Starting phenix.real_space_refine on Sun Nov 17 15:18:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/11_2024/7ckz_30395.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/11_2024/7ckz_30395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/11_2024/7ckz_30395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/11_2024/7ckz_30395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/11_2024/7ckz_30395.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/11_2024/7ckz_30395.cif" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7222 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 53 5.16 5 Cl 2 4.86 5 C 5180 2.51 5 N 1406 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8133 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1906 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2587 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2163 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain breaks: 3 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'CLR': 1, 'G4C': 1, 'LDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.12, per 1000 atoms: 0.63 Number of scatterers: 8133 At special positions: 0 Unit cell: (96, 80, 125, 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) Cl 2 17.00 S 53 16.00 O 1492 8.00 N 1406 7.00 C 5180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.02 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 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: 2.53 Conformation dependent library (CDL) restraints added in 1.0 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 43.1% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.864A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.155A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 293 through 304 removed outlier: 4.357A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.756A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.521A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.828A pdb=" N ILE B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.705A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.992A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 51 removed outlier: 3.572A pdb=" N PHE R 51 " --> pdb=" O ALA R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 76 removed outlier: 3.624A pdb=" N PHE R 61 " --> pdb=" O LYS R 57 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 Processing helix chain 'R' and resid 92 through 94 No H-bonds generated for 'chain 'R' and resid 92 through 94' Processing helix chain 'R' and resid 95 through 127 Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 161 removed outlier: 4.621A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 191 through 203 removed outlier: 3.849A pdb=" N SER R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL R 200 " --> pdb=" O ILE R 196 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE R 201 " --> pdb=" O SER R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 237 removed outlier: 4.324A pdb=" N ALA R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 278 removed outlier: 4.016A pdb=" N LYS R 269 " --> pdb=" O LYS R 265 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 293 Proline residue: R 287 - end of helix removed outlier: 3.882A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 298 Processing helix chain 'R' and resid 309 through 331 removed outlier: 4.129A pdb=" N VAL R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 344 removed outlier: 3.932A pdb=" N ALA R 340 " --> pdb=" O ASP R 336 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR R 343 " --> pdb=" O LYS R 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 3.505A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.899A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.714A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 4.039A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.644A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.584A pdb=" N PHE