Starting phenix.real_space_refine on Thu Mar 13 21:02:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vbh_31879/03_2025/7vbh_31879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vbh_31879/03_2025/7vbh_31879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vbh_31879/03_2025/7vbh_31879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vbh_31879/03_2025/7vbh_31879.map" model { file = "/net/cci-nas-00/data/ceres_data/7vbh_31879/03_2025/7vbh_31879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vbh_31879/03_2025/7vbh_31879.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 5817 2.51 5 N 1577 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9116 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1761 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 3 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 236 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3105 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 13, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2591 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.76, per 1000 atoms: 0.63 Number of scatterers: 9116 At special positions: 0 Unit cell: (81.396, 96.39, 170.289, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 1669 8.00 N 1577 7.00 C 5817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.04 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.04 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 41.2% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.661A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.834A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.660A pdb=" N LEU A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.756A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 333 through 350 removed outlier: 3.750A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.628A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.566A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 28 removed outlier: 3.993A pdb=" N ASP P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 51 removed outlier: 3.715A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 168 Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.727A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 214 Processing helix chain 'R' and resid 219 through 222 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.813A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 291 removed outlier: 3.538A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 336 removed outlier: 3.541A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 365 Processing helix chain 'R' and resid 377 through 403 removed outlier: 3.862A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE R 382 " --> pdb=" O THR R 378 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA R 399 " --> pdb=" O GLY R 395 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 422 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.642A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 22 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.589A pdb=" N GLU G 58 " --> pdb=" O PRO G 55 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 55 through 59' Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.322A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.563A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU N 79 " --> pdb=" O CYS N 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.543A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.382A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.736A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.075A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.643A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.687A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.135A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.845A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1478 1.29 - 1.42: 2571 1.42 - 1.56: 5198 1.56 - 1.69: 3 1.69 - 1.83: 72 Bond restraints: 9322 Sorted by residual: bond pdb=" C02 D6M P 501 " pdb=" C12 D6M P 501 " ideal model delta sigma weight residual 1.517 1.795 -0.278 2.00e-02 2.50e+03 1.93e+02 bond pdb=" C ASP B 228 " pdb=" O ASP B 228 " ideal model delta sigma weight residual 1.234 1.169 0.064 1.23e-02 6.61e+03 2.75e+01 bond pdb=" C07 D6M P 501 " pdb=" O08 D6M P 501 " ideal model delta sigma weight residual 1.247 1.154 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C SER B 227 " pdb=" O SER B 227 " ideal model delta sigma weight residual 1.235 1.178 0.057 1.28e-02 6.10e+03 1.97e+01 bond pdb=" N SER B 227 " pdb=" CA SER B 227 " ideal model delta sigma weight residual 1.455 1.394 0.061 1.41e-02 