Starting phenix.real_space_refine on Fri Mar 15 02:58:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb8_23251/03_2024/7lb8_23251.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb8_23251/03_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_23251/03_2024/7lb8_23251.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb8_23251/03_2024/7lb8_23251.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb8_23251/03_2024/7lb8_23251.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lb8_23251/03_2024/7lb8_23251.pdb" } 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-5265/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: 5.79, per 1000 atoms: 0.55 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: 4.10 Conformation dependent library (CDL) restraints added in 1.9 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: 1.24 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: 3.35 Time building geometry restraints manager: 4.46 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 2.440 nonbonded pdb=" OG1 THR C 231 " pdb=" OE2 GLU C 234 " model vdw 2.207 2.440 nonbonded pdb=" OH TYR U 217 " pdb=" OE1 GLN U 229 " model vdw 2.215 2.440 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 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: 1.340 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: 7.230 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 31.180 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.170 ------------------------------------------------------------------------------- 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 : 1.159 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: 0.2442 time to fit residues: 81.9897 Evaluate side-chains 191 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 176 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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: 0.7980 chunk 35 optimal weight: 0.0370 chunk 71 optimal weight: 0.0570 chunk 56 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.9778 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10671 Z= 0.210 Angle : 0.622 12.959 14561 Z= 0.296 Chirality : 0.042 0.239 1743 Planarity : 0.005 0.049 1827 Dihedral : 5.667 59.692 1521 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.30 % Favored : 96.56 % Rotamer: Outliers : 3.80 % Allowed : 23.27 % Favored : 72.93 % 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: -0.72 (0.22), residues: 1395 helix: 0.86 (0.19), residues: 792 sheet: -1.72 (0.44), residues: 97 loop : -2.43 (0.23), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP U 113 HIS 0.008 0.001 HIS C 114 PHE 0.035 0.002 PHE U 120 TYR 0.011 0.001 TYR U 245 ARG 0.008 0.001 ARG U 85 *********************** 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 244 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 204 time to evaluate : 1.070 Fit side-chains REVERT: B 288 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6321 (tt) REVERT: B 495 MET cc_start: 0.7693 (mmm) cc_final: 0.6831 (mtt) REVERT: U 57 LEU cc_start: 0.6192 (tp) cc_final: 0.5922 (tp) REVERT: U 129 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7345 (tp30) REVERT: U 160 MET cc_start: 0.5942 (tmm) cc_final: 0.5669 (tmm) REVERT: U 210 MET cc_start: 0.7134 (mmp) cc_final: 0.6710 (mmp) REVERT: U 226 MET cc_start: 0.3993 (tpt) cc_final: 0.3175 (tmm) REVERT: C 65 GLU cc_start: 0.6339 (mt-10) cc_final: 0.5019 (tp30) REVERT: C 167 ARG cc_start: 0.7054 (mmp80) cc_final: 0.5368 (ttp80) REVERT: C 213 ARG cc_start: 0.6187 (tpm170) cc_final: 0.5884 (mtp-110) outliers start: 40 outliers final: 27 residues processed: 234 average time/residue: 0.2158 time to fit residues: 71.9654 Evaluate side-chains 210 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 145 THR Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 357 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 565 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 139 THR 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 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 64 SER Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain U residue 186 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 184 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 112 optimal weight: 0.0570 chunk 125 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN D 187 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10671 Z= 0.254 Angle : 0.621 11.132 14561 Z= 0.298 Chirality : 0.043 0.282 1743 Planarity : 0.005 0.046 1827 Dihedral : 5.484 57.301 1507 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.59 % Favored : 95.27 % Rotamer: Outliers : 5.79 % Allowed : 22.79 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.44 (0.22), residues: 1395 helix: 1.06 (0.19), residues: 790 sheet: -1.72 (0.43), residues: 112 loop : -2.22 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 195 HIS 0.007 0.001 HIS C 114 PHE 0.021 0.002 PHE B 54 TYR 0.009 0.001 TYR D 65 ARG 0.004 0.000 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 242 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 181 time to evaluate : 1.191 Fit side-chains REVERT: B 384 ASP cc_start: 0.7736 (m-30) cc_final: 0.7252 (m-30) REVERT: B 395 MET cc_start: 0.7851 (tpp) cc_final: 0.7554 (mmt) REVERT: B 493 LEU cc_start: 0.7457 (mp) cc_final: 0.7057 (mp) REVERT: B 495 MET cc_start: 0.7834 (mmm) cc_final: 0.7040 (mtt) REVERT: B 525 TRP cc_start: 0.6434 (m100) cc_final: 0.6101 (m100) REVERT: B 593 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.6007 (mmt) REVERT: U 30 LEU cc_start: 0.7075 (pt) cc_final: 0.6838 (pt) REVERT: U 53 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7198 (tm) REVERT: U 57 LEU cc_start: 0.6091 (tp) cc_final: 0.5614 (tp) REVERT: U 129 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7363 (tp30) REVERT: U 210 MET cc_start: 0.7223 (mmp) cc_final: 0.6688 (mmt) REVERT: C 65 GLU cc_start: 0.6165 (mt-10) cc_final: 0.4894 (tp30) outliers start: 61 outliers final: 40 residues processed: 230 average time/residue: 0.1819 time to fit residues: 62.6481 Evaluate side-chains 214 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 126 CYS Chi-restraints excluded: chain B residue 145 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 367 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 410 ILE 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 588 SER Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 610 ILE 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 139 THR 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 64 SER Chi-restraints excluded: chain U residue 167 ARG Chi-restraints excluded: chain U residue 169 LEU Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain U residue 249 MET Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 166 SER 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: 1.9990 chunk 95 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 120 optimal weight: 0.0770 chunk 36 optimal weight: 0.7980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN C 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10671 Z= 0.172 Angle : 0.593 10.924 14561 Z= 0.277 Chirality : 0.041 0.334 1743 Planarity : 0.004 0.049 1827 Dihedral : 5.233 55.462 1505 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.16 % Favored : 95.70 % Rotamer: Outliers : 3.99 % Allowed : 25.64 % Favored : 70.37 % 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: -0.10 (0.23), residues: 1395 helix: 1.36 (0.19), residues: 789 sheet: -1.55 (0.45), residues: 112 loop : -2.13 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 389 HIS 0.007 0.001 HIS C 114 PHE 0.018 0.001 PHE B 433 TYR 0.015 0.001 TYR C 214 ARG 0.003 0.000 ARG D 265 *********************** 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 221 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 1.027 Fit side-chains REVERT: B 384 ASP cc_start: 0.7655 (m-30) cc_final: 0.7164 (m-30) REVERT: B 495 MET cc_start: 0.7843 (mmm) cc_final: 0.6944 (mtt) REVERT: B 525 TRP cc_start: 0.6438 (m100) cc_final: 0.6093 (m100) REVERT: B 593 MET cc_start: 0.6243 (OUTLIER) cc_final: 0.5897 (mmt) REVERT: U 53 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7177 (tm) REVERT: U 57 LEU cc_start: 0.6083 (tp) cc_final: 0.5619 (tp) REVERT: U 129 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7307 (tp30) REVERT: U 210 MET cc_start: 0.7201 (mmp) cc_final: 0.6549 (mmt) REVERT: U 226 MET cc_start: 0.4140 (tmm) cc_final: 0.3468 (tmm) REVERT: C 57 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6302 (tt) REVERT: C 65 GLU cc_start: 0.6070 (mt-10) cc_final: 0.4916 (tp30) outliers start: 42 outliers final: 29 residues processed: 211 average time/residue: 0.1752 time to fit residues: 55.6122 Evaluate side-chains 205 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 234 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 368 PHE Chi-restraints excluded: chain B residue 376 THR 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 520 THR Chi-restraints excluded: chain B residue 565 THR 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 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 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 64 SER Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain C residue 57 LEU 