Starting phenix.real_space_refine on Tue Apr 29 08:01:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bya_16325/04_2025/8bya_16325.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bya_16325/04_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_16325/04_2025/8bya_16325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bya_16325/04_2025/8bya_16325.map" model { file = "/net/cci-nas-00/data/ceres_data/8bya_16325/04_2025/8bya_16325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bya_16325/04_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-5669/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: 5.71, per 1000 atoms: 0.68 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: 2.26 Conformation dependent library (CDL) restraints added in 1.1 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: 0.83 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: 2.29 Time building geometry restraints manager: 2.67 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: 1.490 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.000 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- 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= 0.305 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 Details of bonding type rmsd hydrogen bonds : bond 0.18957 ( 306) hydrogen bonds : angle 6.99629 ( 843) covalent geometry : bond 0.00484 ( 8584) covalent geometry : angle 0.80041 (11751) *********************** 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 : 0.867 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: 0.1717 time to fit residues: 37.7495 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 : 0.874 ------------------------------------------------------------------------------- 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 = 0.209338 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 = 10988.145| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 3.22 r_work: 0.3856 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3893 r_free = 0.3893 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 = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.1232 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= 0.179 Angle : 0.626 7.705 11751 Z= 0.325 Chirality : 0.044 0.158 1394 Planarity : 0.005 0.047 1503 Dihedral : 5.419 59.848 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 (0.84), 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 Details of bonding type rmsd hydrogen bonds : bond 0.04078 ( 306) hydrogen bonds : angle 5.20877 ( 843) covalent geometry : bond 0.00418 ( 8584) covalent geometry : angle 0.62648 (11751) *********************** 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 : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.7963 (t70) cc_final: 0.7657 (t70) REVERT: B 180 GLU cc_start: 0.6923 (pt0) cc_final: 0.6056 (mm-30) REVERT: B 238 TYR cc_start: 0.7205 (m-10) cc_final: 0.6842 (m-80) REVERT: D 1126 MET cc_start: 0.7482 (tmm) cc_final: 0.7262 (tmm) REVERT: D 1161 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: E 2127 TRP cc_start: 0.8054 (m-10) cc_final: 0.7786 (m-10) REVERT: E 2269 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.7547 (m-10) REVERT: E 2273 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.7937 (m170) REVERT: G 4185 GLU cc_start: 0.6916 (mp0) cc_final: 0.6142 (mp0) outliers start: 40 outliers final: 20 residues processed: 171 average time/residue: 0.1790 time to fit residues: 45.0734 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 : 0.931 ------------------------------------------------------------------------------- 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: 7.9990 chunk 91 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 0.0270 chunk 25 optimal weight: 0.0770 chunk 43 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- 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 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.207980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.172215 restraints weight = 11265.146| |-----------------------------------------------------------------------------| r_work (start): 0.4142 rms_B_bonded: 3.49 r_work: 0.3830 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 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 = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8584 Z= 0.191 Angle : 0.625 8.283 11751 Z= 0.323 Chirality : 0.044 0.165 1394 Planarity : 0.005 0.045 1503 Dihedral : 4.835 21.679 1206 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 6.40 % Allowed : 18.70 % Favored : 74.91 % 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: -1.43 (0.26), residues: 1117 helix: 0.19 (0.26), residues: 452 sheet: -2.70 (0.83), residues: 40 loop : -1.75 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F3043 HIS 0.007 0.001 HIS F3021 PHE 0.020 0.002 PHE A 193 TYR 0.017 0.002 TYR F3057 ARG 0.005 0.001 ARG E2344 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 