5.03e+03 1.87e+01 ... (remaining 9317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 12176 2.49 - 4.99: 379 4.99 - 7.48: 47 7.48 - 9.97: 18 9.97 - 12.47: 13 Bond angle restraints: 12633 Sorted by residual: angle pdb=" N TYR P 13 " pdb=" CA TYR P 13 " pdb=" C TYR P 13 " ideal model delta sigma weight residual 112.23 100.11 12.12 1.26e+00 6.30e-01 9.25e+01 angle pdb=" C THR P 5 " pdb=" CA THR P 5 " pdb=" CB THR P 5 " ideal model delta sigma weight residual 110.92 100.58 10.34 1.59e+00 3.96e-01 4.23e+01 angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 113.47 121.65 -8.18 1.43e+00 4.89e-01 3.28e+01 angle pdb=" N ASP B 228 " pdb=" CA ASP B 228 " pdb=" C ASP B 228 " ideal model delta sigma weight residual 110.42 118.66 -8.24 1.46e+00 4.69e-01 3.18e+01 angle pdb=" CA LYS A 305 " pdb=" CB LYS A 305 " pdb=" CG LYS A 305 " ideal model delta sigma weight residual 114.10 125.33 -11.23 2.00e+00 2.50e-01 3.15e+01 ... (remaining 12628 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4867 17.97 - 35.95: 521 35.95 - 53.92: 90 53.92 - 71.90: 27 71.90 - 89.87: 12 Dihedral angle restraints: 5517 sinusoidal: 2193 harmonic: 3324 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual -86.00 -160.71 74.71 1 1.00e+01 1.00e-02 7.07e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 44.87 48.13 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA GLU A 327 " pdb=" C GLU A 327 " pdb=" N PRO A 328 " pdb=" CA PRO A 328 " ideal model delta harmonic sigma weight residual 180.00 -151.95 -28.05 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 5514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1154 0.077 - 0.155: 209 0.155 - 0.232: 24 0.232 - 0.310: 2 0.310 - 0.387: 3 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CA ASP B 228 " pdb=" N ASP B 228 " pdb=" C ASP B 228 " pdb=" CB ASP B 228 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CB ILE N 51 " pdb=" CA ILE N 51 " pdb=" CG1 ILE N 51 " pdb=" CG2 ILE N 51 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" C PRO N 100 " pdb=" CB PRO N 100 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1389 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 D6M P 501 " -0.095 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C04 D6M P 501 " 0.348 2.00e-02 2.50e+03 pdb=" C12 D6M P 501 " 0.123 2.00e-02 2.50e+03 pdb=" N03 D6M P 501 " -0.518 2.00e-02 2.50e+03 pdb=" O01 D6M P 501 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 385 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C PHE R 385 " 0.064 2.00e-02 2.50e+03 pdb=" O PHE R 385 " -0.024 2.00e-02 2.50e+03 pdb=" N THR R 386 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 226 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C GLU B 226 " 0.059 2.00e-02 2.50e+03 pdb=" O GLU B 226 " -0.021 2.00e-02 2.50e+03 pdb=" N SER B 227 " -0.021 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 41 2.41 - 3.03: 4872 3.03 - 3.65: 14461 3.65 - 4.28: 22223 4.28 - 4.90: 37221 Nonbonded interactions: 78818 Sorted by model distance: nonbonded pdb=" O LEU P 27 " pdb=" NH2 ARG R 121 " model vdw 1.784 3.120 nonbonded pdb=" CD2 LEU P 26 " pdb=" O GLU R 68 " model vdw 1.908 3.460 nonbonded pdb=" OD1 ASP P 15 " pdb=" N LEU R 32 " model vdw 1.947 3.120 nonbonded pdb=" N HIS P 1 " pdb=" CH2 TRP R 306 " model vdw 1.950 3.420 nonbonded pdb=" O GLY P 29 " pdb=" OE2 GLU R 68 " model vdw 2.182 3.040 ... (remaining 78813 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 23.500 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.278 9322 Z= 0.643 Angle : 1.117 12.466 12633 Z= 0.621 Chirality : 0.062 0.387 1392 Planarity : 0.011 0.294 1604 Dihedral : 15.915 89.873 3349 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.52 % Allowed : 9.91 % Favored : 89.58 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.19), residues: 1117 helix: -2.58 (0.18), residues: 439 sheet: -2.61 (0.29), residues: 212 loop : -2.66 (0.23), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP R 214 HIS 0.010 0.002 HIS A 357 PHE 0.034 0.003 PHE B 151 TYR 0.025 0.003 TYR R 148 ARG 0.009 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 166 average time/residue: 1.1197 time to fit residues: 200.4182 Evaluate side-chains 91 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 239 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 87 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN P 20 GLN ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 302 ASN R 304 ASN R 320 ASN R 394 GLN B 9 GLN B 35 ASN B 155 ASN B 176 GLN B 237 ASN B 259 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.218296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.177257 