B 222 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.890A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.188A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.701A pdb=" N LEU N 20 " --> pdb=" O LEU N 81 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.498A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1167 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: 2.36 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1304 1.31 - 1.44: 2324 1.44 - 1.57: 4601 1.57 - 1.70: 1 1.70 - 1.82: 74 Bond restraints: 8304 Sorted by residual: bond pdb=" C05 G4C R 503 " pdb=" N04 G4C R 503 " ideal model delta sigma weight residual 1.355 1.481 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C16 G4C R 503 " pdb=" C18 G4C R 503 " ideal model delta sigma weight residual 1.508 1.594 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" N ARG N 105 " pdb=" CA ARG N 105 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.80e+00 bond pdb=" N PHE B 234 " pdb=" CA PHE B 234 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.25e-02 6.40e+03 6.34e+00 bond pdb=" C08 G4C R 503 " pdb="CL9 G4C R 503 " ideal model delta sigma weight residual 1.735 1.785 -0.050 2.00e-02 2.50e+03 6.18e+00 ... (remaining 8299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 11131 1.88 - 3.75: 118 3.75 - 5.63: 16 5.63 - 7.50: 4 7.50 - 9.38: 1 Bond angle restraints: 11270 Sorted by residual: angle pdb=" C03 G4C R 503 " pdb=" N04 G4C R 503 " pdb=" C05 G4C R 503 " ideal model delta sigma weight residual 118.75 128.13 -9.38 3.00e+00 1.11e-01 9.77e+00 angle pdb=" N ARG N 105 " pdb=" CA ARG N 105 " pdb=" C ARG N 105 " ideal model delta sigma weight residual 112.72 109.57 3.15 1.14e+00 7.69e-01 7.61e+00 angle pdb=" N VAL R 276 " pdb=" CA VAL R 276 " pdb=" C VAL R 276 " ideal model delta sigma weight residual 111.81 109.50 2.31 8.60e-01 1.35e+00 7.24e+00 angle pdb=" C06 G4C R 503 " pdb=" C05 G4C R 503 " pdb=" N04 G4C R 503 " ideal model delta sigma weight residual 116.82 124.06 -7.24 3.00e+00 1.11e-01 5.82e+00 angle pdb=" C03 G4C R 503 " pdb=" N04 G4C R 503 " pdb=" C16 G4C R 503 " ideal model delta sigma weight residual 119.52 112.47 7.05 3.00e+00 1.11e-01 5.53e+00 ... (remaining 11265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 4656 21.78 - 43.56: 271 43.56 - 65.34: 38 65.34 - 87.12: 10 87.12 - 108.90: 6 Dihedral angle restraints: 4981 sinusoidal: 1959 harmonic: 3022 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -35.36 -50.64 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 186 " pdb=" CB CYS R 186 " ideal model delta sinusoidal sigma weight residual 93.00 58.75 34.25 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" C02 G4C R 503 " pdb=" C03 G4C R 503 " pdb=" C30 G4C R 503 " pdb=" C19 G4C R 503 " ideal model delta sinusoidal sigma weight residual 66.31 175.21 -108.90 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 4978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 796 0.031 - 0.062: 351 0.062 - 0.093: 94 0.093 - 0.124: 37 0.124 - 0.155: 4 Chirality restraints: 1282 Sorted by residual: chirality pdb=" C16 G4C R 503 " pdb=" C17 G4C R 503 " pdb=" C18 G4C R 503 " pdb=" N04 G4C R 503 " both_signs ideal model delta sigma weight residual False -2.47 -2.62 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1279 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 205 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO R 206 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO R 206 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 206 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO A 332 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO G 49 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.017 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 10 2.24 - 2.90: 3347 2.90 - 3.57: 12622 3.57 - 4.23: 21827 4.23 - 4.90: 35825 Nonbonded interactions: 73631 Sorted by model distance: nonbonded pdb=" OD1 ASN B 119 " pdb=" O GLY B 144 " model