306) hydrogen bonds : angle 4.90391 ( 843) covalent geometry : bond 0.00451 ( 8584) covalent geometry : angle 0.62482 (11751) *********************** 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 194 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.8329 (t70) cc_final: 0.8115 (t70) REVERT: B 180 GLU cc_start: 0.6737 (pt0) cc_final: 0.6081 (mm-30) REVERT: B 190 GLU cc_start: 0.5841 (pm20) cc_final: 0.5578 (pm20) REVERT: B 392 MET cc_start: 0.8006 (mmm) cc_final: 0.7726 (mmm) REVERT: D 1126 MET cc_start: 0.7652 (tmm) cc_final: 0.7398 (tmm) REVERT: D 1142 LYS cc_start: 0.6793 (mmtt) cc_final: 0.6367 (mptt) REVERT: E 2269 PHE cc_start: 0.8746 (OUTLIER) cc_final: 0.7599 (m-10) REVERT: E 2273 HIS cc_start: 0.8744 (OUTLIER) cc_final: 0.7983 (m170) REVERT: G 4185 GLU cc_start: 0.7175 (mp0) cc_final: 0.6738 (mp0) outliers start: 51 outliers final: 27 residues processed: 179 average time/residue: 0.2091 time to fit residues: 54.9810 Evaluate side-chains 163 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 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 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 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 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 2348 ILE Chi-restraints excluded: chain E residue 2364 THR Chi-restraints excluded: chain E residue 2401 ILE Chi-restraints excluded: chain F residue 3012 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.205910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.169248 restraints weight = 11236.250| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 3.67 r_work: 0.3787 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3823 r_free = 0.3823 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3823 r_free = 0.3823 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8584 Z= 0.213 Angle : 0.657 8.721 11751 Z= 0.337 Chirality : 0.045 0.164 1394 Planarity : 0.005 0.048 1503 Dihedral : 4.970 21.597 1206 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 6.02 % Allowed : 19.45 % Favored : 74.53 % 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: -1.41 (0.26), residues: 1117 helix: 0.23 (0.26), residues: 445 sheet: -2.83 (0.89), residues: 35 loop : -1.73 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F3043 HIS 0.008 0.001 HIS F3021 PHE 0.020 0.002 PHE A 152 TYR 0.016 0.002 TYR F3057 ARG 0.004 0.001 ARG E2217 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 306) hydrogen bonds : angle 4.96178 ( 843) covalent geometry : bond 0.00503 ( 8584) covalent geometry : angle 0.65744 (11751) *********************** 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 181 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.7887 (t0) cc_final: 0.7632 (t0) REVERT: A 235 ASP cc_start: 0.8454 (t70) cc_final: 0.8219 (t70) REVERT: B 180 GLU cc_start: 0.6908 (pt0) cc_final: 0.6114 (mm-30) REVERT: D 1126 MET cc_start: 0.7665 (tmm) cc_final: 0.7268 (tmm) REVERT: D 1142 LYS cc_start: 0.6788 (mmtt) cc_final: 0.6327 (mptt) REVERT: E 2164 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7256 (ttt180) REVERT: E 2269 PHE cc_start: 0.8836 (OUTLIER) cc_final: 0.7814 (m-10) REVERT: E 2273 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.8044 (m170) REVERT: E 2332 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7441 (t80) REVERT: G 4185 GLU cc_start: 0.7319 (mp0) cc_final: 0.6829 (mp0) outliers start: 48 outliers final: 33 residues processed: 168 average time/residue: 0.2069 time to fit residues: 52.5531 Evaluate side-chains 162 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 111 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 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 315 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 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 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 2332 PHE Chi-restraints excluded: chain E residue 2348 ILE Chi-restraints excluded: chain E residue 2364 THR Chi-restraints excluded: chain E residue 2401 ILE 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: 0.6980 chunk 16 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 54 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4498 r_free = 0.4498 target = 0.209164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.173506 restraints weight = 11058.881| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 3.25 r_work: 0.3862 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3877 r_free = 0.3877 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8584 Z= 0.135 Angle : 0.583 9.047 11751 Z= 0.300 Chirality : 0.043 0.155 1394 Planarity : 0.005 0.057 1503 Dihedral : 4.597 20.458 1206 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.40 % Allowed : 19.20 % Favored : 74.40 % 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: -1.19 (0.26), residues: 1117 helix: 0.41 (0.26), residues: 446 sheet: -2.74 (0.70), residues: 49 loop : -1.57 