Evaluate side-chains 214 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 168 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 43 ILE Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 186 VAL Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain U residue 229 GLN Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 235 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 7.9990 chunk 120 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 44 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10671 Z= 0.168 Angle : 0.593 11.573 14561 Z= 0.280 Chirality : 0.041 0.215 1743 Planarity : 0.005 0.052 1827 Dihedral : 5.058 53.773 1504 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.91 % Rotamer: Outliers : 4.18 % Allowed : 25.74 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.02 (0.23), residues: 1395 helix: 1.32 (0.19), residues: 794 sheet: -0.97 (0.43), residues: 130 loop : -2.09 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 389 HIS 0.007 0.001 HIS C 114 PHE 0.020 0.001 PHE B 433 TYR 0.019 0.001 TYR C 214 ARG 0.005 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 1.060 Fit side-chains REVERT: B 153 VAL cc_start: 0.7060 (t) cc_final: 0.6727 (p) REVERT: B 192 GLU cc_start: 0.7447 (mt-10) cc_final: 0.6876 (mm-30) REVERT: B 384 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: B 480 LEU cc_start: 0.8278 (tt) cc_final: 0.8053 (tt) REVERT: B 493 LEU cc_start: 0.7428 (mp) cc_final: 0.7146 (mp) REVERT: B 495 MET cc_start: 0.7861 (mmm) cc_final: 0.6959 (mtt) REVERT: B 525 TRP cc_start: 0.6541 (m100) cc_final: 0.6169 (m100) REVERT: B 593 MET cc_start: 0.6223 (OUTLIER) cc_final: 0.5877 (mmt) REVERT: U 53 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7238 (tm) REVERT: U 57 LEU cc_start: 0.6132 (tp) cc_final: 0.5839 (tp) REVERT: U 129 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7183 (tp30) REVERT: U 229 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7232 (mt0) REVERT: C 65 GLU cc_start: 0.5967 (mt-10) cc_final: 0.4989 (tp30) outliers start: 44 outliers final: 28 residues processed: 221 average time/residue: 0.1864 time to fit residues: 61.1431 Evaluate side-chains 200 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 168 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 144 LEU Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain U residue 229 GLN Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 235 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 0.2980 chunk 98 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.7415 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10671 Z= 0.180 Angle : 0.605 11.687 14561 Z= 0.286 Chirality : 0.042 0.239 1743 Planarity : 0.005 0.051 1827 Dihedral : 4.911 53.583 1504 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.59 % Favored : 95.27 % Rotamer: Outliers : 4.08 % Allowed : 26.40 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.23), residues: 1395 helix: 1.39 (0.19), residues: 794 sheet: -0.94 (0.43), residues: 130 loop : -2.03 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 195 HIS 0.007 0.001 HIS C 114 PHE 0.018 0.001 PHE B 433 TYR 0.017 0.001 TYR C 214 ARG 0.009 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 179 time to evaluate : 1.192 Fit side-chains REVERT: B 153 VAL cc_start: 0.7080 (t) cc_final: 0.6798 (p) REVERT: B 192 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6911 (mm-30) REVERT: B 384 ASP cc_start: 0.7560 (m-30) cc_final: 0.7220 (m-30) REVERT: B 480 LEU cc_start: 0.8224 (tt) cc_final: 0.8018 (tt) REVERT: B 493 LEU cc_start: 0.7438 (mp) cc_final: 0.7214 (mp) REVERT: B 495 MET cc_start: 0.7846 (mmm) cc_final: 0.6931 (mtt) REVERT: B 525 TRP cc_start: 0.6563 (m100) cc_final: 0.6184 (m100) REVERT: B 593 MET cc_start: 0.6289 (OUTLIER) cc_final: 0.5961 (mmt) REVERT: U 53 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7178 (tm) REVERT: U 57 LEU cc_start: 0.6221 (tp) cc_final: 0.5905 (tp) REVERT: U 119 ARG cc_start: 0.5785 (mpt180) cc_final: 0.5484 (tpt90) REVERT: U 129 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7163 (tp30) REVERT: U 236 MET cc_start: 0.6549 (mmm) cc_final: 0.4650 (pmm) REVERT: C 65 GLU cc_start: 0.5986 (mt-10) cc_final: 0.5059 (tp30) outliers start: 43 outliers final: 33 residues processed: 211 average time/residue: 0.2150 time to fit residues: 67.8751 Evaluate side-chains 206 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 610 ILE Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 144 LEU Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 3.9990 chunk 80 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 121 optimal weight: 0.0370 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10671 Z= 0.160 Angle : 0.594 11.020 14561 Z= 0.279 Chirality : 0.041 0.211 1743 Planarity : 0.005 0.051 1827 Dihedral : 4.754 54.300 1503 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 3.80 % Allowed : 26.69 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.23), residues: 1395 helix: 1.54 (0.19), residues: 794 sheet: -0.85 (0.44), residues: 130 loop : -2.03 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 113 HIS 