Starting phenix.real_space_refine on Fri Mar 15 09:39:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f23_31426/03_2024/7f23_31426_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f23_31426/03_2024/7f23_31426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f23_31426/03_2024/7f23_31426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f23_31426/03_2024/7f23_31426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f23_31426/03_2024/7f23_31426_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f23_31426/03_2024/7f23_31426_updated.pdb" } resolution = 3.58 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= 0.003 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3063 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 53 5.16 5 C 5196 2.51 5 N 1440 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 50": "NH1" <-> "NH2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 130": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F ARG 219": "NH1" <-> "NH2" Residue "F ARG 226": "NH1" <-> "NH2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F ARG 266": "NH1" <-> "NH2" Residue "F ARG 338": "NH1" <-> "NH2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 240": "OD1" <-> "OD2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "D ASP 36": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8211 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2197 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 9, 'TRANS': 266} Chain breaks: 3 Chain: "A" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1937 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2629 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 341, 2605 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 341, 2605 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2624 Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 434 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP B 27 " occ=0.45 ... (14 atoms not shown) pdb=" OD2BASP B 27 " occ=0.55 Time building chain proxies: 6.11, per 1000 atoms: 0.74 Number of scatterers: 8211 At special positions: 0 Unit cell: (84.786, 95.656, 126.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 P 3 15.00 O 1519 8.00 N 1440 7.00 C 5196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 186 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.05 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: 3.31 Conformation dependent library (CDL) restraints added in 2.1 seconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 10 sheets defined 39.5% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'F' and resid 21 through 50 Processing helix chain 'F' and resid 59 through 87 Proline residue: F 79 - end of helix Processing helix chain 'F' and resid 93 through 126 removed outlier: 4.537A pdb=" N SER F 107 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N SER F 110 " --> pdb=" O SER F 107 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE F 111 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER F 126 " --> pdb=" O TRP F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 134 Processing helix chain 'F' and resid 137 through 160 Proline residue: F 158 - end of helix Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 204 through 236 removed outlier: 3.601A pdb=" N ALA F 208 " --> pdb=" O TYR F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 297 Proline residue: F 287 - end of helix Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 310 through 331 removed outlier: 3.777A pdb=" N GLY F 320 " --> pdb=" O PHE F 316 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP F 321 " --> pdb=" O VAL F 317 " (cutoff:3.500A) Proline residue: F 328 - end of helix Processing helix chain 'F' and resid 335 through 345 Processing helix chain 'A' and