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: 0.1980 chunk 76 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 0.0010 chunk 114 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN B 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10671 Z= 0.156 Angle : 0.578 10.771 14561 Z= 0.268 Chirality : 0.040 0.196 1743 Planarity : 0.004 0.049 1827 Dihedral : 5.116 57.604 1505 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.37 % Favored : 95.48 % Rotamer: Outliers : 4.56 % Allowed : 25.93 % 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: 0.14 (0.23), residues: 1395 helix: 1.53 (0.19), residues: 793 sheet: -1.17 (0.44), residues: 122 loop : -2.10 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 389 HIS 0.006 0.001 HIS C 114 PHE 0.017 0.001 PHE B 433 TYR 0.013 0.001 TYR C 214 ARG 0.004 0.000 ARG U 15 *********************** 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: 48 poor density : 185 time to evaluate : 1.126 Fit side-chains REVERT: B 384 ASP cc_start: 0.7651 (m-30) cc_final: 0.7159 (m-30) REVERT: B 495 MET cc_start: 0.7805 (mmm) cc_final: 0.6829 (mtt) REVERT: B 525 TRP cc_start: 0.6490 (m100) cc_final: 0.6146 (m100) REVERT: B 593 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.5975 (mmt) REVERT: U 53 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7127 (tm) REVERT: U 57 LEU cc_start: 0.6161 (tp) cc_final: 0.5777 (tp) REVERT: U 119 ARG cc_start: 0.5542 (mpt180) cc_final: 0.5340 (tpt90) REVERT: U 129 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7272 (tp30) REVERT: U 229 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7272 (mt0) REVERT: C 65 GLU cc_start: 0.6017 (mt-10) cc_final: 0.5020 (tp30) outliers start: 48 outliers final: 34 residues processed: 226 average time/residue: 0.1893 time to fit residues: 62.8620 Evaluate side-chains 213 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 176 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 126 CYS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 376 THR 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 508 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 588 SER 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 44 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 139 THR 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 54 LEU Chi-restraints excluded: chain U residue 64 SER 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 166 SER 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: 4.9990 chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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: 0.7440 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10671 Z= 0.239 Angle : 0.611 10.617 14561 Z= 0.290 Chirality : 0.042 0.184 1743 Planarity : 0.005 0.049 1827 Dihedral : 5.190 57.821 1503 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.66 % Favored : 95.20 % Rotamer: Outliers : 5.03 % Allowed : 25.93 % Favored : 69.04 % 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: 0.03 (0.23), residues: 1395 helix: 1.39 (0.19), residues: 794 sheet: -1.12 (0.42), residues: 128 loop : -2.08 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 195 HIS 0.007 0.001 HIS C 114 PHE 0.030 0.002 PHE B 433 TYR 0.014 0.001 TYR C 214 ARG 0.008 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 226 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 173 time to evaluate : 1.170 Fit side-chains REVERT: B 192 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6849 (mm-30) REVERT: B 384 ASP cc_start: 0.7660 (m-30) cc_final: 0.7241 (m-30) REVERT: B 495 MET cc_start: 0.7823 (mmm) cc_final: 0.6878 (mtt) REVERT: B 525 TRP cc_start: 0.6582 (m100) cc_final: 0.6233 (m100) REVERT: B 593 MET cc_start: 0.6370 (OUTLIER) cc_final: 0.6076 (mmt) REVERT: D 184 ASP cc_start: 0.7386 (p0) cc_final: 0.7150 (p0) REVERT: D 213 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: U 53 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7185 (tm) REVERT: U 57 LEU cc_start: 0.6135 (tp) cc_final: 0.5799 (tp) REVERT: U 119 ARG cc_start: 0.5618 (mpt180) cc_final: 0.5388 (tpt90) REVERT: U 129 GLU cc_start: 0.7875 (tm-30) cc_final: 0.6958 (pt0) REVERT: U 229 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7260 (mt0) REVERT: C 57 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6346 (tt) REVERT: C 65 GLU cc_start: 0.5953 (mt-10) cc_final: 0.5011 (tp30) outliers start: 53 outliers final: 43 residues processed: 215 average time/residue: 0.1919 time to fit residues: 62.3851 Evaluate side-chains 217 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 169 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 126 CYS 