vdw 1.570 3.040 nonbonded pdb=" OD1 ASN B 119 " pdb=" C GLY B 144 " model vdw 1.910 3.270 nonbonded pdb=" OG SER R 202 " pdb=" O2 LDP R 502 " model vdw 2.070 3.040 nonbonded pdb=" O ILE R 154 " pdb=" OH TYR R 194 " model vdw 2.149 3.040 nonbonded pdb=" O ALA R 101 " pdb=" OG SER R 155 " model vdw 2.179 3.040 ... (remaining 73626 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=1.00 max=1.00 mean=1.00 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.370 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 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 : 0.003 0.126 8304 Z= 0.195 Angle : 0.519 9.377 11270 Z= 0.296 Chirality : 0.039 0.155 1282 Planarity : 0.003 0.038 1422 Dihedral : 14.328 108.900 3005 Min Nonbonded Distance : 1.570 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.93 % Allowed : 8.14 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.23), residues: 1017 helix: -1.83 (0.21), residues: 396 sheet: -2.71 (0.31), residues: 200 loop : -2.20 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.009 0.001 PHE R 20 TYR 0.009 0.001 TYR N 117 ARG 0.002 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 270 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5446 (t80) cc_final: 0.4474 (t80) REVERT: A 339 TYR cc_start: 0.8230 (m-80) cc_final: 0.7793 (m-80) REVERT: A 343 ASP cc_start: 0.7415 (m-30) cc_final: 0.7078 (m-30) REVERT: A 386 MET cc_start: 0.7538 (ttp) cc_final: 0.7265 (ttm) REVERT: B 247 ASP cc_start: 0.8084 (p0) cc_final: 0.7806 (p0) REVERT: N 94 TYR cc_start: 0.8186 (m-80) cc_final: 0.7947 (m-80) REVERT: N 95 TYR cc_start: 0.8270 (m-80) cc_final: 0.7959 (m-80) REVERT: R 156 PHE cc_start: 0.6519 (m-10) cc_final: 0.5909 (m-80) REVERT: R 292 ASN cc_start: 0.8348 (t0) cc_final: 0.8064 (t0) outliers start: 8 outliers final: 3 residues processed: 274 average time/residue: 0.2631 time to fit residues: 91.8639 Evaluate side-chains 210 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 207 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 79 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 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 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN A 41 HIS A 267 GLN A 271 ASN A 278 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 259 GLN B 266 HIS B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS N 13 GLN N 31 ASN N 39 GLN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8304 Z= 0.231 Angle : 0.596 13.410 11270 Z= 0.307 Chirality : 0.043 0.323 1282 Planarity : 0.004 0.044 1422 Dihedral : 7.327 80.148 1215 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.21 % Allowed : 16.51 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.25), residues: 1017 helix: -0.48 (0.25), residues: 397 sheet: -2.60 (0.33), residues: 191 loop : -1.58 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.002 PHE B 151 TYR 0.010 0.002 TYR B 264 ARG 0.007 0.001 ARG R 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8135 (tppt) cc_final: 0.7618 (mmtm) REVERT: A 222 PHE cc_start: 0.5409 (t80) cc_final: 0.4670 (t80) REVERT: A 255 MET cc_start: 0.0722 (mmm) cc_final: -0.1608 (mtp) REVERT: A 271 ASN cc_start: 0.7769 (m110) cc_final: 0.7555 (m110) REVERT: A 318 TYR cc_start: 0.7252 (t80) cc_final: 0.6915 (t80) REVERT: A 339 TYR cc_start: 0.8405 (m-80) cc_final: 0.7724 (m-80) REVERT: A 343 ASP cc_start: 0.7566 (m-30) cc_final: 0.7213 (m-30) REVERT: B 124 TYR cc_start: 0.8640 (m-80) cc_final: 0.8372 (m-80) REVERT: B 209 LYS cc_start: 0.8609 (mttp) cc_final: 0.8383 (mmtm) REVERT: B 228 ASP cc_start: 0.6800 (OUTLIER) cc_final: 0.6459 (m-30) REVERT: B 323 ASP cc_start: 0.7076 (p0) cc_final: 0.6568 (p0) REVERT: B 337 LYS cc_start: 0.8116 (mmtp) cc_final: 0.7799 (mptt) REVERT: R 156 PHE cc_start: 0.6557 (m-10) cc_final: 0.6099 (m-80) REVERT: R 319 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7339 (t80) outliers start: 19 outliers final: 14 residues processed: 232 average time/residue: 0.2355 