resid 13 through 39 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 4.051A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 30 through 47 removed outlier: 5.165A pdb=" N LYS D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.324A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.904A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.866A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.704A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.783A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.758A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.244A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.707A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 92 through 98 removed outlier: 6.147A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1077 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2681 1.34 - 1.46: 2060 1.46 - 1.58: 3567 1.58 - 1.71: 5 1.71 - 1.83: 72 Bond restraints: 8385 Sorted by residual: bond pdb=" N CYS F 96 " pdb=" CA CYS F 96 " ideal model delta sigma weight residual 1.458 1.427 0.030 1.33e-02 5.65e+03 5.13e+00 bond pdb=" CA SER F 110 " pdb=" C SER F 110 " ideal model delta sigma weight residual 1.525 1.498 0.027 1.25e-02 6.40e+03 4.68e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.434 0.064 3.10e-02 1.04e+03 4.22e+00 bond pdb=" CG LEU F 66 " pdb=" CD1 LEU F 66 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.15e+00 bond pdb=" C3 LDP F 501 " pdb=" C4 LDP F 501 " ideal model delta sigma weight residual 1.400 1.361 0.039 2.00e-02 2.50e+03 3.87e+00 ... (remaining 8380 not shown) Histogram of bond angle deviations from ideal: 98.48 - 105.62: 127 105.62 - 112.75: 4488 112.75 - 119.88: 3023 119.88 - 127.01: 3630 127.01 - 134.14: 103 Bond angle restraints: 11371 Sorted by residual: angle pdb=" CA CYS E 99 " pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " ideal model delta sigma weight residual 114.40 126.93 -12.53 2.30e+00 1.89e-01 2.97e+01 angle pdb=" C LYS A 233 " pdb=" N TRP A 234 " pdb=" CA TRP A 234 " ideal model delta sigma weight residual 121.58 113.52 8.06 1.95e+00 2.63e-01 1.71e+01 angle pdb=" C THR F 108 " pdb=" N ALA F 109 " pdb=" CA ALA F 109 " ideal model delta sigma weight residual 120.72 114.50 6.22 1.67e+00 3.59e-01 1.39e+01 angle pdb=" C SER B 334 " pdb=" CA SER B 334 " pdb=" CB SER B 334 " ideal model delta sigma weight residual 111.63 106.58 5.05 1.36e+00 5.41e-01 1.38e+01 angle pdb=" C GLY B 131 " pdb=" N ASN B 132 " pdb=" CA ASN B 132 " ideal model delta sigma weight residual 122.81 128.33 -5.52 1.57e+00 4.06e-01 1.24e+01 ... (remaining 11366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.60: 4895 34.60 - 69.20: 87 69.20 - 103.80: 4 103.80 - 138.40: 1 138.40 - 173.00: 2 Dihedral angle restraints: 4989 sinusoidal: 1958 harmonic: 3031 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual -86.00 -18.21 -67.79 1 1.00e+01 1.00e-02 5.97e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -117.73 -173.00 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -36.16 140.75 1 2.00e+01 2.50e-03 4.26e+01 ... (remaining 4986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 956 0.062 - 0.125: 272 0.125 - 0.187: 48 0.187 - 0.250: 1 0.250 - 0.312: 1 Chirality restraints: 1278 Sorted by residual: chirality pdb=" CA CYS E 99 " pdb=" N CYS E 99 " pdb=" C CYS E 99 " pdb=" CB CYS E 99 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA PRO F 206 " pdb=" N PRO F 206 " pdb=" C PRO F 206 " pdb=" CB PRO F 206 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA PHE A 222 " pdb=" N PHE A 222 " pdb=" C PHE A 222 " pdb=" CB PHE A 222 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.58e-01 ... (remaining 1275 not shown) Planarity restraints: 1444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 109 " -0.043 2.00e-02 2.50e+03 8.57e-02 7.34e+01 pdb=" C ALA F 109 " 0.148 2.00e-02 2.50e+03 pdb=" O ALA F 109 " -0.054 2.00e-02 2.50e+03 pdb=" N SER F 110 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 94 " -0.030 2.00e-02 2.50e+03 6.06e-02 3.68e+01 pdb=" C SER F 94 " 0.105 2.00e-02 2.50e+03 pdb=" O SER F 94 " -0.039 2.00e-02 2.50e+03 pdb=" N PHE F 95 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 347 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C ARG A 347 " 0.074 2.00e-02 2.50e+03 pdb=" O ARG A 347 " -0.027 2.00e-02 2.50e+03 pdb=" N ILE A 348 " -0.025 2.00e-02 2.50e+03 ... (remaining 1441 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 217 2.65 - 3.21: 8300 3.21 - 3.77: 13086 3.77 - 4.34: 17763 4.34 - 4.90: 29053 Nonbonded interactions: 68419 Sorted by model distance: nonbonded pdb=" OG SER F 65 " pdb=" ND2 ASN F 113 " model vdw 2.087 2.520 nonbonded pdb=" OG SER B 331 " pdb=" OD2 ASP B 333 " model vdw 2.135 2.440 nonbonded pdb=" OG SER A 54 " pdb=" O1G GTP A 401 " model vdw 2.142 2.440 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.163 2.520 nonbonded pdb=" OG1 THR A 55 " pdb=" O1A GTP A 401 " model vdw 2.164 2.440 ... (remaining 68414 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 1.800 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.230 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 0.010 0.068 8385 Z= 0.671 Angle : 1.006 12.527 11371 Z= 0.572 Chirality : 0.057 0.312 1278 Planarity : 0.007 0.086 1444 Dihedral : 15.075 172.997 3016 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.57 % Allowed : 10.99 % Favored : 88.45 % 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: -2.63 (0.23), residues: 1025 helix: -1.68 (0.21), residues: 416 sheet: -1.41 (0.30), residues: 245 loop : -1.74 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 99 HIS 0.014 0.002 HIS A 357 PHE 0.032 0.003 PHE F 333 TYR 0.018 0.002 TYR E 95 ARG 0.004 0.001 ARG F 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 209 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 86 ILE cc_start: 0.8784 (mm) cc_final: 0.8539 (mt) REVERT: F 194 TYR cc_start: 0.8868 (t80) cc_final: 0.8660 (t80) REVERT: F 225 ILE cc_start: 0.8842 (mt) cc_final: 0.8642 (mp) REVERT: A 20 ARG cc_start: 0.8359 (mtt180) cc_final: 0.8067 (mtt-85) REVERT: A 33 ASP cc_start: 0.8447 (t0) cc_final: 0.8115 (t0) REVERT: A 35 GLN cc_start: 0.8451 (tm-30) cc_final: 0.7814 (tm-30) REVERT: B 214 ARG cc_start: 0.7145 (mtm180) cc_final: 0.6755 (ttp-170) REVERT: B 269 ILE cc_start: 0.9095 (mt) cc_final: 0.8793 (mm) REVERT: E 29 PHE cc_start: 0.9027 (t80) cc_final: 0.8697 (t80) REVERT: E 80 TYR cc_start: 0.7366 (m-80) cc_final: 0.7081 (m-80) REVERT: E 82 GLN cc_start: 0.7631 (tp40) cc_final: 0.7293 (tp40) REVERT: E 83 MET cc_start: 0.7743 (ptp) cc_final: 0.7524 (ptp) REVERT: D 47 GLU cc_start: 0.7750 (pm20) cc_final: 0.6941 (pm20) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.2324 time to fit residues: 63.9643 Evaluate side-chains 160 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 41 ASN F 113 ASN F 164 HIS F 224 GLN A 14 ASN A 267 GLN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 110 ASN B 119 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS E 5 GLN E 13 GLN E 77 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8385 Z= 0.188 Angle : 0.606 9.406 11371 Z= 0.314 Chirality : 0.045 0.178 1278 Planarity : 0.004 0.040 1444 Dihedral : 9.066 171.354 1155 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.49 % Allowed : 16.08 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1025 helix: 0.20 (0.24), residues: 421 sheet: -0.75 (0.32), residues: 235 loop : -0.92 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.007 0.001 HIS F 53 PHE 0.016 0.001 PHE E 108 TYR 0.010 0.001 TYR E 115 ARG 0.003 0.000 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 210 MET cc_start: 0.6491 (mtp) cc_final: 0.5943 (ttm) REVERT: F 211 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7485 (mt) REVERT: F 271 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8625 (mm) REVERT: F 333 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7789 (m-10) REVERT: A 33 ASP cc_start: 0.8308 (t0) cc_final: 0.7929 (t0) REVERT: A 249 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7529 (p0) REVERT: B 46 ARG cc_start: 0.7441 (mtp85) cc_final: 0.7015 (mtm110) REVERT: B 211 TRP cc_start: 0.7719 (m100) cc_final: 0.7432 (m100) REVERT: B 214 ARG cc_start: 0.7114 (mtm180) cc_final: 0.6774 (ptp-170) REVERT: B 289 TYR cc_start: 0.9014 (m-80) cc_final: 0.8781 (m-80) REVERT: B 297 TRP cc_start: 0.8123 (m100) cc_final: 0.7873 (m-10) REVERT: B 318 LEU cc_start: 0.8672 (pp) cc_final: 0.8425 (pp) REVERT: E 4 LEU cc_start: 0.8145 (mt) cc_final: 0.7931 (mt) REVERT: E 29 PHE cc_start: 0.8904 (t80) cc_final: 0.8620 (t80) REVERT: E 36 TRP cc_start: 0.8601 (m100) cc_final: 0.8352 (m100) REVERT: E 80 TYR cc_start: 0.7083 (m-80) cc_final: 0.6832 (m-80) REVERT: E 82 GLN cc_start: 0.7580 (tp40) cc_final: 0.7285 (tp40) REVERT: D 44 HIS cc_start: 0.8499 (m170) cc_final: 0.7705 (m170) REVERT: D 47 GLU cc_start: 0.8039 (pm20) cc_final: 0.7742 (pm20) outliers start: 19 outliers final: 14 residues processed: 210 average time/residue: 0.2031 time to fit residues: 57.9114 Evaluate side-chains 188 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 224 GLN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8385 Z= 0.241 Angle : 0.601 9.071 11371 Z= 0.312 Chirality : 0.044 0.192 1278 Planarity : 0.004 0.038 1444 Dihedral : 8.962 171.173 1155 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.96 % Allowed : 18.80 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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 (0.26), residues: 1025 helix: 0.82 (0.25), residues: 421 sheet: -0.54 (0.32), residues: 236 loop : -0.73 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.009 0.001 HIS F 53 PHE 0.019 0.002 PHE B 235 TYR 0.014 0.001 TYR F 194 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 78 MET cc_start: 0.7415 (mmm) cc_final: 0.7183 (mpp) REVERT: F 214 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7002 (m-80) REVERT: F 271 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8644 (mm) REVERT: F 333 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7922 (m-10) REVERT: A 33 ASP cc_start: 0.8351 (t0) cc_final: 0.7921 (t0) REVERT: A 249 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7569 (p0) REVERT: A 253 TYR cc_start: 0.7343 (m-80) cc_final: 0.6588 (m-80) REVERT: A 270 LEU cc_start: 0.9379 (mp) cc_final: 0.9163 (mp) REVERT: B 188 MET cc_start: 0.8365 (tpp) cc_final: 0.8105 (mmt) REVERT: B 214 ARG cc_start: 0.7140 (mtm180) cc_final: 0.6823 (ptp-170) REVERT: B 289 TYR cc_start: 0.9078 (m-80) cc_final: 0.8866 (m-80) REVERT: E 29 PHE cc_start: 0.8967 (t80) cc_final: 0.8621 (t80) REVERT: E 36 TRP cc_start: 0.8596 (m100) cc_final: 0.8372 (m100) REVERT: E 80 TYR cc_start: 0.7062 (m-80) cc_final: 0.6824 (m-80) REVERT: E 83 MET cc_start: 0.7090 (ptp) cc_final: 0.6875 (ptp) REVERT: E 98 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7765 (tmm-80) REVERT: D 47 GLU cc_start: 0.7949 (pm20) cc_final: 0.7610 (pm20) outliers start: 32 outliers final: 17 residues processed: 194 average time/residue: 0.2071 time to fit residues: 54.3678 Evaluate side-chains 183 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 97 optimal weight: 40.0000 chunk 48 optimal weight: 0.0970 chunk 87 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 81 optimal weight: 4.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8385 Z= 0.230 Angle : 0.588 7.525 11371 Z= 0.306 Chirality : 0.044 0.200 1278 Planarity : 0.004 0.037 1444 Dihedral : 8.922 170.987 1155 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.85 % Allowed : 20.72 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.00 (0.26), residues: 1025 helix: 0.97 (0.26), residues: 419 sheet: -0.57 (0.32), residues: 237 loop : -0.56 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.010 0.001 HIS A 357 PHE 0.016 0.001 PHE E 108 TYR 0.020 0.001 TYR F 194 ARG 0.007 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 214 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: F 271 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8627 (mm) REVERT: F 333 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7826 (m-10) REVERT: A 33 ASP cc_start: 0.8332 (t0) cc_final: 0.7894 (t0) REVERT: A 249 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7397 (p0) REVERT: B 188 MET cc_start: 0.8368 (tpp) cc_final: 0.8098 (mmt) REVERT: B 211 TRP cc_start: 0.7735 (m100) cc_final: 0.7380 (m100) REVERT: B 214 ARG cc_start: 0.7087 (mtm180) cc_final: 0.6826 (ptp-170) REVERT: B 289 TYR cc_start: 0.9084 (m-80) cc_final: 0.8840 (m-80) REVERT: E 4 LEU cc_start: 0.7886 (mt) cc_final: 0.7535 (tp) REVERT: E 36 TRP cc_start: 0.8583 (m100) cc_final: 0.8352 (m100) REVERT: E 80 TYR cc_start: 0.6887 (m-80) cc_final: 0.6570 (m-80) REVERT: E 98 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7782 (tmm-80) REVERT: D 47 GLU cc_start: 0.7971 (pm20) cc_final: 0.7618 (pm20) outliers start: 31 outliers final: 25 residues processed: 190 average time/residue: 0.2126 time to fit residues: 54.4988 Evaluate side-chains 183 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8385 Z= 0.253 Angle : 0.607 9.373 11371 Z= 0.314 Chirality : 0.044 0.216 1278 Planarity : 0.004 0.039 1444 Dihedral : 8.908 170.981 1155 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.42 % Allowed : 21.97 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.05 (0.27), residues: 1025 helix: 0.97 (0.26), residues: 425 sheet: -0.54 (0.32), residues: 239 loop : -0.52 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 281 HIS 0.008 0.001 HIS A 357 PHE 0.020 0.001 PHE B 235 TYR 0.017 0.001 TYR F 194 ARG 0.004 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: F 210 MET cc_start: 0.6853 (mtp) cc_final: 0.6345 (ttm) REVERT: F 214 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: F 271 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8596 (mm) REVERT: F 333 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7741 (m-10) REVERT: A 33 ASP cc_start: 0.8350 (t0) cc_final: 0.7905 (t0) REVERT: A 239 ASN cc_start: 0.8642 (p0) cc_final: 0.8433 (p0) REVERT: A 249 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7562 (p0) REVERT: B 211 TRP cc_start: 0.7749 (m100) cc_final: 0.7332 (m100) REVERT: B 214 ARG cc_start: 0.7067 (mtm180) cc_final: 0.6806 (ptp-170) REVERT: B 289 TYR cc_start: 0.9101 (m-80) cc_final: 0.8852 (m-80) REVERT: E 4 LEU cc_start: 0.8062 (mt) cc_final: 0.7757 (tp) REVERT: E 36 TRP cc_start: 0.8596 (m100) cc_final: 0.8314 (m100) REVERT: E 43 LYS cc_start: 0.7706 (mtmm) cc_final: 0.7445 (ptpt) REVERT: E 47 TRP cc_start: 0.9156 (t60) cc_final: 0.8849 (t60) REVERT: E 51 ILE cc_start: 0.8239 (tt) cc_final: 0.8013 (tt) REVERT: E 80 TYR cc_start: 0.6800 (m-80) cc_final: 0.6494 (m-80) REVERT: E 82 GLN cc_start: 0.7558 (tp40) cc_final: 0.7244 (tp-100) REVERT: E 87 LYS cc_start: 0.6906 (mttt) cc_final: 0.6682 (mtmt) REVERT: E 98 ARG cc_start: 0.8100 (ttp80) cc_final: 0.7861 (tmm-80) REVERT: D 47 GLU cc_start: 0.7968 (pm20) cc_final: 0.7607 (pm20) outliers start: 36 outliers final: 25 residues processed: 185 average time/residue: 0.2033 time to fit residues: 51.6780 Evaluate side-chains 183 