restraints weight = 10688.230| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.44 r_work: 0.3742 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9322 Z= 0.246 Angle : 0.683 8.636 12633 Z= 0.356 Chirality : 0.043 0.152 1392 Planarity : 0.006 0.064 1604 Dihedral : 7.138 58.528 1279 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.76 % Favored : 96.15 % Rotamer: Outliers : 3.41 % Allowed : 16.82 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.23), residues: 1117 helix: 0.03 (0.24), residues: 435 sheet: -1.81 (0.31), residues: 205 loop : -2.15 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 72 HIS 0.005 0.001 HIS A 362 PHE 0.014 0.002 PHE B 151 TYR 0.027 0.002 TYR R 148 ARG 0.007 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8240 (m-30) cc_final: 0.8023 (m-30) REVERT: A 392 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7331 (mt-10) REVERT: N 52 SER cc_start: 0.8591 (p) cc_final: 0.7982 (t) REVERT: N 53 GLN cc_start: 0.7611 (mp10) cc_final: 0.7360 (mp10) REVERT: R 34 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7501 (tm-30) REVERT: R 287 VAL cc_start: 0.5864 (t) cc_final: 0.5646 (p) REVERT: R 293 ASP cc_start: 0.5455 (p0) cc_final: 0.4681 (t0) REVERT: R 320 ASN cc_start: 0.6976 (OUTLIER) cc_final: 0.6266 (m-40) REVERT: B 259 GLN cc_start: 0.6014 (pt0) cc_final: 0.5736 (pt0) REVERT: G 38 MET cc_start: 0.6211 (tmm) cc_final: 0.5716 (ttp) outliers start: 33 outliers final: 10 residues processed: 155 average time/residue: 1.0906 time to fit residues: 182.9216 Evaluate side-chains 115 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 233 MET Chi-restraints excluded: chain R residue 320 ASN Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN N 39 GLN P 1 HIS ** R 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 GLN B 88 ASN B 220 GLN B 230 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.194259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.149791 restraints weight = 10561.620| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.92 r_work: 0.3347 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9322 Z= 0.329 Angle : 0.713 12.638 12633 Z= 0.373 Chirality : 0.046 0.201 1392 Planarity : 0.006 0.067 1604 Dihedral : 6.347 59.149 1273 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.92 % Allowed : 18.89 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.24), residues: 1117 helix: 0.63 (0.24), residues: 443 sheet: -1.44 (0.32), residues: 213 loop : -2.12 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 243 HIS 0.008 0.001 HIS A 220 PHE 0.027 0.002 PHE B 151 TYR 0.023 0.002 TYR R 148 ARG 0.008 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.6630 (mtp85) REVERT: A 392 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7187 (mt-10) REVERT: N 77 ASN cc_start: 0.6158 (p0) cc_final: 0.5906 (p0) REVERT: N 94 TYR cc_start: 0.8033 (m-80) cc_final: 0.7769 (m-80) REVERT: P 21 ASP cc_start: 0.8216 (t70) cc_final: 0.7887 (t70) REVERT: P 26 LEU cc_start: 0.8030 (tp) cc_final: 0.7822 (tp) REVERT: R 139 GLU cc_start: 0.7305 (pm20) cc_final: 0.6443 (tp30) REVERT: R 202 LYS cc_start: 0.6516 (ttpp) cc_final: 0.6030 (tptp) REVERT: R 292 GLU cc_start: 0.7673 (tp30) cc_final: 0.6936 (mp0) REVERT: R 346 LYS cc_start: 0.7953 (mtmm) cc_final: 0.7690 (mtpm) REVERT: B 17 GLN cc_start: 0.6762 (tm-30) cc_final: 0.6467 (tm-30) REVERT: B 46 ARG cc_start: 0.8346 (mtp-110) cc_final: 0.7942 (mtm180) REVERT: B 215 GLU cc_start: 0.8063 (mp0) cc_final: 0.7815 (tt0) REVERT: G 38 MET cc_start: 0.6295 (tmm) cc_final: 0.6091 (ttp) outliers start: 38 outliers final: 13 residues processed: 163 average time/residue: 1.2099 time to fit residues: 211.3652 Evaluate side-chains 125 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 267 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 213 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.194530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151238 restraints weight = 10459.917| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.04 r_work: 0.3410 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.6388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9322 Z= 0.225 Angle : 0.602 7.910 12633 Z= 0.317 Chirality : 0.043 0.138 1392 Planarity : 0.004 0.058 1604 Dihedral : 5.873 59.363 1273 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.23 % Allowed : 21.16 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1117 helix: 1.32 (0.25), residues: 437 sheet: -1.00 (0.33), residues: 226 loop : -1.93 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 243 HIS 0.006 0.001 HIS R 171 PHE 0.017 0.001 PHE B 151 TYR 0.021 0.002 TYR R 148 