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 367 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 490 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 588 SER 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 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 64 ASN Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 213 GLU 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 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 54 LEU Chi-restraints excluded: chain U residue 64 SER 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 57 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 184 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 75 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 83 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3797 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= 0.175 Angle : 0.588 10.717 14561 Z= 0.275 Chirality : 0.040 0.196 1743 Planarity : 0.004 0.050 1827 Dihedral : 5.020 54.169 1503 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.44 % Favored : 95.41 % Rotamer: Outliers : 5.13 % Allowed : 25.83 % Favored : 69.04 % 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: 0.16 (0.23), residues: 1395 helix: 1.50 (0.19), residues: 794 sheet: -0.99 (0.43), residues: 130 loop : -2.07 (0.26), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 195 HIS 0.007 0.001 HIS C 114 PHE 0.028 0.001 PHE B 433 TYR 0.018 0.001 TYR C 214 ARG 0.005 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 234 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 180 time to evaluate : 1.180 Fit side-chains REVERT: B 78 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7111 (mp) REVERT: B 153 VAL cc_start: 0.7214 (t) cc_final: 0.6830 (p) REVERT: B 192 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6860 (mm-30) REVERT: B 384 ASP cc_start: 0.7600 (m-30) cc_final: 0.7216 (m-30) REVERT: B 495 MET cc_start: 0.7783 (mmm) cc_final: 0.6747 (mtt) REVERT: B 525 TRP cc_start: 0.6596 (m100) cc_final: 0.6228 (m100) REVERT: B 593 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.5941 (mmt) REVERT: U 53 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7138 (tm) REVERT: U 57 LEU cc_start: 0.6199 (tp) cc_final: 0.5917 (tp) REVERT: U 119 ARG cc_start: 0.5715 (mpt180) cc_final: 0.5485 (tpt90) REVERT: U 129 GLU cc_start: 0.7872 (tm-30) cc_final: 0.6895 (pt0) REVERT: U 206 HIS cc_start: 0.5233 (OUTLIER) cc_final: 0.4321 (m-70) REVERT: U 226 MET cc_start: 0.4466 (tmm) cc_final: 0.4135 (tmm) REVERT: U 229 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7267 (mt0) REVERT: C 57 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6321 (tt) REVERT: C 65 GLU cc_start: 0.5888 (mt-10) cc_final: 0.4984 (tp30) outliers start: 54 outliers final: 40 residues processed: 222 average time/residue: 0.1918 time to fit residues: 63.3681 Evaluate side-chains 220 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 174 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 78 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 126 CYS 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 367 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 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 588 SER 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 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 139 THR 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 43 ILE Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 64 SER Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 194 SER Chi-restraints excluded: chain U residue 206 HIS 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 57 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 235 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7420 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10671 Z= 0.187 Angle : 0.600 10.645 14561 Z= 0.280 Chirality : 0.041 0.223 1743 Planarity : 0.004 0.049 1827 Dihedral : 4.963 54.275 1503 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.59 % Favored : 95.27 % Rotamer: Outliers : 5.22 % Allowed : 25.17 % Favored : 69.61 % 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: 0.15 (0.23), residues: 1395 helix: 1.47 (0.19), residues: 794 sheet: -0.93 (0.43), residues: 130 loop : -2.03 (0.26), residues: 471 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 0.027 0.001 PHE B 433 TYR 0.018 0.001 TYR C 214 ARG 0.005 0.000 ARG B 556 *********************** 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 232 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 177 time to evaluate : 1.050 Fit side-chains REVERT: B 56 TYR cc_start: 0.5918 (OUTLIER) cc_final: 0.5023 (t80) REVERT: B 78 