Starting phenix.real_space_refine on Sat Sep 12 05:30:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ckz_30395/09_2026/7ckz_30395.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ckz_30395/09_2026/7ckz_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/cci-nas-00/data/ceres_data/7ckz_30395/09_2026/7ckz_30395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ckz_30395/09_2026/7ckz_30395.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ckz_30395/09_2026/7ckz_30395.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ckz_30395/09_2026/7ckz_30395.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ckz_30395/09_2026/7ckz_30395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ckz_30395/09_2026/7ckz_30395.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ASP:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} 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: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU: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: {'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1, '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: 1.22, per 1000 atoms: 0.15 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: 0.78 Conformation dependent library (CDL) restraints added in 294.5 milliseconds 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: 0.22 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: 1.23 Time building geometry restraints manager: 0.94 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 - 17.94: 4466 17.94 - 35.88: 351 35.88 - 53.82: 75 53.82 - 71.76: 9 71.76 - 89.70: 8 Dihedral angle restraints: 4909 sinusoidal: 1887 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=" CA ASP B 258 " pdb=" CB ASP B 258 " pdb=" CG ASP B 258 " pdb=" OD1 ASP B 258 " ideal model delta sinusoidal sigma weight residual -30.00 -87.95 57.95 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 4906 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.760 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 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 8308 Z= 0.178 Angle : 0.519 9.377 11278 Z= 0.296 Chirality : 0.039 0.155 1282 Planarity : 0.003 0.038 1422 Dihedral : 13.746 89.699 2933 Min Nonbonded Distance : 1.570 Molprobity Statistics. All-atom Clashscore : 23.64 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG B 52 TYR 0.009 0.001 TYR N 117 PHE 0.009 0.001 PHE R 20 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.18 ( 8304) covalent geometry : angle 0.51878 / 0.30 (11270) SS BOND : bond 0.00779 / 0.39 ( 4) SS BOND : angle 1.07279 / 0.58 ( 8) hydrogen bonds : bond 0.22163 / 14.51 ( 412) hydrogen bonds : angle 8.40715 / 5.87 ( 1167) *********************** 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 : 0.292 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: 0.4476 (t80) REVERT: A 339 TYR cc_start: 0.8230 (m-80) cc_final: 0.7802 (m-80) REVERT: A 343 ASP cc_start: 0.7415 (m-30) cc_final: 0.7082 (m-30) REVERT: A 386 MET cc_start: 0.7538 (ttp) cc_final: 0.7273 (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: 0.7960 (m-80) REVERT: R 156 PHE cc_start: 0.6519 (m-10) cc_final: 0.5908 (m-80) REVERT: R 292 ASN cc_start: 0.8348 (t0) cc_final: 0.8067 (t0) outliers start: 8 outliers final: 3 residues processed: 274 average time/residue: 0.1128 time to fit residues: 40.0649 Evaluate side-chains 211 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 208 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.0970 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0050 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.189889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.157750 restraints weight = 9318.138| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.04 r_work: 0.3668 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8308 Z= 0.150 Angle : 0.595 14.583 11278 Z= 0.306 Chirality : 0.043 0.323 1282 Planarity : 0.004 0.044 1422 Dihedral : 4.966 50.787 1143 