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8423 (tttt) cc_final: 0.8026 (mmpt) REVERT: A 320 THR cc_start: 0.7191 (OUTLIER) cc_final: 0.6949 (m) REVERT: A 380 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.6609 (mtp85) REVERT: A 386 MET cc_start: 0.7849 (ppp) cc_final: 0.7641 (ptm) REVERT: A 392 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7303 (mt-10) REVERT: N 46 GLU cc_start: 0.7758 (pt0) cc_final: 0.7535 (pt0) REVERT: N 57 SER cc_start: 0.7582 (t) cc_final: 0.7347 (m) REVERT: N 94 TYR cc_start: 0.7882 (m-80) cc_final: 0.7676 (m-80) REVERT: R 192 LEU cc_start: 0.8326 (tt) cc_final: 0.7789 (mp) REVERT: R 202 LYS cc_start: 0.6819 (ttpp) cc_final: 0.6373 (tptp) REVERT: R 346 LYS cc_start: 0.7991 (mtmm) cc_final: 0.7759 (mtpm) REVERT: B 17 GLN cc_start: 0.6924 (tm-30) cc_final: 0.6621 (tm-30) REVERT: B 46 ARG cc_start: 0.8262 (mtp-110) cc_final: 0.7871 (mtp-110) outliers start: 41 outliers final: 23 residues processed: 152 average time/residue: 1.1304 time to fit residues: 185.9136 Evaluate side-chains 142 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN R 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.191703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.147733 restraints weight = 10510.636| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.88 r_work: 0.3342 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9322 Z= 0.243 Angle : 0.619 8.660 12633 Z= 0.325 Chirality : 0.043 0.173 1392 Planarity : 0.004 0.056 1604 Dihedral : 5.738 54.798 1273 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.44 % Allowed : 22.29 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.25), residues: 1117 helix: 1.46 (0.25), residues: 442 sheet: -0.70 (0.35), residues: 222 loop : -1.96 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 243 HIS 0.009 0.001 HIS R 171 PHE 0.016 0.002 PHE B 151 TYR 0.026 0.002 TYR R 289 ARG 0.007 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7489 (pt0) REVERT: A 32 LYS cc_start: 0.8424 (tttt) cc_final: 0.8027 (mmpt) REVERT: A 266 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8060 (tm) REVERT: A 372 ILE cc_start: 0.8472 (mm) cc_final: 0.8258 (mp) REVERT: A 380 ARG cc_start: 0.7550 (ttp-110) cc_final: 0.6633 (mtp85) REVERT: A 386 MET cc_start: 0.7882 (ppp) cc_final: 0.7630 (ptm) REVERT: A 392 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7279 (mt-10) REVERT: N 57 SER cc_start: 0.7683 (OUTLIER) cc_final: 0.7456 (m) REVERT: R 192 LEU cc_start: 0.8332 (tt) cc_final: 0.7837 (mp) REVERT: R 202 LYS cc_start: 0.7099 (ttpp) cc_final: 0.6638 (tptp) REVERT: R 271 SER cc_start: 0.8364 (t) cc_final: 0.7915 (m) REVERT: R 346 LYS cc_start: 0.8135 (mtmm) cc_final: 0.7865 (mtpm) outliers start: 43 outliers final: 24 residues processed: 163 average time/residue: 1.0023 time to fit residues: 176.8115 Evaluate side-chains 148 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN R 171 HIS B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.198828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.154449 restraints weight = 10265.615| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.82 r_work: 0.3559 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.7058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9322 Z= 0.232 Angle : 0.614 8.090 12633 Z= 0.320 Chirality : 0.043 0.158 1392 Planarity : 0.004 0.056 1604 Dihedral : 5.663 55.636 1273 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.92 % Allowed : 23.74 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1117 helix: 1.58 (0.25), residues: 442 sheet: -0.61 (0.35), residues: 224 loop : -1.91 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.005 0.001 HIS R 171 PHE 0.015 0.001 PHE B 151 TYR 0.023 0.002 TYR R 148 ARG 0.003 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8627 (tttt) cc_final: 0.8257 (mmpt) REVERT: A 266 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8217 (tm) REVERT: A 380 ARG cc_start: 0.7798 (ttp-110) cc_final: 0.6889 (mtp85) REVERT: A 386 MET cc_start: 0.8151 (ppp) cc_final: 0.7937 (ptm) REVERT: A 392 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7451 (mt-10) REVERT: N 83 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6885 (mtp) REVERT: R 192 LEU cc_start: 0.8547 (tt) cc_final: 0.8075 (mp) REVERT: R 202 LYS cc_start: 0.7292 (ttpp) cc_final: 0.6863 (tptp) REVERT: R 271 SER cc_start: 0.8588 (t) cc_final: 0.8149 (m) REVERT: R 289 TYR cc_start: 0.7513 (t80) cc_final: 0.7189 (t80) REVERT: R 346 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7867 (mtpm) REVERT: B 118 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6907 (p0) outliers start: 38 outliers final: 26 residues processed: 151 