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D1088 HIS 0.011 0.001 HIS C 48 PHE 0.014 0.001 PHE A 152 TYR 0.010 0.001 TYR F3057 ARG 0.004 0.000 ARG E2217 Details of bonding type rmsd hydrogen bonds : bond 0.03196 ( 306) hydrogen bonds : angle 4.76798 ( 843) covalent geometry : bond 0.00313 ( 8584) covalent geometry : angle 0.58310 (11751) *********************** 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 187 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 136 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 ASP cc_start: 0.7781 (t0) cc_final: 0.7549 (t0) REVERT: A 235 ASP cc_start: 0.8347 (t70) cc_final: 0.8035 (t70) REVERT: B 180 GLU cc_start: 0.6823 (pt0) cc_final: 0.6082 (mm-30) REVERT: B 190 GLU cc_start: 0.5807 (pm20) cc_final: 0.5560 (pm20) REVERT: B 290 GLN cc_start: 0.7459 (mt0) cc_final: 0.6804 (mt0) REVERT: B 392 MET cc_start: 0.8011 (mmm) cc_final: 0.7674 (mmm) REVERT: D 1126 MET cc_start: 0.7730 (tmm) cc_final: 0.7335 (tmm) REVERT: D 1127 ILE cc_start: 0.7778 (mm) cc_final: 0.7546 (mt) REVERT: E 2269 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.7561 (m-10) REVERT: E 2273 HIS cc_start: 0.8692 (OUTLIER) cc_final: 0.8069 (m170) REVERT: E 2332 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7370 (t80) REVERT: E 2396 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8339 (mm) REVERT: G 4185 GLU cc_start: 0.7257 (mp0) cc_final: 0.6800 (mp0) outliers start: 51 outliers final: 32 residues processed: 171 average time/residue: 0.1658 time to fit residues: 41.7846 Evaluate side-chains 165 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 111 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 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 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 2168 SER 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 2332 PHE Chi-restraints excluded: chain E residue 2361 THR Chi-restraints excluded: chain E residue 2396 ILE Chi-restraints excluded: chain E residue 2401 ILE Chi-restraints excluded: chain E residue 2417 THR 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: 10.0000 chunk 31 optimal weight: 0.9980 chunk 71 optimal weight: 0.0020 chunk 11 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1090 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 = 0.4518 r_free = 0.4518 target = 0.211286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.175545 restraints weight = 11124.557| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 3.41 r_work: 0.3879 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 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 = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8584 Z= 0.118 Angle : 0.573 9.542 11751 Z= 0.289 Chirality : 0.042 0.152 1394 Planarity : 0.004 0.053 1503 Dihedral : 4.326 19.101 1206 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.02 % Allowed : 21.58 % 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: -1.00 (0.27), residues: 1117 helix: 0.57 (0.27), residues: 446 sheet: -2.77 (0.70), residues: 49 loop : -1.44 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F3043 HIS 0.005 0.001 HIS C 48 PHE 0.013 0.001 PHE A 152 TYR 0.012 0.001 TYR C 89 ARG 0.005 0.000 ARG E2217 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 306) hydrogen bonds : angle 4.57827 ( 843) covalent geometry : bond 0.00273 ( 8584) covalent geometry : angle 0.57334 (11751) *********************** 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 179 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8341 (mmm) cc_final: 0.8062 (tpt) REVERT: A 210 ASP cc_start: 0.7618 (t0) cc_final: 0.7401 (t0) REVERT: A 235 ASP cc_start: 0.8395 (t70) cc_final: 0.8060 (t70) REVERT: B 180 GLU cc_start: 0.6820 (pt0) cc_final: 0.6080 (mm-30) REVERT: B 290 GLN cc_start: 0.7465 (mt0) cc_final: 0.6741 (mt0) REVERT: B 392 MET cc_start: 0.8123 (mmm) cc_final: 0.7835 (mmm) REVERT: D 1126 MET cc_start: 0.7789 (tmm) cc_final: 0.7423 (tmm) REVERT: D 1127 ILE cc_start: 0.7913 (mm) cc_final: 0.7664 (mt) REVERT: D 1128 LYS cc_start: 0.8275 (mmtt) cc_final: 0.8044 (mmtt) REVERT: E 2269 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7531 (m-10) REVERT: E 2273 HIS cc_start: 0.8701 (OUTLIER) cc_final: 0.8120 (m170) REVERT: E 2332 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7366 (t80) REVERT: E 2396 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8339 (mm) outliers start: 40 outliers final: 27 residues processed: 163 average time/residue: 0.1910 time to fit residues: 46.1683 Evaluate side-chains 165 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 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 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1144 ASP Chi-restraints excluded: chain D residue 1153 VAL Chi-restraints excluded: chain E residue 2105 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 2332 PHE Chi-restraints excluded: chain E residue 2361 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: 