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.09 % Allowed : 16.51 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.25), residues: 1017 helix: -0.49 (0.25), residues: 397 sheet: -2.70 (0.33), residues: 198 loop : -1.62 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 227 TYR 0.011 0.002 TYR B 264 PHE 0.016 0.002 PHE B 151 TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 8304) covalent geometry : angle 0.59464 / 0.31 (11270) SS BOND : bond 0.00170 / 0.08 ( 4) SS BOND : angle 0.90174 / 0.42 ( 8) hydrogen bonds : bond 0.04829 / 3.24 ( 412) hydrogen bonds : angle 5.95709 / 4.08 ( 1167) *********************** 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 239 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 221 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8234 (tppt) cc_final: 0.7695 (mmtm) REVERT: A 222 PHE cc_start: 0.5665 (t80) cc_final: 0.4810 (t80) REVERT: A 255 MET cc_start: 0.0671 (mmm) cc_final: -0.1747 (mtp) REVERT: A 271 ASN cc_start: 0.7967 (m110) cc_final: 0.7730 (m110) REVERT: A 318 TYR cc_start: 0.7396 (t80) cc_final: 0.7055 (t80) REVERT: A 339 TYR cc_start: 0.8536 (m-80) cc_final: 0.7845 (m-80) REVERT: A 343 ASP cc_start: 0.7933 (m-30) cc_final: 0.7588 (m-30) REVERT: A 363 PHE cc_start: 0.8855 (m-80) cc_final: 0.8502 (m-80) REVERT: B 124 TYR cc_start: 0.8755 (m-80) cc_final: 0.8456 (m-80) REVERT: B 209 LYS cc_start: 0.8790 (mttp) cc_final: 0.8570 (mmtm) REVERT: B 228 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6835 (m-30) REVERT: B 323 ASP cc_start: 0.7498 (p0) cc_final: 0.6976 (p0) REVERT: B 337 LYS cc_start: 0.8317 (mmtp) cc_final: 0.8069 (mptt) REVERT: R 142 ILE cc_start: 0.7427 (mt) cc_final: 0.7214 (mt) REVERT: R 156 PHE cc_start: 0.6754 (m-10) cc_final: 0.6074 (m-80) REVERT: R 319 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7526 (t80) outliers start: 18 outliers final: 13 residues processed: 231 average time/residue: 0.1026 time to fit residues: 31.5517 Evaluate side-chains 208 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 20 LEU Chi-restraints excluded: chain N residue 52 SER 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 319 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 84 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 93 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** G 44 HIS N 31 ASN R 60 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.189438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155514 restraints weight = 9275.382| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.13 r_work: 0.3657 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8308 Z= 0.142 Angle : 0.573 14.014 11278 Z= 0.292 Chirality : 0.042 0.314 1282 Planarity : 0.004 0.054 1422 Dihedral : 5.056 51.925 1143 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.72 % Allowed : 18.84 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.26), residues: 1017 helix: -0.02 (0.26), residues: 404 sheet: -2.37 (0.35), residues: 198 loop : -1.50 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 265 TYR 0.015 0.002 TYR B 264 PHE 0.018 0.001 PHE B 151 TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8304) covalent geometry : angle 0.57262 / 0.29 (11270) SS BOND : bond 0.00162 / 0.08 ( 4) SS BOND : angle 0.93580 / 0.44 ( 8) hydrogen bonds : bond 0.04184 / 2.82 ( 412) hydrogen bonds : angle 5.56892 / 3.82 ( 1167) *********************** 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 239 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8268 (tppt) cc_final: 0.7752 (mmtm) REVERT: A 208 PHE cc_start: 0.3479 (m-80) cc_final: 0.2846 (t80) REVERT: A 222 PHE cc_start: 0.5587 (t80) cc_final: 0.5180 (t80) REVERT: A 255 MET cc_start: 0.0834 (mmm) cc_final: -0.1365 (mtp) REVERT: A 318 TYR cc_start: 0.7512 (t80) cc_final: 0.7224 (t80) REVERT: A 332 PRO cc_start: 0.7928 (Cg_exo) cc_final: 0.7679 (Cg_endo) REVERT: A 339 TYR cc_start: 0.8614 (m-80) cc_final: 0.7945 (m-80) REVERT: A 343 ASP cc_start: 0.8075 (m-30) cc_final: 0.7773 (m-30) REVERT: B 124 TYR cc_start: 0.8858 (m-80) cc_final: 0.8423 (m-80) REVERT: B 228 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7123 (m-30) REVERT: B 262 MET cc_start: 0.8560 (tpp) cc_final: 0.8251 (tpp) REVERT: B 323 ASP cc_start: 0.7898 (p0) cc_final: 0.7433 (p0) REVERT: B 337 LYS cc_start: 0.8482 (mmtp) cc_final: 0.8243 (mttp) REVERT: G 21 MET cc_start: 0.7808 (mtp) cc_final: 0.7539 (ttt) REVERT: G 29 LYS cc_start: 0.8340 (mmtm) cc_final: 0.7958 (mmtm) REVERT: N 95 TYR cc_start: 0.8879 (m-80) cc_final: 0.8324 (m-80) REVERT: R 81 LYS cc_start: 0.8403 (tptt) cc_final: 0.7950 (tptt) REVERT: R 142 ILE cc_start: 0.7565 (mt) cc_final: 0.7292 (mt) REVERT: R 319 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7397 (t80) outliers start: 32 outliers final: 21 residues processed: 218 average time/residue: 0.1006 time to fit residues: 29.3397 Evaluate side-chains 214 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 A residue 386 MET Chi-restraints excluded: chain B residue 105 TYR 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 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 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 52 SER 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 207 VAL Chi-restraints excluded: chain R residue 211 ILE Chi-restraints excluded: chain R residue 295 LEU Chi-restraints excluded: chain R residue 319 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 29 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.174548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138640 restraints weight = 9394.523| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.13 r_work: 0.3444 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 8308 Z= 0.282 Angle : 0.674 14.372 11278 Z= 0.344 Chirality : 0.045 0.319 1282 Planarity : 0.004 0.053 1422 Dihedral : 5.104 53.367 1141 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.88 % Allowed : 18.84 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.26), residues: 1017 helix: 0.01 (0.26), residues: 398 sheet: -2.35 (0.36), residues: 189 loop : -1.35 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 333 TYR 0.027 0.003 TYR B 264 PHE 0.018 0.002 PHE B 151 TRP 0.018 0.002 TRP B 99 HIS 0.008 0.002 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.28 ( 8304) covalent geometry : angle 0.67308 / 0.34 (11270) SS BOND : bond 0.00505 / 0.25 ( 4) SS BOND : angle 1.70905 / 0.88 ( 8) hydrogen bonds : bond 0.04682 / 3.14 ( 412) hydrogen bonds : angle 5.70228 / 3.89 ( 1167) *********************** 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 245 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 203 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8220 (tppt) cc_final: 0.7749 (mmtm) REVERT: A 31 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7733 (mm110) REVERT: A 208 PHE cc_start: 0.3950 (m-80) cc_final: 0.3597 (t80) REVERT: A 222 PHE cc_start: 0.6250 (t80) cc_final: 0.5640 (t80) REVERT: A 318 TYR cc_start: 0.7964 (t80) cc_final: 0.7671 (t80) REVERT: A 339 TYR cc_start: 0.8746 (m-80) cc_final: 0.8132 (m-80) REVERT: A 343 ASP cc_start: 0.8297 (m-30) cc_final: 0.8079 (m-30) REVERT: B 124 TYR cc_start: 0.9038 (m-80) cc_final: 0.8722 (m-80) REVERT: B 176 GLN cc_start: 0.8526 (mt0) cc_final: 0.8308 (mt0) REVERT: B 209 LYS cc_start: 0.9076 (mttp) cc_final: 0.8742 (mmtm) REVERT: B 262 MET cc_start: 0.8664 (tpp) cc_final: 0.8366 (tpp) REVERT: B 289 TYR cc_start: 0.8955 (m-80) cc_final: 0.8739 (m-80) REVERT: B 297 TRP cc_start: 0.9179 (m100) cc_final: 0.8683 (m100) REVERT: B 336 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8571 (mp) outliers start: 42 outliers final: 26 residues processed: 226 average time/residue: 0.0927 time to fit residues: 28.5066 Evaluate side-chains 212 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR 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 242 THR 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 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 181 