Starting phenix.real_space_refine on Thu Feb 13 00:18:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bya_16325/02_2025/8bya_16325.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bya_16325/02_2025/8bya_16325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bya_16325/02_2025/8bya_16325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bya_16325/02_2025/8bya_16325.map" model { file = "/net/cci-nas-00/data/ceres_data/8bya_16325/02_2025/8bya_16325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bya_16325/02_2025/8bya_16325.cif" } resolution = 3.38 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= 0.029 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 35 5.16 5 C 5392 2.51 5 N 1432 2.21 5 O 1528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8389 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2025 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 19, 'TRANS': 257} Chain breaks: 2 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'TPO:plan-1': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 114 Chain: "B" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1871 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 242} Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 6, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 115 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 499 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 6, 'TRANS': 62} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 855 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 6, 'ARG:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 12, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 157 Chain: "E" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2481 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "F" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 589 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 63} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 69 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" N LEU A 25 " occ=0.73 ... (3 atoms not shown) pdb=" CB LEU A 25 " occ=0.73 residue: pdb=" N ASP A 68 " occ=0.38 ... (3 atoms not shown) pdb=" CB ASP A 68 " occ=0.38 residue: pdb=" N PRO A 294 " occ=0.52 ... (5 atoms not shown) pdb=" CD PRO A 294 " occ=0.52 residue: pdb=" N HIS A 295 " occ=0.67 ... (8 atoms not shown) pdb=" NE2 HIS A 295 " occ=0.67 residue: pdb=" N LEU A 296 " occ=0.52 ... (6 atoms not shown) pdb=" CD2 LEU A 296 " occ=0.52 residue: pdb=" N THR D1082 " occ=0.22 ... (5 atoms not shown) pdb=" CG2 THR D1082 " occ=0.22 residue: pdb=" N ASP D1083 " occ=0.52 ... (6 atoms not shown) pdb=" OD2 ASP D1083 " occ=0.52 residue: pdb=" N ASP D1084 " occ=0.40 ... (3 atoms not shown) pdb=" CB ASP D1084 " occ=0.40 residue: pdb=" N ILE D1085 " occ=0.53 ... (6 atoms not shown) pdb=" CD1 ILE D1085 " occ=0.53 residue: pdb=" N PRO E2101 " occ=0.63 ... (5 atoms not shown) pdb=" CD PRO E2101 " occ=0.63 Time building chain proxies: 5.16, per 1000 atoms: 0.62 Number of scatterers: 8389 At special positions: 0 Unit cell: (82.39, 115.56, 115.56, 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 35 16.00 P 2 15.00 O 1528 8.00 N 1432 7.00 C 5392 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 - 3.00 Amino acid : True - 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: 2.22 Conformation dependent library (CDL) restraints added in 1.0 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 11 sheets defined 43.1% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.511A pdb=" N ILE A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 108 through 120 Processing helix chain 'A' and resid 129 through 132 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 183 through 189 removed outlier: 3.966A pdb=" N TRP A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 183 through 189' Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 207 through 220 removed outlier: 3.667A pdb=" N THR A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.894A pdb=" N VAL B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS B 192 " --> pdb=" O GLU B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.580A pdb=" N MET B 200 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 202 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 226 Processing helix chain 'B' and resid 228 through 244 Processing helix chain 'B' and resid 252 through 269 Processing helix chain 'B' and resid 274 through 281 Processing helix chain 'B' and resid 287 through 302 Processing helix chain 'B' and resid 310 through 318 removed outlier: 3.679A pdb=" N TYR B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 343 removed outlier: 3.521A pdb=" N LEU B 341 " --> pdb=" O GLY B 337 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 342 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 368 removed outlier: 3.835A pdb=" N LEU B 364 " --> pdb=" O PHE B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 381 removed outlier: 3.713A pdb=" N ILE B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 removed outlier: 3.526A pdb=" N ASP B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 414 removed outlier: 3.555A pdb=" N LYS B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 37 through 52 removed outlier: 3.992A pdb=" N LEU C 41 " --> pdb=" O ASP C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'D' and resid 1024 through 1031 Processing helix chain 'D' and resid 1045 through 1063 removed outlier: 3.898A pdb=" N ASN D1051 " --> pdb=" O LEU D1047 " (cutoff:3.500A) Processing helix chain 'D' and resid 1086 through 1092 Processing helix chain 'D' and resid 1096 through 1111 Processing helix chain 'D' and resid 1113 through 1128 Processing helix chain 'D' and resid 1131 through 1139 Processing helix chain 'D' and resid 1148 through 1157 removed outlier: 4.098A pdb=" N GLN D1152 " --> pdb=" O GLU D1148 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN D1157 " --> pdb=" O VAL D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1158 through 1160 No H-bonds generated for 'chain 'D' and resid 1158 through 1160' Processing helix chain 'E' and resid 2101 through 2111 removed outlier: 3.868A pdb=" N CYS E2111 " --> pdb=" O GLY E2107 " (cutoff:3.500A) Processing helix chain 'E' and resid 2113 through 2119 Processing helix chain 'E' and resid 2125 through 2132 removed outlier: 3.846A pdb=" N ARG E2129 " --> pdb=" O LYS E2125 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU E2130 " --> pdb=" O ARG E2126 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER E2132 " --> pdb=" O TYR E2128 " (cutoff:3.500A) Processing helix chain 'E' and resid 2151 through 2158 removed outlier: 3.597A pdb=" N GLN E2158 " --> pdb=" O ARG E2154 " (cutoff:3.500A) Processing helix chain 'E' and resid 2194 through 2203 Processing helix chain 'E' and resid 2219 through 2226 Processing helix chain 'E' and resid 2244 through 2255 Processing helix chain 'E' and resid 2270 through 2280 Processing helix chain 'E' and resid 2298 through 2309 Processing helix chain 'E' and resid 2327 through 2332 removed outlier: 3.506A pdb=" N PHE E2331 " --> pdb=" O CYS E2327 " (cutoff:3.500A) Processing helix chain 'E' and resid 2350 through 2359 removed outlier: 3.589A pdb=" N ILE E2359 " --> pdb=" O LEU E2356 " (cutoff:3.500A) Processing helix chain 'E' and resid 2374 through 2383 Processing helix chain 'F' and resid 3042 through 3047 removed outlier: 3.592A pdb=" N GLY F3047 " --> pdb=" O TRP F3043 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.229A pdb=" N VAL A 18 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 79 " --> pdb=" O VAL A 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 4.213A pdb=" N ASP A 68 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLU A 81 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU A 66 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'C' and resid 62 through 63 Processing sheet with id=AA6, first strand: chain 'E' and resid 2185 through 2187 Processing sheet with id=AA7, first strand: chain 'E' and resid 2210 through 2212 Processing sheet with id=AA8, first strand: chain 'E' and resid 2287 through 2288 removed outlier: 3.530A pdb=" N LEU E2288 " --> pdb=" O HIS E2314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 2364 through 2365 removed outlier: 3.826A pdb=" N LEU E2365 " --> pdb=" O GLN E2387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 2408 through 2409 Processing sheet with id=AB2, first strand: chain 'F' and resid 3007 through 3008 removed outlier: 3.521A pdb=" N TYR F3007 " --> pdb=" O MET F3023 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET F3023 " --> pdb=" O TYR F3007 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE F3066 " --> pdb=" O ILE F3059 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE F3059 " --> pdb=" O ILE F3066 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N LEU F3068 " --> pdb=" O TYR F3057 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 843 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: 2.42 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1487 1.33 - 1.45: 2137 1.45 - 1.57: 4911 1.57 - 1.69: 2 1.69 - 1.81: 47 Bond restraints: 8584 Sorted by residual: bond pdb=" OG1 TPO G4187 " pdb=" P TPO G4187 " ideal model delta sigma weight residual 1.717 1.593 0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" OG1 TPO A 159 " pdb=" P TPO A 159 " ideal model delta sigma weight residual 1.717 1.621 0.096 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C PRO B 426 " pdb=" O PRO B 426 " ideal model delta sigma weight residual 1.243 1.213 0.031 8.50e-03 1.38e+04 1.29e+01 bond pdb=" CB TPO A 159 " pdb=" OG1 TPO A 159 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.94e+00 bond pdb=" N ILE F3006 " pdb=" CA ILE F3006 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.32e-02 5.74e+03 8.73e+00 ... (remaining 8579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 10996 1.50 - 3.01: 617 3.01 - 4.51: 112 4.51 - 6.01: 22 6.01 - 7.51: 4 Bond angle restraints: 11751 Sorted by residual: angle pdb=" N ILE F3028 " pdb=" CA ILE F3028 " pdb=" C ILE F3028 " ideal model delta sigma weight residual 113.53 107.69 5.84 9.80e-01 1.04e+00 3.55e+01 angle pdb=" N VAL E2233 " pdb=" CA VAL E2233 " pdb=" C VAL E2233 " ideal model delta sigma weight residual 113.47 108.68 4.79 1.01e+00 9.80e-01 2.25e+01 angle pdb=" C PRO B 426 " pdb=" CA PRO B 426 " pdb=" CB PRO B 426 " ideal model delta sigma weight residual 111.17 106.89 4.28 9.40e-01 1.13e+00 2.08e+01 angle pdb=" N MET B 210 " pdb=" CA MET B 210 " pdb=" C MET B 210 " ideal model delta sigma weight residual 111.07 106.73 4.34 1.07e+00 8.73e-01 1.64e+01 angle pdb=" C LYS D1130 " pdb=" CA LYS D1130 " pdb=" CB LYS D1130 " ideal model delta sigma weight residual 116.34 111.13 5.21 1.40e+00 5.10e-01 1.38e+01 ... (remaining 11746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4503 17.53 - 35.06: 458 35.06 - 52.60: 109 52.60 - 70.13: 21 70.13 - 87.66: 9 Dihedral angle restraints: 5100 sinusoidal: 1735 harmonic: 3365 Sorted by residual: dihedral pdb=" CA ASP B 345 " pdb=" C ASP B 345 " pdb=" N PRO B 346 " pdb=" CA PRO B 346 " ideal model delta harmonic sigma weight residual 0.00 -20.57 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU A 267 " pdb=" C LEU A 267 " pdb=" N HIS A 268 " pdb=" CA HIS A 268 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLN E2158 " pdb=" C GLN E2158 " pdb=" N GLY E2159 " pdb=" CA GLY E2159 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 948 0.042 - 0.084: 328 0.084 - 0.126: 94 0.126 - 0.168: 15 0.168 - 0.210: 9 Chirality restraints: 1394 Sorted by residual: chirality pdb=" CA ARG E2344 " pdb=" N ARG E2344 " pdb=" C ARG E2344 " pdb=" CB ARG E2344 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA GLU C 75 " pdb=" N GLU C 75 " pdb=" C GLU C 75 " pdb=" CB GLU C 75 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CA MET B 392 " pdb=" N MET B 392 " pdb=" C MET B 392 " pdb=" CB MET B 392 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.85e-01 ... (remaining 1391 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 31 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ASN C 31 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN C 31 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU C 32 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 323 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO B 324 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 324 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 324 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D1045 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO D1046 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO D1046 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D1046 " 0.027 5.00e-02 4.00e+02 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 3 2.14 - 2.83: 2721 2.83 - 3.52: 11369 3.52 - 4.21: 18358 4.21 - 4.90: 31994 Nonbonded interactions: 64445 Sorted by model distance: nonbonded pdb=" CD ARG D1136 " pdb=" OD2 ASP D1144 " model vdw 1.446 3.440 nonbonded pdb=" NE2 GLN A 85 " pdb=" OH TYR A 107 " model vdw 1.977 3.120 nonbonded pdb=" OE1 GLN A 85 " pdb=" CE2 TYR A 107 " model vdw 2.049 3.340 nonbonded pdb=" OD1 ASP F3014 " pdb=" N GLU F3015 " model vdw 2.158 3.120 nonbonded pdb=" OD1 ASP A 86 " pdb=" CD2 LEU A 134 " model vdw 2.182 3.460 ... (remaining 64440 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 max=1.00 mean=0.99 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: 6.770 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.210 Find NCS groups from input model: 0.150 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 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 : 0.005 0.124 8584 Z= 0.336 Angle : 0.800 7.514 11751 Z= 0.511 Chirality : 0.047 0.210 1394 Planarity : 0.005 0.050 1503 Dihedral : 15.658 87.660 2904 Min Nonbonded Distance : 1.446 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 0.88 % Allowed : 21.83 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.67 (0.25), residues: 1117 helix: -0.01 (0.26), residues: 422 sheet: -2.53 (0.71), residues: 59 loop : -1.79 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 217 HIS 0.003 0.001 HIS E2185 PHE 0.010 0.001 PHE A 152 TYR 0.018 0.001 TYR B 280 ARG 0.004 0.000 ARG D1136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 GLU cc_start: 0.6614 (pt0) cc_final: 0.5986 (mm-30) REVERT: D 1161 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7676 (tt0) REVERT: E 2134 GLU cc_start: 0.8358 (pt0) cc_final: 0.8153 (pt0) REVERT: E 2332 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.5999 (m-80) REVERT: E 2355 GLU cc_start: 0.7652 (tp30) cc_final: 0.7300 (tp30) outliers start: 7 outliers final: 1 residues processed: 154 average time/residue: 0.1921 time to fit residues: 42.1544 Evaluate side-chains 137 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain E residue 2344 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS D1157 ASN F3052 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.209342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.172171 restraints weight = 10987.850| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 3.22 r_work: 0.3856 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8584 Z= 0.280 Angle : 0.626 7.708 11751 Z= 0.325 Chirality : 0.044 0.158 1394 Planarity : 0.005 0.047 1503 Dihedral : 5.419 59.850 1212 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.45 % Favored : 93.46 % Rotamer: Outliers : 5.02 % Allowed : 17.82 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.52 (0.26), residues: 1117 helix: 0.13 (0.26), residues: 449 sheet: -2.65 (0.83), residues: 41 loop : -1.81 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F3043 HIS 0.009 0.001 HIS A 84 PHE 0.019 0.002 PHE A 152 TYR 0.014 0.002 TYR F3057 ARG 0.004 0.001 ARG E2217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7964 (t70) cc_final: 0.7660 (t70) REVERT: B 180 GLU cc_start: 0.6924 (pt0) cc_final: 0.6059 (mm-30) REVERT: B 238 TYR cc_start: 0.7203 (m-10) cc_final: 0.6844 (m-80) REVERT: D 1126 MET cc_start: 0.7483 (tmm) cc_final: 0.7263 (tmm) REVERT: D 1161 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: E 2127 TRP cc_start: 0.8054 (m-10) cc_final: 0.7785 (m-10) REVERT: E 2269 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7548 (m-10) REVERT: E 2273 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.7936 (m170) REVERT: G 4185 GLU cc_start: 0.6915 (mp0) cc_final: 0.6142 (mp0) outliers start: 40 outliers final: 20 residues processed: 171 average time/residue: 0.1796 time to fit residues: 44.3508 Evaluate side-chains 155 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1059 ILE Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1153 VAL Chi-restraints excluded: chain D residue 1161 GLU Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2168 SER Chi-restraints excluded: chain E residue 2190 ASN Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2273 HIS Chi-restraints excluded: chain E residue 2337 LEU Chi-restraints excluded: chain E residue 2364 THR Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 63 optimal weight: 0.0270 chunk 25 optimal weight: 0.0870 chunk 43 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** 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 = 0.4535 r_free = 0.4535 target = 0.213546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.177882 restraints weight = 11199.439| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 3.27 r_work: 0.3885 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8584 Z= 0.177 Angle : 0.547 8.288 11751 Z= 0.281 Chirality : 0.041 0.154 1394 Planarity : 0.004 0.050 1503 Dihedral : 4.329 19.691 1206 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.14 % Allowed : 19.70 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.18 (0.26), residues: 1117 helix: 0.35 (0.26), residues: 453 sheet: -2.74 (0.91), residues: 35 loop : -1.57 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D1088 HIS 0.005 0.001 HIS C 48 PHE 0.012 0.001 PHE A 193 TYR 0.010 0.001 TYR F3057 ARG 0.004 0.000 ARG E2217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 GLU cc_start: 0.6778 (pt0) cc_final: 0.5959 (mm-30) REVERT: B 392 MET cc_start: 0.7965 (mmm) cc_final: 0.7690 (mmm) REVERT: D 1126 MET cc_start: 0.7594 (tmm) cc_final: 0.7178 (tmm) REVERT: D 1142 LYS cc_start: 0.6659 (mmtt) cc_final: 0.6255 (mptt) REVERT: D 1161 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: E 2128 TYR cc_start: 0.7907 (t80) cc_final: 0.7643 (t80) REVERT: E 2269 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.7404 (m-10) REVERT: E 2273 HIS cc_start: 0.8651 (OUTLIER) cc_final: 0.7909 (m170) REVERT: G 4185 GLU cc_start: 0.6903 (mp0) cc_final: 0.6309 (mp0) outliers start: 41 outliers final: 22 residues processed: 171 average time/residue: 0.1826 time to fit residues: 44.9207 Evaluate side-chains 161 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1153 VAL Chi-restraints excluded: chain D residue 1161 GLU Chi-restraints excluded: chain E residue 2123 VAL Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2168 SER Chi-restraints excluded: chain E residue 2190 ASN Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2273 HIS Chi-restraints excluded: chain F residue 3012 TYR Chi-restraints excluded: chain F residue 3016 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** 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 = 0.4489 r_free = 0.4489 target = 0.208500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.172773 restraints weight = 11213.376| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 3.39 r_work: 0.3832 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8584 Z= 0.297 Angle : 0.632 8.791 11751 Z= 0.320 Chirality : 0.044 0.162 1394 Planarity : 0.005 0.048 1503 Dihedral : 4.685 20.271 1206 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 6.02 % Allowed : 18.44 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.22 (0.26), residues: 1117 helix: 0.41 (0.27), residues: 446 sheet: -2.90 (0.81), residues: 40 loop : -1.63 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F3043 HIS 0.009 0.001 HIS C 48 PHE 0.020 0.002 PHE A 152 TYR 0.016 0.002 TYR F3057 ARG 0.004 0.001 ARG E2217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.7704 (t0) cc_final: 0.7484 (t0) REVERT: B 180 GLU cc_start: 0.6924 (pt0) cc_final: 0.6171 (mm-30) REVERT: D 1126 MET cc_start: 0.7467 (tmm) cc_final: 0.7014 (tmm) REVERT: D 1142 LYS cc_start: 0.6680 (mmtt) cc_final: 0.6242 (mptt) REVERT: D 1161 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: E 2269 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7436 (m-10) REVERT: E 2273 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.8033 (m170) REVERT: E 2332 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7313 (t80) REVERT: G 4185 GLU cc_start: 0.7124 (mp0) cc_final: 0.6843 (mp0) outliers start: 48 outliers final: 28 residues processed: 166 average time/residue: 0.1862 time to fit residues: 45.7119 Evaluate side-chains 161 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1153 VAL Chi-restraints excluded: chain D residue 1161 GLU Chi-restraints excluded: chain E residue 2105 LEU Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2168 SER Chi-restraints excluded: chain E residue 2190 ASN Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2273 HIS Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain E residue 2364 THR Chi-restraints excluded: chain E residue 2417 THR Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 97 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.211149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.175362 restraints weight = 11072.955| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 3.22 r_work: 0.3879 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8584 Z= 0.203 Angle : 0.578 8.702 11751 Z= 0.295 Chirality : 0.042 0.154 1394 Planarity : 0.004 0.049 1503 Dihedral : 4.441 19.653 1206 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.14 % Allowed : 19.07 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.12 (0.26), residues: 1117 helix: 0.45 (0.26), residues: 453 sheet: -2.90 (0.69), residues: 49 loop : -1.51 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D1088 HIS 0.010 0.001 HIS C 48 PHE 0.013 0.001 PHE A 193 TYR 0.011 0.001 TYR F3057 ARG 0.005 0.000 ARG E2217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.7652 (t0) cc_final: 0.7409 (t0) REVERT: B 180 GLU cc_start: 0.6819 (pt0) cc_final: 0.6084 (mm-30) REVERT: B 290 GLN cc_start: 0.7455 (mt0) cc_final: 0.6785 (mt0) REVERT: B 392 MET cc_start: 0.8008 (mmm) cc_final: 0.7708 (mmm) REVERT: C 44 ASP cc_start: 0.8529 (m-30) cc_final: 0.7583 (p0) REVERT: D 1126 MET cc_start: 0.7612 (tmm) cc_final: 0.7234 (tmm) REVERT: D 1127 ILE cc_start: 0.7768 (mm) cc_final: 0.7471 (mt) REVERT: D 1161 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: E 2269 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7321 (m-10) REVERT: E 2273 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8024 (m170) REVERT: E 2332 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7287 (t80) REVERT: G 4185 GLU cc_start: 0.7099 (mp0) cc_final: 0.6848 (mp0) outliers start: 41 outliers final: 27 residues processed: 159 average time/residue: 0.1726 time to fit residues: 40.0290 Evaluate side-chains 157 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1090 GLN Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1153 VAL Chi-restraints excluded: chain D residue 1161 GLU Chi-restraints excluded: chain E residue 2105 LEU Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2168 SER Chi-restraints excluded: chain E residue 2190 ASN Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2273 HIS Chi-restraints excluded: chain E residue 2297 LEU Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 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 = 0.4472 r_free = 0.4472 target = 0.206241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.169208 restraints weight = 11188.131| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 3.80 r_work: 0.3794 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3827 r_free = 0.3827 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8584 Z= 0.341 Angle : 0.669 9.546 11751 Z= 0.340 Chirality : 0.046 0.162 1394 Planarity : 0.005 0.056 1503 Dihedral : 4.882 22.554 1206 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 6.27 % Allowed : 19.57 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.27 (0.26), residues: 1117 helix: 0.39 (0.26), residues: 445 sheet: -2.85 (0.69), residues: 49 loop : -1.65 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F3043 HIS 0.008 0.001 HIS F3021 PHE 0.022 0.002 PHE A 152 TYR 0.017 0.002 TYR F3057 ARG 0.003 0.001 ARG E2217 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.7626 (t0) cc_final: 0.7362 (t0) REVERT: B 180 GLU cc_start: 0.6926 (pt0) cc_final: 0.6159 (mm-30) REVERT: B 392 MET cc_start: 0.8065 (mmm) cc_final: 0.7764 (mmm) REVERT: D 1126 MET cc_start: 0.7716 (tmm) cc_final: 0.7352 (tmm) REVERT: D 1127 ILE cc_start: 0.7693 (mm) cc_final: 0.7436 (mt) REVERT: D 1161 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: E 2164 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7305 (ttt180) REVERT: E 2269 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.7495 (m-10) REVERT: E 2273 HIS cc_start: 0.8761 (OUTLIER) cc_final: 0.8152 (m170) REVERT: E 2332 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7301 (t80) REVERT: E 2396 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8396 (mm) REVERT: F 3016 GLU cc_start: 0.8077 (pt0) cc_final: 0.7631 (pp20) REVERT: G 4185 GLU cc_start: 0.7334 (mp0) cc_final: 0.6880 (mp0) outliers start: 50 outliers final: 33 residues processed: 171 average time/residue: 0.1722 time to fit residues: 42.7663 Evaluate side-chains 170 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1090 GLN Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1153 VAL Chi-restraints excluded: chain D residue 1161 GLU Chi-restraints excluded: chain E residue 2105 LEU Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL Chi-restraints excluded: chain E residue 2164 ARG Chi-restraints excluded: chain E residue 2168 SER Chi-restraints excluded: chain E residue 2190 ASN Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2273 HIS Chi-restraints excluded: chain E residue 2297 LEU Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain E residue 2361 THR Chi-restraints excluded: chain E residue 2364 THR Chi-restraints excluded: chain E residue 2396 ILE Chi-restraints excluded: chain E residue 2417 THR Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 chunk 109 optimal weight: 0.0060 chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.211797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.177064 restraints weight = 11136.797| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 3.30 r_work: 0.3890 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3923 r_free = 0.3923 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8584 Z= 0.177 Angle : 0.584 9.455 11751 Z= 0.297 Chirality : 0.042 0.153 1394 Planarity : 0.004 0.055 1503 Dihedral : 4.386 19.302 1206 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.27 % Allowed : 21.71 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.06 (0.27), residues: 1117 helix: 0.48 (0.27), residues: 452 sheet: -2.98 (0.65), residues: 54 loop : -1.43 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D1088 HIS 0.009 0.001 HIS C 48 PHE 0.013 0.001 PHE B 335 TYR 0.009 0.001 TYR D1109 ARG 0.005 0.000 ARG E2217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.7612 (t0) cc_final: 0.7358 (t0) REVERT: B 180 GLU cc_start: 0.6825 (pt0) cc_final: 0.6116 (mm-30) REVERT: B 290 GLN cc_start: 0.7437 (mt0) cc_final: 0.6774 (mt0) REVERT: B 392 MET cc_start: 0.8156 (mmm) cc_final: 0.7870 (mmm) REVERT: D 1126 MET cc_start: 0.7736 (tmm) cc_final: 0.7336 (tmm) REVERT: D 1127 ILE cc_start: 0.7921 (mm) cc_final: 0.7684 (mt) REVERT: E 2105 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6572 (tp) REVERT: E 2269 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.7445 (m-10) REVERT: E 2273 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.8105 (m170) REVERT: E 2332 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.7233 (t80) outliers start: 34 outliers final: 24 residues processed: 159 average time/residue: 0.1617 time to fit residues: 37.8507 Evaluate side-chains 163 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1090 GLN Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1153 VAL Chi-restraints excluded: chain E residue 2105 LEU Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2273 HIS Chi-restraints excluded: chain E residue 2297 LEU Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 92 optimal weight: 0.0040 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.203518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.167621 restraints weight = 11325.591| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 3.87 r_work: 0.3767 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 8584 Z= 0.449 Angle : 0.743 10.269 11751 Z= 0.379 Chirality : 0.048 0.172 1394 Planarity : 0.005 0.056 1503 Dihedral : 5.194 23.727 1206 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 5.14 % Allowed : 21.46 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.48 (0.26), residues: 1117 helix: 0.25 (0.26), residues: 445 sheet: -2.91 (0.65), residues: 54 loop : -1.78 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP F3043 HIS 0.009 0.002 HIS C 48 PHE 0.026 0.003 PHE A 193 TYR 0.020 0.002 TYR F3057 ARG 0.004 0.001 ARG E2217 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.7650 (t0) cc_final: 0.7433 (t0) REVERT: B 180 GLU cc_start: 0.6999 (pt0) cc_final: 0.6400 (mm-30) REVERT: B 284 ASP cc_start: 0.8839 (t70) cc_final: 0.8533 (m-30) REVERT: D 1126 MET cc_start: 0.7800 (tmm) cc_final: 0.7436 (tmm) REVERT: D 1127 ILE cc_start: 0.7813 (mm) cc_final: 0.7573 (mt) REVERT: E 2105 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6687 (tp) REVERT: E 2164 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7413 (ttt180) REVERT: E 2269 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.7684 (m-10) REVERT: E 2273 HIS cc_start: 0.8812 (OUTLIER) cc_final: 0.8167 (m170) REVERT: E 2332 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7306 (t80) REVERT: E 2396 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8483 (mm) REVERT: G 4185 GLU cc_start: 0.7596 (mp0) cc_final: 0.7015 (mp0) outliers start: 41 outliers final: 31 residues processed: 159 average time/residue: 0.1814 time to fit residues: 42.0336 Evaluate side-chains 164 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1090 GLN Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain E residue 2105 LEU Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL Chi-restraints excluded: chain E residue 2164 ARG Chi-restraints excluded: chain E residue 2197 THR Chi-restraints excluded: chain E residue 2208 LEU Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2273 HIS Chi-restraints excluded: chain E residue 2297 LEU Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain E residue 2361 THR Chi-restraints excluded: chain E residue 2364 THR Chi-restraints excluded: chain E residue 2396 ILE Chi-restraints excluded: chain E residue 2417 THR Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.210318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.175528 restraints weight = 11337.202| |-----------------------------------------------------------------------------| r_work (start): 0.4168 rms_B_bonded: 3.20 r_work: 0.3872 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8584 Z= 0.197 Angle : 0.609 10.055 11751 Z= 0.311 Chirality : 0.043 0.154 1394 Planarity : 0.005 0.056 1503 Dihedral : 4.599 19.595 1206 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.64 % Allowed : 23.96 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.24 (0.26), residues: 1117 helix: 0.34 (0.26), residues: 458 sheet: -2.74 (0.70), residues: 49 loop : -1.61 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D1088 HIS 0.010 0.001 HIS C 48 PHE 0.013 0.001 PHE F3017 TYR 0.010 0.001 TYR D1109 ARG 0.007 0.000 ARG B 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.7617 (t0) cc_final: 0.7390 (t0) REVERT: B 180 GLU cc_start: 0.6868 (pt0) cc_final: 0.6179 (mm-30) REVERT: B 284 ASP cc_start: 0.8768 (t70) cc_final: 0.8464 (m-30) REVERT: B 290 GLN cc_start: 0.7452 (mt0) cc_final: 0.6774 (mt0) REVERT: B 392 MET cc_start: 0.7752 (mmm) cc_final: 0.7501 (mmm) REVERT: D 1127 ILE cc_start: 0.7839 (mm) cc_final: 0.7597 (mt) REVERT: E 2105 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6565 (tp) REVERT: E 2269 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.7617 (m-10) REVERT: E 2273 HIS cc_start: 0.8701 (OUTLIER) cc_final: 0.8178 (m170) REVERT: E 2332 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7196 (t80) outliers start: 29 outliers final: 23 residues processed: 153 average time/residue: 0.1768 time to fit residues: 39.5429 Evaluate side-chains 158 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain D residue 1090 GLN Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain E residue 2105 LEU Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2273 HIS Chi-restraints excluded: chain E residue 2297 LEU Chi-restraints excluded: chain E residue 2323 LEU Chi-restraints excluded: chain E residue 2332 PHE Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 18 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 23 optimal weight: 0.0870 chunk 71 optimal weight: 0.0040 chunk 89 optimal weight: 0.0670 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.1886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.214652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.179666 restraints weight = 11211.130| |-----------------------------------------------------------------------------| r_work (start): 0.4213 rms_B_bonded: 3.23 r_work: 0.3928 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3958 r_free = 0.3958 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3958 r_free = 0.3958 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8584 Z= 0.155 Angle : 0.578 10.173 11751 Z= 0.294 Chirality : 0.041 0.152 1394 Planarity : 0.005 0.054 1503 Dihedral : 4.151 18.298 1206 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.76 % Allowed : 24.47 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -0.99 (0.27), residues: 1117 helix: 0.48 (0.26), residues: 460 sheet: -2.37 (0.73), residues: 49 loop : -1.44 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D1088 HIS 0.011 0.001 HIS C 48 PHE 0.015 0.001 PHE B 242 TYR 0.014 0.001 TYR C 89 ARG 0.007 0.000 ARG B 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8273 (mmm) cc_final: 0.8036 (tpt) REVERT: B 180 GLU cc_start: 0.6778 (pt0) cc_final: 0.6108 (mm-30) REVERT: B 181 ASP cc_start: 0.7302 (t0) cc_final: 0.6936 (t0) REVERT: B 290 GLN cc_start: 0.7418 (mt0) cc_final: 0.6711 (mt0) REVERT: B 378 ARG cc_start: 0.7070 (ptp90) cc_final: 0.6734 (mtm-85) REVERT: B 392 MET cc_start: 0.7977 (mmm) cc_final: 0.7700 (mmm) REVERT: D 1127 ILE cc_start: 0.7884 (mm) cc_final: 0.7644 (mt) REVERT: E 2105 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6574 (tp) REVERT: E 2217 ARG cc_start: 0.8417 (ttm-80) cc_final: 0.7937 (ttm-80) REVERT: E 2269 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7392 (m-10) REVERT: E 2273 HIS cc_start: 0.8664 (OUTLIER) cc_final: 0.8025 (m170) REVERT: E 2332 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7202 (t80) outliers start: 22 outliers final: 14 residues processed: 159 average time/residue: 0.1767 time to fit residues: 41.3532 Evaluate side-chains 156 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain D residue 1090 GLN Chi-restraints excluded: chain E residue 2105 LEU Chi-restraints excluded: chain E residue 2142 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL Chi-restraints excluded: chain E residue 2269 PHE Chi-restraints excluded: chain E residue 2273 HIS Chi-restraints excluded: chain E residue 2332 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 3.9990 chunk 80 optimal weight: 0.0170 chunk 52 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 HIS A 132 ASN B 361 HIS C 48 HIS ** F3060 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.201046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.166003 restraints weight = 11428.571| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 4.00 r_work: 0.3732 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 8584 Z= 0.560 Angle : 0.834 8.683 11751 Z= 0.424 Chirality : 0.051 0.216 1394 Planarity : 0.006 0.053 1503 Dihedral : 5.577 26.116 1206 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 3.64 % Allowed : 23.84 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % 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: -1.66 (0.26), residues: 1117 helix: 0.09 (0.26), residues: 447 sheet: -2.87 (0.63), residues: 63 loop : -1.87 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D1088 HIS 0.011 0.002 HIS C 48 PHE 0.034 0.004 PHE A 193 TYR 0.025 0.003 TYR F3012 ARG 0.007 0.001 ARG B 378 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4265.52 seconds wall clock time: 76 minutes 45.42 seconds (4605.42 seconds total)