average time/residue: 1.0227 time to fit residues: 167.3662 Evaluate side-chains 146 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 37 optimal weight: 30.0000 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN R 171 HIS B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.195630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154731 restraints weight = 10316.845| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.46 r_work: 0.3562 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.7257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9322 Z= 0.250 Angle : 0.618 8.367 12633 Z= 0.323 Chirality : 0.044 0.156 1392 Planarity : 0.004 0.055 1604 Dihedral : 5.673 56.174 1273 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.75 % Allowed : 22.60 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1117 helix: 1.67 (0.25), residues: 440 sheet: -0.59 (0.35), residues: 224 loop : -1.85 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.006 0.001 HIS A 220 PHE 0.015 0.002 PHE B 151 TYR 0.019 0.002 TYR R 289 ARG 0.008 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8604 (tttt) cc_final: 0.8221 (mmpt) REVERT: A 266 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8217 (tm) REVERT: A 380 ARG cc_start: 0.7818 (ttp-110) cc_final: 0.6897 (mtp85) REVERT: A 392 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7442 (mm-30) REVERT: R 202 LYS cc_start: 0.7359 (ttpp) cc_final: 0.6934 (tptp) REVERT: R 271 SER cc_start: 0.8659 (t) cc_final: 0.8232 (m) REVERT: R 289 TYR cc_start: 0.7540 (t80) cc_final: 0.7230 (t80) REVERT: R 346 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7958 (mtpm) REVERT: B 45 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7397 (mmt) REVERT: B 96 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7327 (mtm-85) REVERT: B 118 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.6918 (p0) outliers start: 46 outliers final: 34 residues processed: 154 average time/residue: 1.1448 time to fit residues: 191.2039 Evaluate side-chains 154 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 355 THR Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 22 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 73 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.198775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156024 restraints weight = 10441.055| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.92 r_work: 0.3556 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.7497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9322 Z= 0.198 Angle : 0.593 8.396 12633 Z= 0.307 Chirality : 0.042 0.155 1392 Planarity : 0.004 0.054 1604 Dihedral : 5.527 54.298 1273 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.23 % Allowed : 23.01 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.26), residues: 1117 helix: 1.85 (0.25), residues: 439 sheet: -0.54 (0.35), residues: 224 loop : -1.77 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.005 0.001 HIS A 387 PHE 0.015 0.001 PHE R 280 TYR 0.019 0.002 TYR R 148 ARG 0.009 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8506 (tttt) cc_final: 0.8203 (mmpt) REVERT: A 266 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8137 (tm) REVERT: A 380 ARG cc_start: 0.7564 (ttp-110) cc_final: 0.6740 (mtp85) REVERT: A 392 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7218 (mm-30) REVERT: P 12 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7502 (mtpt) REVERT: R 202 LYS cc_start: 0.7213 (ttpp) cc_final: 0.6808 (tptp) REVERT: R 271 SER cc_start: 0.8498 (t) cc_final: 0.8047 (m) REVERT: R 289 TYR cc_start: 0.7394 (t80) cc_final: 0.7087 (t80) REVERT: R 346 LYS cc_start: 0.8304 (mtmm) cc_final: 0.8053 (mtpm) REVERT: B 45 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7146 (mmt) outliers start: 41 outliers final: 26 residues processed: 161 average time/residue: 1.0466 time to fit residues: 184.3816 Evaluate side-chains 153 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.0570 chunk 34 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 0.0030 chunk 62 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 HIS B 237 ASN G 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.198881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156906 restraints weight = 10305.926| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.71 r_work: 0.3533 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.7650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9322 Z= 0.189 Angle : 0.598 9.155 12633 Z= 0.312 Chirality : 0.042 0.152 1392 Planarity : 0.004 0.053 1604 Dihedral : 5.463 53.749 1273 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.23 % Allowed : 23.84 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1117 helix: 1.92 (0.25), residues: 441 sheet: -0.37 (0.35), residues: 221 loop : -1.77 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.008 0.001 HIS A 387 PHE 0.014 0.001 PHE R 280 TYR 0.036 0.002 TYR R 220 ARG 0.007 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 1.936 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8505 (tttt) cc_final: 0.8227 (mmpt) REVERT: A 266 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8141 (tm) REVERT: A 380 ARG cc_start: 0.7590 (ttp-110) cc_final: 0.6776 (mtp85) REVERT: A 392 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7299 (mm-30) REVERT: N 87 LYS cc_start: 0.7612 (mttm) cc_final: 0.7141 (mtpm) REVERT: P 12 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7565 (mtpt) REVERT: R 202 LYS cc_start: 0.7244 (ttpp) cc_final: 0.6847 (tptp) REVERT: R 271 SER cc_start: 0.8510 (t) cc_final: 0.8072 (m) REVERT: R 289 TYR cc_start: 0.7377 (t80) cc_final: 0.7076 (t80) REVERT: R 346 LYS cc_start: 0.8288 (mtmm) cc_final: 0.8022 (mtpm) REVERT: B 57 LYS cc_start: 0.9165 (pttm) cc_final: 0.8955 (pttp) REVERT: B 118 ASP cc_start: 0.7064 (OUTLIER) cc_final: 0.6678 (p0) outliers start: 41 outliers final: 30 residues processed: 156 average time/residue: 1.1707 time to fit residues: 199.3342 Evaluate side-chains 161 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 272 ILE Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 422 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 0.5980 chunk 99 optimal weight: 0.0270 chunk 40 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 171 HIS R 213 GLN R 263 GLN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.198342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155908 restraints weight = 10478.522| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.83 r_work: 0.3549 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.7786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9322 Z= 0.202 Angle : 0.611 8.611 12633 Z= 0.318 Chirality : 0.042 0.157 1392 Planarity : 0.004 0.053 1604 Dihedral : 5.464 55.069 1273 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.51 % Allowed : 25.08 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.26), residues: 1117 helix: 2.07 (0.25), residues: 434 sheet: -0.34 (0.35), residues: 218 loop : -1.63 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.005 0.001 HIS A 220 PHE 0.015 0.001 PHE R 280 TYR 0.025 0.002 TYR R 220 ARG 0.006 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8522 (tttt) cc_final: 0.8206 (mmpt) REVERT: A 266 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8134 (tm) REVERT: A 380 ARG cc_start: 0.7574 (ttp-110) cc_final: 0.6747 (mtp85) REVERT: A 392 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7264 (mm-30) REVERT: N 87 LYS cc_start: 0.7682 (mttm) cc_final: 0.7283 (mtpm) REVERT: P 12 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7534 (mtpt) REVERT: R 202 LYS cc_start: 0.7265 (ttpp) cc_final: 0.6846 (tptp) REVERT: R 271 SER cc_start: 0.8568 (t) cc_final: 0.8107 (m) REVERT: R 279 LEU cc_start: 0.8281 (tm) cc_final: 0.7569 (mp) REVERT: R 289 TYR cc_start: 0.7346 (t80) cc_final: 0.7071 (t80) REVERT: R 346 LYS cc_start: 0.8281 (mtmm) cc_final: 0.8032 (mtpm) REVERT: B 118 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6633 (p0) REVERT: B 264 TYR cc_start: 0.7978 (m-80) cc_final: 0.7359 (m-80) outliers start: 34 outliers final: 26 residues processed: 152 average time/residue: 1.0040 time to fit residues: 165.6804 Evaluate side-chains 155 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 106 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 171 HIS B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.196225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.156719 restraints weight = 10261.508| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.65 r_work: 0.3524 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.7909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9322 Z= 0.202 Angle : 0.595 8.834 12633 Z= 0.313 Chirality : 0.042 0.158 1392 Planarity : 0.004 0.053 1604 Dihedral : 5.477 59.259 1273 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.72 % Allowed : 24.66 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1117 helix: 2.02 (0.25), residues: 440 sheet: -0.28 (0.35), residues: 218 loop : -1.69 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.005 0.001 HIS A 220 PHE 0.015 0.001 PHE R 280 TYR 0.023 0.002 TYR R 220 ARG 0.006 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6968.92 seconds wall clock time: 123 minutes 49.57 seconds (7429.57 seconds total)