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 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 B residue 336 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 64 VAL 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 202 SER 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 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 278 ASN A 371 ASN A 377 ASN A 390 GLN B 32 GLN B 239 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.178516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.143656 restraints weight = 9344.392| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.12 r_work: 0.3509 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8308 Z= 0.176 Angle : 0.608 14.095 11278 Z= 0.308 Chirality : 0.043 0.307 1282 Planarity : 0.004 0.054 1422 Dihedral : 5.083 52.432 1141 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.12 % Allowed : 20.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.26), residues: 1017 helix: 0.13 (0.25), residues: 408 sheet: -2.22 (0.36), residues: 196 loop : -1.20 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 333 TYR 0.021 0.002 TYR B 264 PHE 0.016 0.001 PHE B 151 TRP 0.014 0.002 TRP B 99 HIS 0.006 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 ( 8304) covalent geometry : angle 0.60749 / 0.31 (11270) SS BOND : bond 0.00280 / 0.13 ( 4) SS BOND : angle 1.14131 / 0.56 ( 8) hydrogen bonds : bond 0.04178 / 2.82 ( 412) hydrogen bonds : angle 5.51878 / 3.76 ( 1167) *********************** 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 237 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8298 (tppt) cc_final: 0.7858 (mmtm) REVERT: A 20 ARG cc_start: 0.7608 (ttp80) cc_final: 0.7316 (ttm-80) REVERT: A 222 PHE cc_start: 0.5979 (t80) cc_final: 0.5528 (t80) REVERT: A 318 TYR cc_start: 0.7725 (t80) cc_final: 0.7497 (t80) REVERT: A 338 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8258 (ttmt) REVERT: A 339 TYR cc_start: 0.8687 (m-80) cc_final: 0.7998 (m-80) REVERT: A 343 ASP cc_start: 0.8245 (m-30) cc_final: 0.8006 (m-30) REVERT: B 124 TYR cc_start: 0.8988 (m-80) cc_final: 0.8743 (m-80) REVERT: B 262 MET cc_start: 0.8462 (tpp) cc_final: 0.8209 (mmm) REVERT: B 329 THR cc_start: 0.8988 (m) cc_final: 0.8685 (p) REVERT: B 336 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8354 (mp) REVERT: N 87 LYS cc_start: 0.7642 (mttt) cc_final: 0.7358 (mmtm) REVERT: R 81 LYS cc_start: 0.8442 (tptt) cc_final: 0.7989 (tptt) REVERT: R 125 ILE cc_start: 0.8495 (mm) cc_final: 0.7747 (mt) REVERT: R 142 ILE cc_start: 0.7701 (mt) cc_final: 0.7474 (mt) REVERT: R 154 ILE cc_start: 0.8671 (mm) cc_final: 0.8361 (mt) outliers start: 44 outliers final: 30 residues processed: 213 average time/residue: 0.0955 time to fit residues: 27.4319 Evaluate side-chains 208 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR 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 292 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 57 LYS 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 243 THR 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 B residue 336 LEU Chi-restraints excluded: chain N residue 125 THR 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 19 optimal weight: 10.0000 chunk 33 optimal weight: 0.4980 chunk 58 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 0.0170 chunk 66 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 377 ASN B 32 GLN R 60 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.182578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.149310 restraints weight = 9238.426| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.01 r_work: 0.3573 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8308 Z= 0.140 Angle : 0.596 14.021 11278 Z= 0.298 Chirality : 0.042 0.313 1282 Planarity : 0.004 0.052 1422 Dihedral : 5.021 51.783 1141 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.77 % Allowed : 20.58 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.26), residues: 1017 helix: 0.31 (0.25), residues: 408 sheet: -2.10 (0.36), residues: 181 loop : -1.13 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 333 TYR 0.018 0.002 TYR B 289 PHE 0.015 0.001 PHE B 151 TRP 0.014 0.002 TRP A 234 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 8304) covalent geometry : angle 0.59614 / 0.30 (11270) SS BOND : bond 0.00189 / 0.09 ( 4) SS BOND : angle 0.92825 / 0.43 ( 8) hydrogen bonds : bond 0.03895 / 2.62 ( 412) hydrogen bonds : angle 5.35678 / 3.65 ( 1167) *********************** 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: 41 poor density : 193 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8327 (tppt) cc_final: 0.7894 (mmtm) REVERT: A 20 ARG cc_start: 0.7648 (ttp80) cc_final: 0.7368 (ttm-80) REVERT: A 208 PHE cc_start: 0.4811 (OUTLIER) cc_final: 0.3695 (t80) REVERT: A 222 PHE cc_start: 0.6036 (t80) cc_final: 0.5394 (t80) REVERT: A 318 TYR cc_start: 0.7682 (t80) cc_final: 0.7469 (t80) REVERT: A 338 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8206 (ttmt) REVERT: A 339 TYR cc_start: 0.8678 (m-80) cc_final: 0.7976 (m-80) REVERT: A 343 ASP cc_start: 0.8104 (m-30) cc_final: 0.7882 (m-30) REVERT: B 124 TYR cc_start: 0.8918 (m-80) cc_final: 0.8678 (m-80) REVERT: B 262 MET cc_start: 0.8307 (tpp) cc_final: 0.8056 (mmm) REVERT: B 297 TRP cc_start: 0.9177 (m100) cc_final: 0.8811 (m100) REVERT: B 323 ASP cc_start: 0.7993 (p0) cc_final: 0.7499 (p0) REVERT: N 95 TYR cc_start: 0.9023 (m-80) cc_final: 0.8519 (m-80) REVERT: R 125 ILE cc_start: 0.8419 (mm) cc_final: 0.7724 (mt) REVERT: R 142 ILE cc_start: 0.7823 (mt) cc_final: 0.7562 (mt) REVERT: R 163 TRP cc_start: 0.6123 (m100) cc_final: 0.5827 (m100) outliers start: 41 outliers final: 29 residues processed: 213 average time/residue: 0.0983 time to fit residues: 28.2877 Evaluate side-chains 208 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 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 A residue 386 MET Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 105 TYR 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 190 LEU Chi-restraints excluded: chain B residue 213 VAL 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 N residue 6 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN B 32 GLN R 60 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.179495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144652 restraints weight = 9309.498| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.13 r_work: 0.3533 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8308 Z= 0.174 Angle : 0.618 14.126 11278 Z= 0.309 Chirality : 0.043 0.317 1282 Planarity : 0.004 0.053 1422 Dihedral : 5.074 52.042 1141 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.30 % Allowed : 21.16 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.27), residues: 1017 helix: 0.37 (0.26), residues: 408 sheet: -2.01 (0.36), residues: 181 loop : -1.09 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 314 TYR 0.017 0.002 TYR B 264 PHE 0.012 0.001 PHE A 238 TRP 0.013 0.002 TRP A 234 HIS 0.006 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 8304) covalent geometry : angle 0.61779 / 0.31 (11270) SS BOND : bond 0.00210 / 0.10 ( 4) SS BOND : angle 1.06635 / 0.51 ( 8) hydrogen bonds : bond 0.04030 / 2.69 ( 412) hydrogen bonds : angle 5.34026 / 3.64 ( 1167) *********************** 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 218 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8299 (tppt) cc_final: 0.7887 (mmtm) REVERT: A 20 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7295 (ttm-80) REVERT: A 208 PHE cc_start: 0.4782 (OUTLIER) cc_final: 0.3894 (t80) REVERT: A 222 PHE cc_start: 0.6054 (t80) cc_final: 0.5500 (t80) REVERT: A 318 TYR cc_start: 0.7774 (t80) cc_final: 0.7547 (t80) REVERT: A 338 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8238 (ttmt) REVERT: A 339 TYR cc_start: 0.8710 (m-80) cc_final: 0.8026 (m-80) REVERT: A 343 ASP cc_start: 0.8201 (m-30) cc_final: 0.7975 (m-30) REVERT: B 124 TYR cc_start: 0.8955 (m-80) cc_final: 0.8702 (m-80) REVERT: B 297 TRP cc_start: 0.9176 (m100) cc_final: 0.8881 (m100) REVERT: B 325 MET cc_start: 0.8857 (tpp) cc_final: 0.8432 (mmm) REVERT: N 95 TYR cc_start: 0.9032 (m-80) cc_final: 0.8474 (m-80) REVERT: R 81 LYS cc_start: 0.8529 (tptt) cc_final: 0.8168 (tptt) REVERT: R 125 ILE cc_start: 0.8506 (mm) cc_final: 0.7835 (mt) REVERT: R 142 ILE cc_start: 0.7750 (mt) cc_final: 0.7472 (mt) REVERT: R 163 TRP cc_start: 0.6081 (m100) cc_final: 0.5784 (m100) outliers start: 37 outliers final: 31 residues processed: 202 average time/residue: 0.0961 time to fit residues: 26.5114 Evaluate side-chains 208 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 263 THR 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 B residue 57 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 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL 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 274 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 6 GLU 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 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 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 81 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN A 236 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 377 ASN B 32 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.182071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.147217 restraints weight = 9332.763| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.15 r_work: 0.3560 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8308 Z= 0.149 Angle : 0.617 14.080 11278 Z= 0.304 Chirality : 0.043 0.318 1282 Planarity : 0.004 0.049 1422 Dihedral : 5.083 52.619 1141 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.42 % Allowed : 21.86 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.27), residues: 1017 helix: 0.51 (0.26), residues: 407 sheet: -1.96 (0.37), residues: 181 loop : -1.08 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 333 TYR 0.016 0.002 TYR B 289 PHE 0.012 0.001 PHE A 238 TRP 0.014 0.002 TRP A 281 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 8304) covalent geometry : angle 0.61649 / 0.30 (11270) SS BOND : bond 0.00183 / 0.09 ( 4) SS BOND : angle 0.91999 / 0.44 ( 8) hydrogen bonds : bond 0.03876 / 2.59 ( 412) hydrogen bonds : angle 5.28144 / 3.59 ( 1167) *********************** 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 226 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8282 (tppt) cc_final: 0.7872 (mmtm) REVERT: A 20 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7287 (ttm-80) REVERT: A 208 PHE cc_start: 0.4708 (t80) cc_final: 0.3809 (t80) REVERT: A 222 PHE cc_start: 0.6006 (t80) cc_final: 0.5505 (t80) REVERT: A 318 TYR cc_start: 0.7746 (t80) cc_final: 0.7526 (t80) REVERT: A 338 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8220 (ttmt) REVERT: A 339 TYR cc_start: 0.8694 (m-80) cc_final: 0.8003 (m-80) REVERT: A 343 ASP cc_start: 0.8204 (m-30) cc_final: 0.7970 (m-30) REVERT: A 360 TYR cc_start: 0.8913 (m-80) cc_final: 0.8606 (m-80) REVERT: A 362 HIS cc_start: 0.7709 (m170) cc_final: 0.7331 (m-70) REVERT: B 124 TYR cc_start: 0.8921 (m-80) cc_final: 0.8663 (m-80) REVERT: B 297 TRP cc_start: 0.9177 (m100) cc_final: 0.8910 (m100) REVERT: B 336 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8222 (mp) REVERT: N 80 TYR cc_start: 0.8428 (m-80) cc_final: 0.7947 (m-80) REVERT: N 95 TYR cc_start: 0.8979 (m-80) cc_final: 0.8432 (m-80) REVERT: R 60 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8679 (t0) REVERT: R 81 LYS cc_start: 0.8511 (tptt) cc_final: 0.8036 (tptt) REVERT: R 142 ILE cc_start: 0.7752 (mt) cc_final: 0.7456 (mt) REVERT: R 163 TRP cc_start: 0.6095 (m100) cc_final: 0.5833 (m100) outliers start: 38 outliers final: 33 residues processed: 210 average time/residue: 0.0900 time to fit residues: 26.1124 Evaluate side-chains 214 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 57 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 