0.007 0.001 HIS C 114 PHE 0.016 0.001 PHE B 433 TYR 0.015 0.001 TYR C 214 ARG 0.007 0.000 ARG B 526 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 177 time to evaluate : 0.987 Fit side-chains REVERT: B 153 VAL cc_start: 0.7091 (t) cc_final: 0.6801 (p) REVERT: B 192 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6904 (mm-30) REVERT: B 384 ASP cc_start: 0.7534 (m-30) cc_final: 0.7166 (m-30) REVERT: B 495 MET cc_start: 0.7882 (mmm) cc_final: 0.6849 (mtt) REVERT: B 525 TRP cc_start: 0.6599 (m100) cc_final: 0.6183 (m100) REVERT: B 593 MET cc_start: 0.6263 (OUTLIER) cc_final: 0.5916 (mmt) REVERT: U 53 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7209 (tm) REVERT: U 57 LEU cc_start: 0.6284 (tp) cc_final: 0.5981 (tp) REVERT: U 119 ARG cc_start: 0.5808 (mpt180) cc_final: 0.5527 (tpt90) REVERT: U 129 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7148 (tp30) REVERT: U 236 MET cc_start: 0.6604 (mmm) cc_final: 0.4761 (pmm) REVERT: C 65 GLU cc_start: 0.5961 (mt-10) cc_final: 0.5067 (tp30) REVERT: C 213 ARG cc_start: 0.6469 (tpm170) cc_final: 0.6010 (mtp-110) outliers start: 40 outliers final: 27 residues processed: 209 average time/residue: 0.1912 time to fit residues: 59.0695 Evaluate side-chains 199 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 171 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 124 optimal weight: 0.0010 chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10671 Z= 0.167 Angle : 0.600 11.026 14561 Z= 0.282 Chirality : 0.041 0.217 1743 Planarity : 0.005 0.050 1827 Dihedral : 4.683 54.386 1503 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 3.61 % Allowed : 26.50 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.23), residues: 1395 helix: 1.57 (0.19), residues: 794 sheet: -0.77 (0.44), residues: 129 loop : -2.01 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP U 113 HIS 0.006 0.001 HIS C 114 PHE 0.025 0.001 PHE B 433 TYR 0.015 0.001 TYR C 214 ARG 0.010 0.000 ARG B 556 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 1.003 Fit side-chains REVERT: B 153 VAL cc_start: 0.7097 (t) cc_final: 0.6823 (p) REVERT: B 192 GLU cc_start: 0.7509 (mt-10) cc_final: 0.6911 (mm-30) REVERT: B 384 ASP cc_start: 0.7484 (m-30) cc_final: 0.7150 (m-30) REVERT: B 423 GLU cc_start: 0.7335 (mp0) cc_final: 0.7075 (mp0) REVERT: B 495 MET cc_start: 0.7800 (mmm) cc_final: 0.6744 (mtt) REVERT: B 525 TRP cc_start: 0.6585 (m100) cc_final: 0.6186 (m100) REVERT: B 593 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.5925 (mmt) REVERT: D 165 MET cc_start: 0.6959 (mmt) cc_final: 0.6728 (mmt) REVERT: U 53 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7207 (tm) REVERT: U 57 LEU cc_start: 0.6305 (tp) cc_final: 0.6004 (tp) REVERT: U 119 ARG cc_start: 0.5767 (mpt180) cc_final: 0.5538 (tpt90) REVERT: C 65 GLU cc_start: 0.5932 (mt-10) cc_final: 0.5069 (tp30) REVERT: C 213 ARG cc_start: 0.6418 (tpm170) cc_final: 0.6047 (mtp-110) outliers start: 38 outliers final: 32 residues processed: 206 average time/residue: 0.1881 time to fit residues: 57.4177 Evaluate side-chains 204 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 424 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 189 LEU Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 79 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.7276 > 50: distance: 79 - 84: 6.696 distance: 84 - 85: 24.758 distance: 84 - 138: 11.619 distance: 85 - 86: 30.810 distance: 85 - 88: 9.812 distance: 86 - 87: 9.713 distance: 86 - 89: 3.876 distance: 89 - 90: 10.413 distance: 90 - 91: 40.936 distance: 90 - 93: 26.083 distance: 91 - 92: 17.104 distance: 91 - 97: 23.146 distance: 93 - 94: 24.058 distance: 94 - 95: 40.203 distance: 94 - 96: 20.165 distance: 97 - 98: 21.259 distance: 98 - 99: 8.716 distance: 98 - 101: 19.218 distance: 99 - 100: 6.486 distance: 99 - 102: 25.905 distance: 102 - 103: 14.991 distance: 103 - 104: 29.975 distance: 104 - 105: 8.805 distance: 104 - 106: 39.717 distance: 106 - 107: 17.321 distance: 107 - 108: 22.316 distance: 108 - 109: 25.178 distance: 108 - 110: 32.595 distance: 110 - 111: 30.275 distance: 111 - 112: 16.218 distance: 111 - 114: 28.419 distance: 112 - 113: 20.324 distance: 112 - 119: 18.164 distance: 114 - 115: 17.856 distance: 115 - 116: 10.838 distance: 116 - 117: 23.883 distance: 116 - 118: 28.749 distance: 119 - 120: 4.753 distance: 120 - 121: 26.045 distance: 120 - 123: 30.640 distance: 121 - 127: 19.002 distance: 123 - 124: 40.887 distance: 124 - 125: 10.332 distance: 125 - 126: 26.101 distance: 127 - 128: 16.425 distance: 128 - 129: 30.399 distance: 128 - 131: 29.803 distance: 129 - 130: 16.188 distance: 129 - 135: 14.692 distance: 131 - 132: 17.139 distance: 131 - 133: 28.425 distance: 132 - 134: 21.605 distance: 135 - 136: 18.672 distance: 136 - 137: 14.683 distance: 136 - 139: 12.862 distance: 137 - 138: 22.759 distance: 137 - 140: 35.093 distance: 140 - 141: 53.364 distance: 141 - 142: 48.552 distance: 141 - 144: 51.713 distance: 142 - 143: 36.109 distance: 142 - 149: 25.324 distance: 144 - 145: 28.444 distance: 145 - 146: 9.888 distance: 146 - 147: 30.462 distance: 146 - 148: 5.666