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.0570 chunk 51 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN E 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8385 Z= 0.208 Angle : 0.594 9.832 11371 Z= 0.304 Chirality : 0.043 0.230 1278 Planarity : 0.004 0.040 1444 Dihedral : 8.837 170.706 1155 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.74 % Allowed : 24.01 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.17 (0.27), residues: 1025 helix: 1.06 (0.26), residues: 424 sheet: -0.36 (0.32), residues: 237 loop : -0.53 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS A 357 PHE 0.021 0.001 PHE B 235 TYR 0.024 0.001 TYR F 194 ARG 0.004 0.000 ARG E 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 210 MET cc_start: 0.6610 (mtp) cc_final: 0.6267 (ttm) REVERT: F 214 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.6923 (m-10) REVERT: F 271 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8617 (mm) REVERT: F 333 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7730 (m-10) REVERT: A 33 ASP cc_start: 0.8294 (t0) cc_final: 0.7810 (t0) REVERT: A 249 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7509 (p0) REVERT: B 37 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8014 (mp) REVERT: B 211 TRP cc_start: 0.7682 (m100) cc_final: 0.7291 (m100) REVERT: B 214 ARG cc_start: 0.6958 (mtm180) cc_final: 0.6745 (ptp-170) REVERT: B 234 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8202 (t80) REVERT: B 289 TYR cc_start: 0.9077 (m-80) cc_final: 0.8777 (m-80) REVERT: E 4 LEU cc_start: 0.8057 (mt) cc_final: 0.7663 (tp) REVERT: E 36 TRP cc_start: 0.8514 (m100) cc_final: 0.8292 (m100) REVERT: E 43 LYS cc_start: 0.7705 (mtmm) cc_final: 0.7472 (ptpt) REVERT: E 80 TYR cc_start: 0.6710 (m-80) cc_final: 0.6387 (m-80) REVERT: E 87 LYS cc_start: 0.7078 (mttt) cc_final: 0.6863 (mtmt) REVERT: D 17 GLU cc_start: 0.7614 (pt0) cc_final: 0.7402 (pt0) REVERT: D 47 GLU cc_start: 0.7887 (pm20) cc_final: 0.7590 (pm20) outliers start: 30 outliers final: 21 residues processed: 187 average time/residue: 0.2014 time to fit residues: 51.2796 Evaluate side-chains 177 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.0770 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8385 Z= 0.206 Angle : 0.601 10.557 11371 Z= 0.305 Chirality : 0.044 0.247 1278 Planarity : 0.004 0.040 1444 Dihedral : 8.803 170.586 1155 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.96 % Allowed : 24.69 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.20 (0.27), residues: 1025 helix: 1.09 (0.26), residues: 424 sheet: -0.33 (0.32), residues: 237 loop : -0.53 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.006 0.001 HIS F 53 PHE 0.021 0.001 PHE B 235 TYR 0.021 0.001 TYR F 194 ARG 0.004 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 160 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7740 (tm-30) REVERT: F 210 MET cc_start: 0.6602 (mtp) cc_final: 0.6283 (ttm) REVERT: F 214 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.6922 (m-10) REVERT: F 271 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8614 (mm) REVERT: F 333 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7727 (m-10) REVERT: A 33 ASP cc_start: 0.8296 (t0) cc_final: 0.7858 (t0) REVERT: A 249 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7412 (p0) REVERT: B 37 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8172 (mp) REVERT: B 211 TRP cc_start: 0.7715 (m100) cc_final: 0.7323 (m100) REVERT: B 214 ARG cc_start: 0.7002 (mtm180) cc_final: 0.6753 (ptp-170) REVERT: B 234 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8179 (t80) REVERT: B 289 TYR cc_start: 0.9082 (m-80) cc_final: 0.8723 (m-80) REVERT: E 4 LEU cc_start: 0.8001 (mt) cc_final: 0.7612 (tp) REVERT: E 36 TRP cc_start: 0.8552 (m100) cc_final: 0.8305 (m100) REVERT: E 47 TRP cc_start: 0.9108 (t60) cc_final: 0.8856 (t60) REVERT: E 80 TYR cc_start: 0.6689 (m-80) cc_final: 0.6354 (m-80) REVERT: D 47 GLU cc_start: 0.7865 (pm20) cc_final: 0.7513 (pm20) outliers start: 32 outliers final: 23 residues processed: 179 average time/residue: 0.1838 time to fit residues: 46.0199 Evaluate side-chains 178 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8385 Z= 0.237 Angle : 0.615 9.545 11371 Z= 0.312 Chirality : 0.044 0.254 1278 Planarity : 0.004 0.040 1444 Dihedral : 8.807 170.512 1155 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.08 % Allowed : 25.14 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.21 (0.27), residues: 1025 helix: 1.11 (0.26), residues: 426 sheet: -0.32 (0.32), residues: 235 loop : -0.58 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 281 HIS 0.006 0.001 HIS F 53 PHE 0.021 0.001 PHE B 235 TYR 0.020 0.001 TYR F 194 ARG 0.004 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 210 MET cc_start: 0.6703 (mtp) cc_final: 0.6392 (ttm) REVERT: F 214 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.6920 (m-10) REVERT: F 271 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8598 (mm) REVERT: F 333 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7746 (m-10) REVERT: A 33 ASP cc_start: 0.8386 (t0) cc_final: 0.7878 (t0) REVERT: A 44 LEU cc_start: 0.8782 (tp) cc_final: 0.8437 (tp) REVERT: A 60 MET cc_start: 0.8338 (mmm) cc_final: 0.7943 (mmm) REVERT: A 222 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8474 (p90) REVERT: A 249 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7492 (p0) REVERT: B 37 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8154 (mp) REVERT: B 211 TRP cc_start: 0.7705 (m100) cc_final: 0.7325 (m100) REVERT: B 214 ARG cc_start: 0.7045 (mtm180) cc_final: 0.6772 (ptp-170) REVERT: B 289 TYR cc_start: 0.9082 (m-80) cc_final: 0.8690 (m-80) REVERT: E 4 LEU cc_start: 0.7884 (mt) cc_final: 0.7488 (tp) REVERT: E 36 TRP cc_start: 0.8565 (m100) cc_final: 0.8298 (m100) REVERT: E 80 TYR cc_start: 0.6735 (m-80) cc_final: 0.6398 (m-80) REVERT: E 87 LYS cc_start: 0.7194 (mttt) cc_final: 0.6982 (mtmt) REVERT: E 123 GLN cc_start: 0.8245 (tt0) cc_final: 0.7870 (tp-100) REVERT: D 47 GLU cc_start: 0.7860 (pm20) cc_final: 0.7539 (pm20) outliers start: 33 outliers final: 26 residues processed: 178 average time/residue: 0.1852 time to fit residues: 45.9652 Evaluate side-chains 180 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9980 chunk 93 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8385 Z= 0.204 Angle : 0.617 11.391 11371 Z= 0.312 Chirality : 0.044 0.272 1278 Planarity : 0.004 0.050 1444 Dihedral : 8.776 170.071 1155 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.85 % Allowed : 25.93 % Favored : 70.22 % 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: 0.22 (0.27), residues: 1025 helix: 1.23 (0.26), residues: 415 sheet: -0.38 (0.32), residues: 234 loop : -0.60 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 281 HIS 0.006 0.001 HIS F 53 PHE 0.021 0.001 PHE B 235 TYR 0.026 0.001 TYR F 194 ARG 0.004 0.000 ARG F 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 160 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7775 (tm-30) REVERT: F 210 MET cc_start: 0.6666 (mtp) cc_final: 0.6385 (ttm) REVERT: F 214 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.6895 (m-10) REVERT: F 271 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8559 (mt) REVERT: F 333 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7766 (m-10) REVERT: A 44 LEU cc_start: 0.8717 (tp) cc_final: 0.8315 (tp) REVERT: A 249 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7375 (p0) REVERT: B 37 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8131 (mp) REVERT: B 211 TRP cc_start: 0.7672 (m100) cc_final: 0.7304 (m100) REVERT: B 214 ARG cc_start: 0.6964 (mtm180) cc_final: 0.6758 (ptp-170) REVERT: B 289 TYR cc_start: 0.9058 (m-80) cc_final: 0.8612 (m-80) REVERT: E 4 LEU cc_start: 0.7971 (mt) cc_final: 0.7549 (tp) REVERT: E 36 TRP cc_start: 0.8501 (m100) cc_final: 0.8259 (m100) REVERT: E 87 LYS cc_start: 0.7191 (mttt) cc_final: 0.6989 (mtmt) REVERT: E 123 GLN cc_start: 0.8230 (tt0) cc_final: 0.7901 (tp-100) outliers start: 31 outliers final: 22 residues processed: 181 average time/residue: 0.1967 time to fit residues: 49.4081 Evaluate side-chains 181 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8385 Z= 0.216 Angle : 0.629 11.503 11371 Z= 0.317 Chirality : 0.044 0.278 1278 Planarity : 0.004 0.065 1444 Dihedral : 8.776 169.878 1155 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.62 % Allowed : 26.39 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.38 (0.27), residues: 1025 helix: 1.39 (0.26), residues: 408 sheet: -0.25 (0.33), residues: 222 loop : -0.55 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 281 HIS 0.009 0.001 HIS F 53 PHE 0.021 0.001 PHE B 235 TYR 0.025 0.001 TYR F 194 ARG 0.003 0.000 ARG F 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 160 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7793 (tm-30) REVERT: F 210 MET cc_start: 0.6656 (mtp) cc_final: 0.6384 (ttm) REVERT: F 214 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.6899 (m-10) REVERT: F 271 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8554 (mt) REVERT: F 333 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7745 (m-10) REVERT: A 44 LEU cc_start: 0.8682 (tp) cc_final: 0.8263 (tp) REVERT: A 60 MET cc_start: 0.8300 (mmm) cc_final: 0.7980 (mmm) REVERT: A 222 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8506 (p90) REVERT: A 249 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7346 (p0) REVERT: B 37 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8159 (mp) REVERT: B 211 TRP cc_start: 0.7697 (m100) cc_final: 0.7301 (m100) REVERT: B 214 ARG cc_start: 0.6967 (mtm180) cc_final: 0.6749 (ptp-170) REVERT: B 289 TYR cc_start: 0.9056 (m-80) cc_final: 0.8621 (m-80) REVERT: E 36 TRP cc_start: 0.8522 (m100) cc_final: 0.8253 (m100) REVERT: E 77 ASN cc_start: 0.7337 (t0) cc_final: 0.6973 (t0) REVERT: E 87 LYS cc_start: 0.7200 (mttt) cc_final: 0.6999 (mtmt) outliers start: 29 outliers final: 22 residues processed: 176 average time/residue: 0.2006 time to fit residues: 48.7380 Evaluate side-chains 181 residues out of total 885 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 9.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 0.1980 chunk 33 optimal weight: 0.4980 chunk 82 optimal weight: 0.0270 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.163999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.115628 restraints weight = 36424.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123362 restraints weight = 12600.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126595 restraints weight = 6191.688| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8385 Z= 0.163 Angle : 0.615 10.541 11371 Z= 0.308 Chirality : 0.043 0.283 1278 Planarity : 0.004 0.069 1444 Dihedral : 8.692 168.895 1155 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.49 % Allowed : 27.86 % Favored : 69.65 % 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: 0.47 (0.27), residues: 1025 helix: 1.54 (0.26), residues: 399 sheet: -0.23 (0.33), residues: 223 loop : -0.53 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 281 HIS 0.009 0.001 HIS F 53 PHE 0.020 0.001 PHE B 235 TYR 0.025 0.001 TYR D 40 ARG 0.004 0.000 ARG A 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.49 seconds wall clock time: 34 minutes 57.22 seconds (2097.22 seconds total)