time to fit residues: 71.7440 Evaluate side-chains 212 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 295 LEU Chi-restraints excluded: chain R residue 319 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 60 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8304 Z= 0.239 Angle : 0.565 9.528 11270 Z= 0.292 Chirality : 0.042 0.194 1282 Planarity : 0.004 0.045 1422 Dihedral : 5.401 53.108 1215 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.72 % Allowed : 18.95 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.26), residues: 1017 helix: -0.03 (0.26), residues: 404 sheet: -2.41 (0.35), residues: 194 loop : -1.38 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.019 0.001 PHE B 151 TYR 0.016 0.002 TYR B 264 ARG 0.005 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8162 (tppt) cc_final: 0.7640 (mmtm) REVERT: A 255 MET cc_start: 0.1021 (mmm) cc_final: -0.1254 (mtp) REVERT: A 294 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7456 (mm-40) REVERT: A 318 TYR cc_start: 0.7396 (t80) cc_final: 0.7105 (t80) REVERT: A 339 TYR cc_start: 0.8461 (m-80) cc_final: 0.7809 (m-80) REVERT: A 343 ASP cc_start: 0.7568 (m-30) cc_final: 0.7249 (m-30) REVERT: B 124 TYR cc_start: 0.8703 (m-80) cc_final: 0.8375 (m-80) REVERT: B 228 ASP cc_start: 0.6802 (OUTLIER) cc_final: 0.6469 (m-30) REVERT: B 262 MET cc_start: 0.7649 (tpp) cc_final: 0.7447 (tpp) REVERT: B 337 LYS cc_start: 0.8176 (mmtp) cc_final: 0.7907 (mttp) REVERT: G 29 LYS cc_start: 0.8379 (mmtm) cc_final: 0.8117 (mmtm) REVERT: N 95 TYR cc_start: 0.8479 (m-80) cc_final: 0.8003 (m-80) REVERT: R 81 LYS cc_start: 0.8290 (tptt) cc_final: 0.7989 (tptt) outliers start: 32 outliers final: 19 residues processed: 220 average time/residue: 0.2435 time to fit residues: 70.8061 Evaluate side-chains 200 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.0040 chunk 47 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 0.0000 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8304 Z= 0.211 Angle : 0.538 6.212 11270 Z= 0.281 Chirality : 0.041 0.133 1282 Planarity : 0.004 0.047 1422 Dihedral : 4.565 54.023 1213 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.19 % Allowed : 19.65 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.26), residues: 1017 helix: 0.21 (0.26), residues: 403 sheet: -2.22 (0.36), residues: 192 loop : -1.30 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.022 0.001 PHE A 238 TYR 0.019 0.002 TYR B 264 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.917 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8168 (tppt) cc_final: 0.7687 (mmtm) REVERT: A 38 ARG cc_start: 0.7484 (mmt90) cc_final: 0.7276 (mmt-90) REVERT: A 208 PHE cc_start: 0.3975 (OUTLIER) cc_final: 0.3246 (t80) REVERT: A 222 PHE cc_start: 0.5375 (t80) cc_final: 0.5086 (t80) REVERT: A 318 TYR cc_start: 0.7354 (t80) cc_final: 0.7087 (t80) REVERT: A 332 PRO cc_start: 0.8170 (Cg_exo) cc_final: 0.7908 (Cg_endo) REVERT: A 339 TYR cc_start: 0.8451 (m-80) cc_final: 0.7786 (m-80) REVERT: A 343 ASP cc_start: 0.7594 (m-30) cc_final: 0.7268 (m-30) REVERT: B 124 TYR cc_start: 0.8723 (m-80) cc_final: 0.8520 (m-80) REVERT: B 228 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6524 (m-30) REVERT: B 323 ASP cc_start: 0.7172 (p0) cc_final: 0.6628 (p0) REVERT: B 337 LYS cc_start: 0.8135 (mmtp) cc_final: 0.7804 (mttp) REVERT: G 29 LYS cc_start: 0.8367 (mmtm) cc_final: 0.8101 (mmtm) REVERT: N 95 TYR cc_start: 0.8437 (m-80) cc_final: 0.7851 (m-80) REVERT: R 154 ILE cc_start: 0.8336 (mm) cc_final: 0.8114 (mt) outliers start: 36 outliers final: 24 residues processed: 214 average time/residue: 0.2217 time to fit residues: 62.9189 Evaluate side-chains 205 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 0.0030 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 67 optimal weight: 0.7980 chunk 0 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 0.0870 overall best weight: 0.3968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 