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7106 (mp) REVERT: B 153 VAL cc_start: 0.7211 (t) cc_final: 0.6895 (p) REVERT: B 192 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6856 (mm-30) REVERT: B 384 ASP cc_start: 0.7573 (m-30) cc_final: 0.7181 (m-30) REVERT: B 495 MET cc_start: 0.7856 (mmm) cc_final: 0.6809 (mtt) REVERT: B 525 TRP cc_start: 0.6590 (m100) cc_final: 0.6241 (m100) REVERT: B 593 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.5996 (mmt) REVERT: D 213 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6592 (pm20) REVERT: U 53 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7146 (tm) REVERT: U 57 LEU cc_start: 0.6150 (tp) cc_final: 0.5890 (tp) REVERT: U 119 ARG cc_start: 0.5740 (mpt180) cc_final: 0.5510 (tpt90) REVERT: U 206 HIS cc_start: 0.5191 (OUTLIER) cc_final: 0.4266 (m-70) REVERT: U 226 MET cc_start: 0.4685 (tmm) cc_final: 0.4278 (tmm) REVERT: U 236 MET cc_start: 0.6485 (mmm) cc_final: 0.4618 (pmm) REVERT: C 57 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6271 (tt) REVERT: C 65 GLU cc_start: 0.5898 (mt-10) cc_final: 0.5049 (tp30) outliers start: 55 outliers final: 42 residues processed: 219 average time/residue: 0.1893 time to fit residues: 61.3850 Evaluate side-chains 222 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 173 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 56 TYR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 97 THR 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 320 LEU Chi-restraints excluded: chain B residue 367 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 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 588 SER 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 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 139 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 PHE 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 64 SER Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 194 SER Chi-restraints excluded: chain U residue 206 HIS Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 235 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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: 0.7436 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10671 Z= 0.196 Angle : 0.602 10.422 14561 Z= 0.283 Chirality : 0.041 0.207 1743 Planarity : 0.004 0.049 1827 Dihedral : 4.933 53.862 1503 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.66 % Favored : 95.20 % Rotamer: Outliers : 5.70 % Allowed : 24.79 % 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: 0.15 (0.23), residues: 1395 helix: 1.44 (0.19), residues: 793 sheet: -0.87 (0.43), residues: 130 loop : -2.00 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP U 113 HIS 0.007 0.001 HIS C 114 PHE 0.028 0.001 PHE B 433 TYR 0.019 0.001 TYR C 214 ARG 0.008 0.000 ARG B 526 *********************** 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 236 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 176 time to evaluate : 1.244 Fit side-chains REVERT: B 56 TYR cc_start: 0.5978 (OUTLIER) cc_final: 0.4986 (t80) REVERT: B 78 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7109 (mp) REVERT: B 153 VAL cc_start: 0.7166 (t) cc_final: 0.6857 (p) REVERT: B 192 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6844 (mm-30) REVERT: B 384 ASP cc_start: 0.7566 (m-30) cc_final: 0.7173 (m-30) REVERT: B 495 MET cc_start: 0.7890 (mmm) cc_final: 0.6850 (mtt) REVERT: B 525 TRP cc_start: 0.6671 (m100) cc_final: 0.6238 (m100) REVERT: B 593 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.6008 (mmt) REVERT: D 213 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6580 (pm20) REVERT: U 53 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7258 (tm) REVERT: U 57 LEU cc_start: 0.6201 (tp) cc_final: 0.5984 (tp) REVERT: U 206 HIS cc_start: 0.5199 (OUTLIER) cc_final: 0.4262 (m-70) REVERT: U 226 MET cc_start: 0.4680 (tmm) cc_final: 0.4478 (tmm) REVERT: C 57 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6286 (tt) REVERT: C 65 GLU cc_start: 0.5877 (mt-10) cc_final: 0.5013 (tp30) outliers start: 60 outliers final: 48 residues processed: 222 average time/residue: 0.1785 time to fit residues: 59.0417 Evaluate side-chains 225 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 170 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 56 TYR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 145 THR 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 320 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 387 MET 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 492 MET Chi-restraints excluded: chain B residue 520 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 