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 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 6 GLU 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 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 96 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 377 ASN B 75 GLN R 60 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.181110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.146485 restraints weight = 9356.277| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.12 r_work: 0.3550 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8308 Z= 0.161 Angle : 0.639 14.120 11278 Z= 0.313 Chirality : 0.044 0.320 1282 Planarity : 0.004 0.048 1422 Dihedral : 5.106 52.681 1141 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.12 % Allowed : 21.51 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.27), residues: 1017 helix: 0.55 (0.26), residues: 407 sheet: -1.99 (0.35), residues: 191 loop : -1.04 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 333 TYR 0.026 0.002 TYR B 264 PHE 0.012 0.001 PHE A 238 TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 8304) covalent geometry : angle 0.63864 / 0.31 (11270) SS BOND : bond 0.00205 / 0.10 ( 4) SS BOND : angle 0.97119 / 0.47 ( 8) hydrogen bonds : bond 0.03893 / 2.61 ( 412) hydrogen bonds : angle 5.26350 / 3.60 ( 1167) *********************** 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 229 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8240 (tppt) cc_final: 0.7846 (mmtm) REVERT: A 20 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7261 (ttm-80) REVERT: A 208 PHE cc_start: 0.4638 (OUTLIER) cc_final: 0.4216 (t80) REVERT: A 222 PHE cc_start: 0.6058 (t80) cc_final: 0.5565 (t80) REVERT: A 318 TYR cc_start: 0.7804 (t80) cc_final: 0.7593 (t80) REVERT: A 338 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8261 (ttmt) REVERT: A 339 TYR cc_start: 0.8710 (m-80) cc_final: 0.8023 (m-80) REVERT: A 343 ASP cc_start: 0.8208 (m-30) cc_final: 0.7984 (m-30) REVERT: A 360 TYR cc_start: 0.8900 (m-80) cc_final: 0.8605 (m-80) REVERT: A 362 HIS cc_start: 0.7660 (m170) cc_final: 0.7341 (m-70) REVERT: B 124 TYR cc_start: 0.8909 (m-80) cc_final: 0.8643 (m-80) REVERT: B 197 ARG cc_start: 0.7988 (tpp80) cc_final: 0.7280 (tpp80) REVERT: B 297 TRP cc_start: 0.9159 (m100) cc_final: 0.8950 (m100) REVERT: B 336 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8220 (mp) REVERT: N 80 TYR cc_start: 0.8418 (m-80) cc_final: 0.7946 (m-80) REVERT: N 95 TYR cc_start: 0.8997 (m-80) cc_final: 0.8453 (m-80) REVERT: R 81 LYS cc_start: 0.8523 (tptt) cc_final: 0.8132 (tptt) REVERT: R 125 ILE cc_start: 0.8480 (mm) cc_final: 0.7800 (mt) REVERT: R 142 ILE cc_start: 0.7761 (mt) cc_final: 0.7462 (mt) REVERT: R 163 TRP cc_start: 0.6063 (m100) cc_final: 0.5814 (m100) outliers start: 44 outliers final: 35 residues processed: 211 average time/residue: 0.0875 time to fit residues: 25.4394 Evaluate side-chains 216 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 178 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 250 SER 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 30 LEU Chi-restraints excluded: chain B residue 57 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 190 LEU 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 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 6 GLU 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 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 32 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 85 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 377 ASN R 60 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.182344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.148126 restraints weight = 9315.053| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.10 r_work: 0.3569 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8308 Z= 0.147 Angle : 0.635 14.073 11278 Z= 0.311 Chirality : 0.043 0.322 1282 Planarity : 0.004 0.048 1422 Dihedral : 5.109 53.116 1141 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.77 % Allowed : 22.