32 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 323 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8304 Z= 0.191 Angle : 0.534 8.254 11270 Z= 0.277 Chirality : 0.041 0.130 1282 Planarity : 0.004 0.051 1422 Dihedral : 4.516 54.551 1213 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.72 % Allowed : 21.51 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.27), residues: 1017 helix: 0.44 (0.26), residues: 408 sheet: -2.19 (0.36), residues: 176 loop : -1.18 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 41 PHE 0.017 0.001 PHE A 238 TYR 0.016 0.002 TYR R 214 ARG 0.008 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8140 (tppt) cc_final: 0.7649 (mmtm) REVERT: A 38 ARG cc_start: 0.7432 (mmt90) cc_final: 0.7207 (mmt-90) REVERT: A 208 PHE cc_start: 0.4018 (OUTLIER) cc_final: 0.3332 (t80) REVERT: A 318 TYR cc_start: 0.7316 (t80) cc_final: 0.7048 (t80) REVERT: A 332 PRO cc_start: 0.8044 (Cg_exo) cc_final: 0.7793 (Cg_endo) REVERT: A 339 TYR cc_start: 0.8441 (m-80) cc_final: 0.7761 (m-80) REVERT: A 343 ASP cc_start: 0.7541 (m-30) cc_final: 0.7211 (m-30) REVERT: B 169 TRP cc_start: 0.9135 (m100) cc_final: 0.8921 (m100) REVERT: B 337 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7679 (mptt) REVERT: N 80 TYR cc_start: 0.8293 (m-80) cc_final: 0.8080 (m-80) REVERT: N 95 TYR cc_start: 0.8500 (m-80) cc_final: 0.7936 (m-80) REVERT: R 81 LYS cc_start: 0.8512 (tptt) cc_final: 0.8143 (tptt) REVERT: R 125 ILE cc_start: 0.7954 (mm) cc_final: 0.7281 (mt) REVERT: R 154 ILE cc_start: 0.8314 (mm) cc_final: 0.8103 (mt) outliers start: 32 outliers final: 21 residues processed: 210 average time/residue: 0.2298 time to fit residues: 64.0326 Evaluate side-chains 202 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 29 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 32 GLN B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 8304 Z= 0.380 Angle : 0.617 8.004 11270 Z= 0.322 Chirality : 0.044 0.160 1282 Planarity : 0.004 0.048 1422 Dihedral : 4.872 55.162 1213 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.19 % Allowed : 21.74 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.26), residues: 1017 helix: 0.20 (0.26), residues: 404 sheet: -2.31 (0.35), residues: 198 loop : -1.10 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 63 HIS 0.009 0.002 HIS B 311 PHE 0.018 0.002 PHE A 376 TYR 0.016 0.002 TYR B 264 ARG 0.009 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8143 (tppt) cc_final: 0.7671 (mmtm) REVERT: A 31 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7445 (mm110) REVERT: A 318 TYR cc_start: 0.7629 (t80) cc_final: 0.7363 (t80) REVERT: A 332 PRO cc_start: 0.8150 (Cg_exo) cc_final: 0.7796 (Cg_endo) REVERT: A 338 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8318 (ttmt) REVERT: A 339 TYR cc_start: 0.8560 (m-80) cc_final: 0.7922 (m-80) REVERT: A 343 ASP cc_start: 0.7616 (m-30) cc_final: 0.7351 (m-30) REVERT: B 124 TYR cc_start: 0.8928 (m-80) cc_final: 0.8547 (m-80) REVERT: B 146 LEU cc_start: 0.8883 (tt) cc_final: 0.8676 (tt) REVERT: B 209 LYS cc_start: 0.8843 (mttp) cc_final: 0.8464 (mmtm) REVERT: B 228 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6825 (m-30) REVERT: B 289 TYR cc_start: 0.8760 (m-80) cc_final: 0.8539 (m-80) REVERT: B 297 TRP cc_start: 0.9002 (m100) cc_final: 0.8650 (m100) REVERT: R 154 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8174 (mt) REVERT: R 163 TRP cc_start: 0.6352 (m100) cc_final: 0.5860 (m100) outliers start: 36 outliers final: 29 residues processed: 219 average time/residue: 0.1627 time to fit residues: 47.6687 Evaluate side-chains 216 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 44 optimal weight: 0.0050 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 371 ASN A 377 ASN B 32 GLN R 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8304 Z= 0.227 Angle : 0.563 8.561 11270 Z= 0.293 Chirality : 0.042 0.157 1282 Planarity : 0.004 0.048 1422 Dihedral : 4.786 56.775 1213 