588 SER 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 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 139 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 213 GLU 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 D residue 274 PHE 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 64 SER Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 194 SER Chi-restraints excluded: chain U residue 206 HIS Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 235 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.0770 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 127 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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: 0.7400 moved from start: 0.4175 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= 0.167 Angle : 0.596 10.493 14561 Z= 0.279 Chirality : 0.040 0.214 1743 Planarity : 0.005 0.049 1827 Dihedral : 4.799 54.820 1502 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.01 % Favored : 95.84 % Rotamer: Outliers : 4.75 % Allowed : 25.93 % Favored : 69.33 % 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: 0.26 (0.23), residues: 1395 helix: 1.54 (0.19), residues: 795 sheet: -0.77 (0.44), residues: 130 loop : -2.02 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP U 113 HIS 0.006 0.001 HIS C 114 PHE 0.026 0.001 PHE B 433 TYR 0.017 0.001 TYR C 214 ARG 0.008 0.000 ARG B 526 ********************** REFINEMENT MACRO_CYCLE 10 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 223 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 173 time to evaluate : 1.107 Fit side-chains REVERT: B 56 TYR cc_start: 0.5934 (OUTLIER) cc_final: 0.4942 (t80) REVERT: B 153 VAL cc_start: 0.7184 (t) cc_final: 0.6877 (p) REVERT: B 192 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6863 (mm-30) REVERT: B 384 ASP cc_start: 0.7604 (m-30) cc_final: 0.7217 (m-30) REVERT: B 495 MET cc_start: 0.7864 (mmm) cc_final: 0.6776 (mtt) REVERT: B 525 TRP cc_start: 0.6685 (m100) cc_final: 0.6263 (m100) REVERT: D 213 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6538 (pm20) REVERT: U 53 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7244 (tm) REVERT: U 57 LEU cc_start: 0.6235 (tp) cc_final: 0.6019 (tp) REVERT: U 226 MET cc_start: 0.4712 (tmm) cc_final: 0.4493 (tmm) REVERT: U 236 MET cc_start: 0.6454 (mmm) cc_final: 0.4734 (pmm) REVERT: C 57 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6272 (tt) REVERT: C 65 GLU cc_start: 0.5777 (mt-10) cc_final: 0.5005 (tp30) outliers start: 50 outliers final: 37 residues processed: 213 average time/residue: 0.1891 time to fit residues: 59.8260 Evaluate side-chains 212 residues out of total 1114 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 171 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 56 TYR 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 362 VAL Chi-restraints excluded: chain B residue 367 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 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 588 SER 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 B residue 637 ILE 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 213 GLU 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 43 ILE Chi-restraints excluded: chain U residue 53 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 64 SER Chi-restraints excluded: chain U residue 108 ILE Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain U residue 264 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 166 SER Chi-restraints excluded: chain C residue 184 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.192113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 139)---------------| | r_work = 0.3797 r_free = 0.3797 target = 0.164998 restraints weight = 11796.751| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 0.88 r_work: 0.3658 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10671 Z= 0.211 Angle : 0.620 10.252 14561 Z= 0.292 Chirality : 0.041 0.206 1743 Planarity : 0.005 0.049 1827 Dihedral : 4.857 54.148 1502 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.37 % Favored : 95.48 % Rotamer: Outliers : 4.65 % Allowed : 25.64 % Favored : 69.71 % 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: 0.16 (0.23), residues: 1395 helix: 1.46 (0.19), residues: 793 sheet: -0.86 (0.43), residues: 131 loop : -2.00 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP U 113 HIS 0.007 0.001 HIS C 114 PHE 0.029 0.002 PHE B 433 TYR 0.018 0.001 TYR C 214 ARG 0.009 0.000 ARG B 556 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2423.74 seconds wall clock time: 43 minutes 57.12 seconds (2637.12 seconds total)