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.27), residues: 1017 helix: 0.75 (0.26), residues: 401 sheet: -1.90 (0.35), residues: 190 loop : -0.99 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 333 TYR 0.018 0.002 TYR B 264 PHE 0.012 0.001 PHE A 238 TRP 0.014 0.002 TRP A 281 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 8304) covalent geometry : angle 0.63477 / 0.31 (11270) SS BOND : bond 0.00171 / 0.08 ( 4) SS BOND : angle 0.89485 / 0.42 ( 8) hydrogen bonds : bond 0.03838 / 2.58 ( 412) hydrogen bonds : angle 5.20385 / 3.56 ( 1167) ********************** 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 236 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8235 (tppt) cc_final: 0.7842 (mmtm) REVERT: A 20 ARG cc_start: 0.7525 (ttp80) cc_final: 0.7263 (ttm-80) REVERT: A 222 PHE cc_start: 0.5723 (t80) cc_final: 0.5335 (t80) REVERT: A 265 ARG cc_start: 0.8004 (ttt90) cc_final: 0.7596 (ttm170) REVERT: A 338 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8141 (ttmt) REVERT: A 339 TYR cc_start: 0.8621 (m-80) cc_final: 0.7910 (m-80) REVERT: A 343 ASP cc_start: 0.8018 (m-30) cc_final: 0.7775 (m-30) REVERT: A 360 TYR cc_start: 0.8783 (m-80) cc_final: 0.8495 (m-80) REVERT: A 362 HIS cc_start: 0.7260 (m170) cc_final: 0.6999 (m-70) REVERT: B 124 TYR cc_start: 0.8810 (m-80) cc_final: 0.8608 (m-80) REVERT: B 197 ARG cc_start: 0.7680 (tpp80) cc_final: 0.7119 (tpp80) REVERT: B 297 TRP cc_start: 0.9099 (m100) cc_final: 0.8867 (m100) REVERT: B 323 ASP cc_start: 0.7794 (p0) cc_final: 0.7320 (p0) REVERT: B 336 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8127 (mp) REVERT: G 29 LYS cc_start: 0.8450 (tppt) cc_final: 0.7891 (tptt) REVERT: N 80 TYR cc_start: 0.8319 (m-80) cc_final: 0.7881 (m-80) REVERT: N 95 TYR cc_start: 0.8823 (m-80) cc_final: 0.8263 (m-80) REVERT: R 60 ASN cc_start: 0.8985 (OUTLIER) cc_final: 0.8779 (t0) REVERT: R 81 LYS cc_start: 0.8488 (tptt) cc_final: 0.8122 (tptt) REVERT: R 142 ILE cc_start: 0.7692 (mt) cc_final: 0.7390 (mt) outliers start: 41 outliers final: 33 residues processed: 219 average time/residue: 0.0881 time to fit residues: 26.8441 Evaluate side-chains 221 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 250 SER 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 30 LEU Chi-restraints excluded: chain B residue 57 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 190 LEU 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 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 6 GLU 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 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 87 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 377 ASN R 60 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.181092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.146636 restraints weight = 9321.043| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.11 r_work: 0.3551 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8308 Z= 0.167 Angle : 0.646 14.132 11278 Z= 0.315 Chirality : 0.044 0.324 1282 Planarity : 0.004 0.047 1422 Dihedral : 5.156 53.027 1141 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.19 % Allowed : 22.79 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.27), residues: 1017 helix: 0.72 (0.26), residues: 401 sheet: -1.82 (0.35), residues: 194 loop : -0.98 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 333 TYR 0.017 0.002 TYR B 264 PHE 0.014 0.001 PHE A 238 TRP 0.019 0.002 TRP B 63 HIS 0.005 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 8304) covalent geometry : angle 0.64572 / 0.32 (11270) SS BOND : bond 0.00197 / 0.10 ( 4) SS BOND : angle 0.97201 / 0.48 ( 8) hydrogen bonds : bond 0.03908 / 2.62 ( 412) hydrogen bonds : angle 5.21324 / 3.57 ( 1167) =============================================================================== Job complete usr+sys time: 2281.62 seconds wall clock time: 40 minutes 0.80 seconds (2400.80 seconds total)