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.72 % Allowed : 23.14 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.27), residues: 1017 helix: 0.40 (0.26), residues: 407 sheet: -2.04 (0.37), residues: 179 loop : -1.07 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 41 PHE 0.016 0.002 PHE A 238 TYR 0.009 0.001 TYR B 264 ARG 0.009 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8139 (tppt) cc_final: 0.7617 (mmtm) REVERT: A 208 PHE cc_start: 0.4643 (t80) cc_final: 0.3993 (t80) REVERT: A 222 PHE cc_start: 0.5722 (t80) cc_final: 0.5310 (t80) REVERT: A 318 TYR cc_start: 0.7433 (t80) cc_final: 0.7153 (t80) REVERT: A 332 PRO cc_start: 0.8042 (Cg_exo) cc_final: 0.7823 (Cg_endo) REVERT: A 338 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8308 (ttmt) REVERT: A 339 TYR cc_start: 0.8522 (m-80) cc_final: 0.7836 (m-80) REVERT: A 343 ASP cc_start: 0.7548 (m-30) cc_final: 0.7248 (m-30) REVERT: B 99 TRP cc_start: 0.8050 (m100) cc_final: 0.7847 (m-90) REVERT: B 146 LEU cc_start: 0.8823 (tt) cc_final: 0.8602 (tt) REVERT: B 197 ARG cc_start: 0.7565 (tpp80) cc_final: 0.7164 (tpp80) REVERT: B 243 THR cc_start: 0.8272 (p) cc_final: 0.7927 (p) REVERT: B 297 TRP cc_start: 0.8990 (m100) cc_final: 0.8620 (m100) REVERT: B 329 THR cc_start: 0.8769 (m) cc_final: 0.8413 (p) REVERT: N 95 TYR cc_start: 0.8625 (m-80) cc_final: 0.8160 (m-80) REVERT: R 81 LYS cc_start: 0.8428 (tptt) cc_final: 0.8158 (tptt) REVERT: R 125 ILE cc_start: 0.8139 (mm) cc_final: 0.7455 (mt) REVERT: R 163 TRP cc_start: 0.6394 (m100) cc_final: 0.5987 (m100) outliers start: 32 outliers final: 25 residues processed: 209 average time/residue: 0.2238 time to fit residues: 62.3368 Evaluate side-chains 205 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 377 ASN R 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8304 Z= 0.244 Angle : 0.574 8.768 11270 Z= 0.298 Chirality : 0.042 0.163 1282 Planarity : 0.004 0.049 1422 Dihedral : 4.791 55.854 1213 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.49 % Allowed : 23.95 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.27), residues: 1017 helix: 0.44 (0.25), residues: 407 sheet: -1.99 (0.37), residues: 175 loop : -1.09 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.007 0.001 HIS A 41 PHE 0.016 0.001 PHE A 238 TYR 0.016 0.002 TYR B 289 ARG 0.009 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8158 (tppt) cc_final: 0.7711 (mmtm) REVERT: A 208 PHE cc_start: 0.4645 (t80) cc_final: 0.4029 (t80) REVERT: A 318 TYR cc_start: 0.7501 (t80) cc_final: 0.7180 (t80) REVERT: A 338 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8325 (ttmt) REVERT: A 339 TYR cc_start: 0.8511 (m-80) cc_final: 0.7821 (m-80) REVERT: A 343 ASP cc_start: 0.7554 (m-30) cc_final: 0.7246 (m-30) REVERT: A 381 ASP cc_start: 0.7983 (m-30) cc_final: 0.7569 (t0) REVERT: B 99 TRP cc_start: 0.8326 (m100) cc_final: 0.7824 (m-90) REVERT: B 243 THR cc_start: 0.8201 (p) cc_final: 0.7834 (p) REVERT: B 297 TRP cc_start: 0.8977 (m100) cc_final: 0.8732 (m100) REVERT: B 329 THR cc_start: 0.8762 (m) cc_final: 0.8392 (p) REVERT: N 80 TYR cc_start: 0.8240 (m-80) cc_final: 0.7857 (m-80) REVERT: N 95 TYR cc_start: 0.8607 (m-80) cc_final: 0.8150 (m-80) REVERT: R 81 LYS cc_start: 0.8423 (tptt) cc_final: 0.8040 (tptt) REVERT: R 163 TRP cc_start: 0.6410 (m100) cc_final: 0.6028 (m100) outliers start: 30 outliers final: 26 residues processed: 206 average time/residue: 0.2265 time to fit residues: 62.4227 Evaluate side-chains 204 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.0040 chunk 93 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 377 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8304 Z= 0.235 Angle : 0.584 9.311 11270 Z= 0.299 Chirality : 0.043 0.154 1282 Planarity : 0.004 0.048 1422 Dihedral : 4.826 56.653 1213 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.60 % Allowed : 23.49 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.27), residues: 1017 helix: 0.51 (0.26), residues: 