1.9990 chunk 58 optimal weight: 0.0000 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 109 optimal weight: 0.0040 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** 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 = 0.4512 r_free = 0.4512 target = 0.210565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.175226 restraints weight = 11119.786| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 3.32 r_work: 0.3846 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3846 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8584 Z= 0.127 Angle : 0.579 9.230 11751 Z= 0.292 Chirality : 0.042 0.183 1394 Planarity : 0.004 0.051 1503 Dihedral : 4.315 19.642 1206 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 5.02 % Allowed : 21.83 % Favored : 73.15 % 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: -0.93 (0.27), residues: 1117 helix: 0.63 (0.27), residues: 446 sheet: -2.95 (0.65), residues: 54 loop : -1.37 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D1088 HIS 0.008 0.001 HIS C 48 PHE 0.014 0.001 PHE A 152 TYR 0.010 0.001 TYR F3057 ARG 0.005 0.000 ARG E2217 Details of bonding type rmsd hydrogen bonds : bond 0.02917 ( 306) hydrogen bonds : angle 4.55778 ( 843) covalent geometry : bond 0.00295 ( 8584) covalent geometry : angle 0.57936 (11751) *********************** 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 177 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8344 (mmm) cc_final: 0.8069 (tpt) REVERT: A 111 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7113 (mt) REVERT: A 235 ASP cc_start: 0.8434 (t70) cc_final: 0.8120 (t70) REVERT: B 180 GLU cc_start: 0.6893 (pt0) cc_final: 0.6151 (mm-30) REVERT: B 284 ASP cc_start: 0.8748 (t70) cc_final: 0.8451 (m-30) REVERT: B 290 GLN cc_start: 0.7408 (mt0) cc_final: 0.6729 (mt0) REVERT: B 392 MET cc_start: 0.8133 (mmm) cc_final: 0.7861 (mmm) REVERT: D 1126 MET cc_start: 0.7788 (tmm) cc_final: 0.7405 (tmm) REVERT: D 1127 ILE cc_start: 0.7834 (mm) cc_final: 0.7577 (mt) REVERT: D 1128 LYS cc_start: 0.8256 (mmtt) cc_final: 0.8036 (mmtt) REVERT: E 2105 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6449 (tp) REVERT: E 2269 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.7549 (m-10) REVERT: E 2273 HIS cc_start: 0.8712 (OUTLIER) cc_final: 0.8093 (m170) REVERT: E 2332 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7350 (t80) REVERT: E 2396 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8359 (mm) outliers start: 40 outliers final: 28 residues processed: 162 average time/residue: 0.1822 time to fit residues: 44.1225 Evaluate side-chains 167 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 111 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 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 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 1144 ASP Chi-restraints excluded: chain E residue 2105 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL 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 2332 PHE Chi-restraints excluded: chain E residue 2361 THR Chi-restraints excluded: chain E residue 2396 ILE Chi-restraints excluded: chain E residue 2401 ILE Chi-restraints excluded: chain E residue 2417 THR Chi-restraints excluded: chain F residue 3009 SER 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: 0.0980 chunk 94 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 92 optimal weight: 0.0980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1090 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 = 0.4491 r_free = 0.4491 target = 0.208039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.172466 restraints weight = 11226.480| |-----------------------------------------------------------------------------| r_work (start): 0.4138 rms_B_bonded: 3.74 r_work: 0.3792 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 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 = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8584 Z= 0.167 Angle : 0.631 8.985 11751 Z= 0.318 Chirality : 0.044 0.156 1394 Planarity : 0.005 0.052 1503 Dihedral : 4.558 20.797 1206 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 5.02 % Allowed : 22.71 % Favored : 72.27 % 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: -1.05 (0.27), residues: 1117 helix: 0.56 (0.27), residues: 445 sheet: -2.74 (0.69), residues: 49 loop : -1.50 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D1088 HIS 0.009 0.001 HIS C 48 PHE 0.018 0.002 PHE A 152 TYR 0.013 0.002 TYR F3057 ARG 0.005 0.000 ARG E2217 Details of bonding type rmsd hydrogen bonds : bond 0.03204 ( 306) hydrogen bonds : angle 4.66904 ( 843) covalent geometry : bond 0.00394 ( 8584) covalent geometry : angle 0.63085 (11751) *********************** 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 175 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8417 (mmm) cc_final: 0.8122 (tpt) REVERT: A 235 ASP cc_start: 0.8534 (t70) cc_final: 0.8214 (t70) REVERT: B 180 GLU cc_start: 0.6952 (pt0) cc_final: 0.6219 (mm-30) REVERT: B 277 GLU cc_start: 0.7900 (mp0) cc_final: 0.7681 (mm-30) REVERT: B 284 ASP cc_start: 0.8805 (t70) cc_final: 0.8547 (m-30) REVERT: B 290 GLN cc_start: 0.7492 (mt0) cc_final: 0.6790 (mt0) REVERT: D 1127 ILE cc_start: 0.7860 (mm) cc_final: 0.7646 (mt) REVERT: D 1128 LYS cc_start: 0.8287 (mmtt) cc_final: 0.8087 (mmtt) REVERT: E 2105 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6614 (tp) REVERT: E 2269 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.7524 (m-10) REVERT: E 2273 HIS cc_start: 0.8763 (OUTLIER) cc_final: 0.8072 (m170) REVERT: E 2332 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7429 (t80) REVERT: E 2391 SER cc_start: 0.8724 (t) cc_final: 0.8488 (p) REVERT: E 2396 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8394 (mm) REVERT: G 4185 GLU cc_start: 0.7441 (mp0) cc_final: 0.6987 (mp0) outliers start: 40 outliers final: 29 residues processed: 160 average time/residue: 0.1737 time to fit residues: 40.6163 Evaluate side-chains 165 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 111 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 214 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 289 LYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 331 SER 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 E residue 2105 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL 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 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 2401 ILE Chi-restraints excluded: chain E residue 2417 THR Chi-restraints excluded: chain F residue 3009 SER 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: 0.0770 chunk 45 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 16 optimal weight: 0.0010 chunk 39 optimal weight: 3.9990 overall best weight: 1.3548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1090 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 = 0.4476 r_free = 0.4476 target = 0.206481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.170993 restraints weight = 11364.423| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 3.99 r_work: 0.3787 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3807 r_free = 0.3807 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3807 r_free = 0.3807 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8584 Z= 0.189 Angle : 0.649 9.023 11751 Z= 0.329 Chirality : 0.045 0.178 1394 Planarity : 0.005 0.054 1503 Dihedral : 4.768 21.458 1206 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 5.27 % Allowed : 22.46 % Favored : 72.27 % 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: 0.42 (0.26), residues: 451 sheet: -2.86 (0.68), residues: 49 loop : -1.64 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D1088 HIS 0.007 0.001 HIS F3021 PHE 0.018 0.002 PHE A 152 TYR 0.014 0.002 TYR F3057 ARG 0.005 0.001 ARG E2217 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 306) hydrogen bonds : angle 4.79798 ( 843) covalent geometry : bond 0.00448 ( 8584) covalent geometry : angle 0.64907 (11751) *********************** 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 179 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ASP cc_start: 0.8541 (t70) cc_final: 0.8210 (t70) REVERT: B 180 GLU cc_start: 0.6940 (pt0) cc_final: 0.6244 (mm-30) REVERT: B 277 GLU cc_start: 0.7872 (mp0) cc_final: 0.7669 (mm-30) REVERT: B 284 ASP cc_start: 0.8806 (t70) cc_final: 0.8550 (m-30) REVERT: B 290 GLN cc_start: 0.7521 (mt0) cc_final: 0.6816 (mt0) REVERT: B 392 MET cc_start: 0.7757 (mmm) cc_final: 0.7502 (mmm) REVERT: D 1128 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7964 (mmtt) REVERT: E 2105 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6563 (tp) REVERT: E 2269 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.7723 (m-10) REVERT: E 2273 HIS cc_start: 0.8774 (OUTLIER) cc_final: 0.8130 (m170) REVERT: E 2332 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7404 (t80) REVERT: E 2391 SER cc_start: 0.8738 (t) cc_final: 0.8514 (p) REVERT: G 4185 GLU cc_start: 0.7635 (mp0) cc_final: 0.7056 (mp0) outliers start: 42 outliers final: 31 residues processed: 165 average time/residue: 0.1708 time to fit residues: 41.5900 Evaluate side-chains 168 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 111 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 214 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 289 LYS 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 1095 VAL Chi-restraints excluded: chain D residue 1116 LEU Chi-restraints excluded: chain D residue 1144 ASP Chi-restraints excluded: chain E residue 2105 LEU Chi-restraints excluded: chain E residue 2143 THR Chi-restraints excluded: chain E residue 2151 VAL 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 2332 PHE Chi-restraints excluded: chain E residue 2361 THR Chi-restraints excluded: chain E residue 2364 THR Chi-restraints excluded: chain E residue 2417 THR Chi-restraints excluded: chain F residue 3009 SER Chi-restraints excluded: chain F residue 3012 TYR Chi-restraints excluded: chain F residue 3035 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 18 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 89 optimal weight: 0.0980 chunk 69 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** ** D1090 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 = 0.4516 r_free = 0.4516 target = 0.210998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.174531 restraints weight = 11205.613| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 3.95 r_work: 0.3849 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3894 r_free = 0.3894 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 = 0.3893 r_free = 0.3893 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8584 Z= 0.119 Angle : 0.599 9.648 11751 Z= 0.302 Chirality : 0.043 0.152 1394 Planarity : 0.004 0.050 1503 Dihedral : 4.366 21.477 1206 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.89 % Allowed : 23.96 % Favored : 72.15 % 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: -1.06 (0.26), residues: 1117 helix: 0.59 (0.27), residues: 451 sheet: -2.69 (0.70), residues: 49 loop : -1.56 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D1088 HIS 0.007 0.001 HIS C 48 PHE 0.011 0.001 PHE A 152 TYR 0.013 0.001 TYR C 89 ARG 0.005 0.000 ARG E2217 Details of bonding type rmsd hydrogen bonds : bond 0.02871 ( 306) hydrogen bonds : angle 4.59571 ( 843) covalent geometry : bond 0.00276 ( 8584) covalent geometry : angle 0.59866 (11751) ********************** 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: 31 poor density : 138 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8345 (mmm) cc_final: 0.8072 (tpt) REVERT: A 111 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7075 (mt) REVERT: A 235 ASP cc_start: 0.8487 (t70) cc_final: 0.8107 (t70) REVERT: B 180 GLU cc_start: 0.6901 (pt0) cc_final: 0.6159 (mm-30) REVERT: B 277 GLU cc_start: 0.7880 (mp0) cc_final: 0.7675 (mm-30) REVERT: B 290 GLN cc_start: 0.7383 (mt0) cc_final: 0.6711 (mt0) REVERT: B 392 MET cc_start: 0.7785 (mmm) cc_final: 0.7485 (mmm) REVERT: D 1128 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7660 (mttt) REVERT: E 2105 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6534 (tp) REVERT: E 2217 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.7869 (ttm-80) REVERT: E 2269 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.7547 (m-10) REVERT: E 2273 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8098 (m170) REVERT: E 2332 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7172 (t80) REVERT: E 2391 SER cc_start: 0.8656 (t) cc_final: 0.8442 (p) outliers start: 31 outliers final: 22 residues processed: 157 average time/residue: 0.1801 time to fit residues: 41.0891 Evaluate side-chains 162 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 84 HIS Chi-restraints excluded: chain A residue 111 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 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 C residue 84 LEU Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain E residue 2105 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 2332 PHE Chi-restraints excluded: chain E residue 2361 THR Chi-restraints excluded: chain E residue 2417 THR Chi-restraints excluded: chain F residue 3009 SER 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 109 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 76 optimal weight: 0.0770 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 overall best weight: 1.2740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1090 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 = 0.4484 r_free = 0.4484 target = 0.207295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.171923 restraints weight = 11351.526| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 3.86 r_work: 0.3779 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3824 r_free = 0.3824 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3824 r_free = 0.3824 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8584 Z= 0.182 Angle : 0.646 8.961 11751 Z= 0.326 Chirality : 0.044 0.159 1394 Planarity : 0.005 0.050 1503 Dihedral : 4.626 21.922 1206 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.14 % Allowed : 24.22 % Favored : 71.64 % 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: -1.15 (0.26), residues: 1117 helix: 0.52 (0.27), residues: 452 sheet: -2.74 (0.69), residues: 49 loop : -1.63 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D1088 HIS 0.007 0.001 HIS C 48 PHE 0.018 0.002 PHE A 152 TYR 0.014 0.001 TYR F3057 ARG 0.004 0.000 ARG E2217 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 306) hydrogen bonds : angle 4.71996 ( 843) covalent geometry : bond 0.00433 ( 8584) covalent geometry : angle 0.64576 (11751) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4586.86 seconds wall clock time: 80 minutes 54.95 seconds (4854.95 seconds total)