407 sheet: -1.92 (0.37), residues: 174 loop : -1.12 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.006 0.001 HIS A 41 PHE 0.016 0.001 PHE A 238 TYR 0.013 0.002 TYR B 124 ARG 0.009 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8154 (tppt) cc_final: 0.7699 (mmtm) REVERT: A 208 PHE cc_start: 0.4622 (t80) cc_final: 0.4059 (t80) REVERT: A 255 MET cc_start: 0.0616 (mmm) cc_final: -0.1069 (mtp) REVERT: A 318 TYR cc_start: 0.7480 (t80) cc_final: 0.7184 (t80) REVERT: A 338 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8277 (ttmt) REVERT: A 339 TYR cc_start: 0.8525 (m-80) cc_final: 0.7844 (m-80) REVERT: A 343 ASP cc_start: 0.7550 (m-30) cc_final: 0.7255 (m-30) REVERT: B 99 TRP cc_start: 0.8327 (m100) cc_final: 0.7825 (m-90) REVERT: B 243 THR cc_start: 0.8234 (p) cc_final: 0.7866 (p) REVERT: B 323 ASP cc_start: 0.7423 (p0) cc_final: 0.6944 (p0) REVERT: N 80 TYR cc_start: 0.8210 (m-80) cc_final: 0.7834 (m-80) REVERT: N 95 TYR cc_start: 0.8607 (m-80) cc_final: 0.8154 (m-80) REVERT: R 81 LYS cc_start: 0.8429 (tptt) cc_final: 0.8134 (tptt) outliers start: 31 outliers final: 27 residues processed: 198 average time/residue: 0.2150 time to fit residues: 57.4892 Evaluate side-chains 205 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 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 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 377 ASN R 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8304 Z= 0.257 Angle : 0.601 9.386 11270 Z= 0.308 Chirality : 0.043 0.155 1282 Planarity : 0.004 0.047 1422 Dihedral : 4.902 57.300 1213 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.72 % Allowed : 23.02 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.26), residues: 1017 helix: 0.52 (0.26), residues: 407 sheet: -1.86 (0.37), residues: 168 loop : -1.15 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.006 0.001 HIS A 41 PHE 0.016 0.002 PHE A 238 TYR 0.022 0.002 TYR B 264 ARG 0.009 0.001 ARG A 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8142 (tppt) cc_final: 0.7683 (mmtm) REVERT: A 208 PHE cc_start: 0.4701 (t80) cc_final: 0.4254 (t80) REVERT: A 255 MET cc_start: 0.0501 (mmm) cc_final: -0.1224 (mtp) REVERT: A 318 TYR cc_start: 0.7506 (t80) cc_final: 0.7210 (t80) REVERT: A 338 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8231 (ttmt) REVERT: A 339 TYR cc_start: 0.8527 (m-80) cc_final: 0.7847 (m-80) REVERT: A 343 ASP cc_start: 0.7557 (m-30) cc_final: 0.7259 (m-30) REVERT: B 99 TRP cc_start: 0.8329 (m100) cc_final: 0.7767 (m-90) REVERT: B 243 THR cc_start: 0.8269 (p) cc_final: 0.7920 (p) REVERT: B 323 ASP cc_start: 0.7417 (p0) cc_final: 0.6950 (p0) REVERT: N 80 TYR cc_start: 0.8211 (m-80) cc_final: 0.7832 (m-80) REVERT: N 95 TYR cc_start: 0.8624 (m-80) cc_final: 0.8191 (m-80) REVERT: R 81 LYS cc_start: 0.8429 (tptt) cc_final: 0.8132 (tptt) outliers start: 32 outliers final: 29 residues processed: 200 average time/residue: 0.2214 time to fit residues: 59.4183 Evaluate side-chains 207 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.0970 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 377 ASN R 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.182792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.148519 restraints weight = 9212.369| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.13 r_work: 0.3574 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8304 Z= 0.226 Angle : 0.583 9.374 11270 Z= 0.300 Chirality : 0.042 0.153 1282 Planarity : 0.004 0.047 1422 Dihedral : 4.916 58.362 1213 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.84 % Allowed : 23.84 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.27), residues: 1017 helix: 0.70 (0.26), residues: 401 sheet: -1.88 (0.37), residues: 174 loop : -1.04 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 163 HIS 0.006 0.001 HIS A 41 PHE 0.019 0.002 PHE A 363 TYR 0.020 0.002 TYR B 264 ARG 0.011 0.001 ARG A 333 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: