Starting phenix.real_space_refine on Wed Sep 17 10:23:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lup_63401/09_2025/9lup_63401.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lup_63401/09_2025/9lup_63401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lup_63401/09_2025/9lup_63401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lup_63401/09_2025/9lup_63401.map" model { file = "/net/cci-nas-00/data/ceres_data/9lup_63401/09_2025/9lup_63401.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lup_63401/09_2025/9lup_63401.cif" } resolution = 2.8 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 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= 0.001 sd= 1.040 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 38 5.16 5 C 5133 2.51 5 N 1394 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8081 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3403 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 16, 'TRANS': 421} Chain breaks: 2 Chain: "B" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2647 Classifications: {'peptide': 334} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 315} Chain: "C" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 907 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "D" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1099 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain breaks: 2 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'GA3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.19, per 1000 atoms: 0.27 Number of scatterers: 8081 At special positions: 0 Unit cell: (73.7649, 96.1179, 125.177, 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 38 16.00 O 1516 8.00 N 1394 7.00 C 5133 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 434.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 5 sheets defined 58.3% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 58 through 87 removed outlier: 7.102A pdb=" N GLU A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP A 79 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 108 Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.731A pdb=" N VAL A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 254 removed outlier: 3.917A pdb=" N ALA A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER A 253 " --> pdb=" O CYS A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 274 removed outlier: 4.172A pdb=" N LYS A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 300 through 317 removed outlier: 3.718A pdb=" N ALA A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.765A pdb=" N LEU A 339 " --> pdb=" O GLN A 335 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 removed outlier: 3.835A pdb=" N HIS A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 401 through 406 removed outlier: 3.641A pdb=" N MET A 404 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 405 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A 406 " --> pdb=" O SER A 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 406' Processing helix chain 'A' and resid 422 through 427 removed outlier: 3.567A pdb=" N LEU A 427 " --> pdb=" O HIS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.530A pdb=" N LYS A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 480 Processing helix chain 'A' and resid 486 through 505 removed outlier: 3.519A pdb=" N VAL A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 517 through 529 Processing helix chain 'A' and resid 536 through 550 removed outlier: 3.657A pdb=" N SER A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 34 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 126 through 139 removed outlier: 3.510A pdb=" N LEU B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 170 removed outlier: 3.567A pdb=" N TRP B 163 " --> pdb=" O TYR B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 5.755A pdb=" N TRP B 174 " --> pdb=" O SER B 171 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS B 176 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 207 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 291 through 304 Processing helix chain 'B' and resid 320 through 324 removed outlier: 3.530A pdb=" N LEU B 323 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 324 " --> pdb=" O PHE B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 320 through 324' Processing helix chain 'B' and resid 327 through 342 removed outlier: 3.671A pdb=" N HIS B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 36 through 45 Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 59 through 67 Processing helix chain 'C' and resid 68 through 79 removed outlier: 3.693A pdb=" N TRP C 72 " --> pdb=" O ASP C 68 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 97 Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.860A pdb=" N TYR C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 122 through 141 removed outlier: 4.208A pdb=" N SER C 141 " --> pdb=" O TYR C 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 49 through 68 Processing helix chain 'D' and resid 89 through 103 removed outlier: 3.784A pdb=" N LYS D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 121 through 137 Processing helix chain 'D' and resid 140 through 148 removed outlier: 3.648A pdb=" N ILE D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 166 removed outlier: 3.581A pdb=" N ASN D 166 " --> pdb=" O VAL D 162 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 211 removed outlier: 4.388A pdb=" N LEU B 77 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL B 141 " --> pdb=" O PRO B 107 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 108 " --> pdb=" O PHE B 186 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA B 188 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU B 110 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ASP B 190 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE B 112 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ILE B 185 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ILE B 215 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU B 187 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU B 217 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY B 189 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N SER B 281 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N MET B 312 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 283 " --> pdb=" O MET B 312 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU B 314 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 285 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 390 removed outlier: 7.090A pdb=" N ARG A 322 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ALA A 416 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS A 324 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN A 418 " --> pdb=" O HIS A 324 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 326 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N VAL A 420 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE A 447 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA A 579 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 390 removed outlier: 7.090A pdb=" N ARG A 322 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ALA A 416 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS A 324 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ASN A 418 " --> pdb=" O HIS A 324 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 326 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N VAL A 420 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE A 447 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TRP A 569 " --> pdb=" O PRO A 573 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 35 through 36 removed outlier: 3.787A pdb=" N THR B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 7 through 10 450 hydrogen bonds defined for protein. 1317 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: 1.34 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1448 1.32 - 1.44: 2094 1.44 - 1.57: 4655 1.57 - 1.69: 0 1.69 - 1.81: 59 Bond restraints: 8256 Sorted by residual: bond pdb=" C10 GA3 B 401 " pdb=" C9 GA3 B 401 " ideal model delta sigma weight residual 1.506 1.560 -0.054 2.00e-02 2.50e+03 7.36e+00 bond pdb=" C7 GA3 B 401 " pdb=" O71 GA3 B 401 " ideal model delta sigma weight residual 1.247 1.215 0.032 2.00e-02 2.50e+03 2.54e+00 bond pdb=" C7 GA3 B 401 " pdb=" O72 GA3 B 401 " ideal model delta sigma weight residual 1.248 1.217 0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C13 GA3 B 401 " pdb=" C14 GA3 B 401 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" CG PRO D 156 " pdb=" CD PRO D 156 " ideal model delta sigma weight residual 1.503 1.548 -0.045 3.40e-02 8.65e+02 1.71e+00 ... (remaining 8251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 10954 1.64 - 3.27: 189 3.27 - 4.91: 44 4.91 - 6.54: 5 6.54 - 8.18: 4 Bond angle restraints: 11196 Sorted by residual: angle pdb=" N TRP A 336 " pdb=" CA TRP A 336 " pdb=" C TRP A 336 " ideal model delta sigma weight residual 109.81 115.96 -6.15 2.21e+00 2.05e-01 7.74e+00 angle pdb=" CA PRO D 156 " pdb=" N PRO D 156 " pdb=" CD PRO D 156 " ideal model delta sigma weight residual 112.00 108.43 3.57 1.40e+00 5.10e-01 6.51e+00 angle pdb=" C10 GA3 B 401 " pdb=" C5 GA3 B 401 " pdb=" C6 GA3 B 401 " ideal model delta sigma weight residual 106.02 98.62 7.40 3.00e+00 1.11e-01 6.09e+00 angle pdb=" CB GLU C 42 " pdb=" CG GLU C 42 " pdb=" CD GLU C 42 " ideal model delta sigma weight residual 112.60 116.74 -4.14 1.70e+00 3.46e-01 5.93e+00 angle pdb=" C LYS D 139 " pdb=" N THR D 140 " pdb=" CA THR D 140 " ideal model delta sigma weight residual 121.80 127.60 -5.80 2.44e+00 1.68e-01 5.64e+00 ... (remaining 11191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4274 18.01 - 36.02: 530 36.02 - 54.04: 164 54.04 - 72.05: 32 72.05 - 90.06: 14 Dihedral angle restraints: 5014 sinusoidal: 2058 harmonic: 2956 Sorted by residual: dihedral pdb=" CA ARG A 271 " pdb=" C ARG A 271 " pdb=" N ARG A 272 " pdb=" CA ARG A 272 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CG ARG B 73 " pdb=" CD ARG B 73 " pdb=" NE ARG B 73 " pdb=" CZ ARG B 73 " ideal model delta sinusoidal sigma weight residual -90.00 -39.96 -50.04 2 1.50e+01 4.44e-03 1.25e+01 dihedral pdb=" CA THR D 155 " pdb=" C THR D 155 " pdb=" N PRO D 156 " pdb=" CA PRO D 156 " ideal model delta harmonic sigma weight residual 180.00 -162.31 -17.69 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 5011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1155 0.079 - 0.158: 90 0.158 - 0.237: 3 0.237 - 0.315: 0 0.315 - 0.394: 2 Chirality restraints: 1250 Sorted by residual: chirality pdb=" C5 GA3 B 401 " pdb=" C10 GA3 B 401 " pdb=" C4 GA3 B 401 " pdb=" C6 GA3 B 401 " both_signs ideal model delta sigma weight residual False -2.80 -3.19 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" C9 GA3 B 401 " pdb=" C10 GA3 B 401 " pdb=" C11 GA3 B 401 " pdb=" C8 GA3 B 401 " both_signs ideal model delta sigma weight residual False 2.24 2.56 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C4 GA3 B 401 " pdb=" C19 GA3 B 401 " pdb=" C3 GA3 B 401 " pdb=" C5 GA3 B 401 " both_signs ideal model delta sigma weight residual False 3.16 2.92 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 1247 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 155 " -0.072 5.00e-02 4.00e+02 1.07e-01 1.85e+01 pdb=" N PRO D 156 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 43 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.23e+00 pdb=" N PRO D 44 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 44 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 44 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 140 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO D 141 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 141 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 141 " 0.022 5.00e-02 4.00e+02 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 103 2.66 - 3.22: 7335 3.22 - 3.78: 12181 3.78 - 4.34: 17078 4.34 - 4.90: 28375 Nonbonded interactions: 65072 Sorted by model distance: nonbonded pdb=" O LEU A 470 " pdb=" OG SER A 474 " model vdw 2.104 3.040 nonbonded pdb=" OD1 ASP C 48 " pdb=" OG1 THR C 51 " model vdw 2.190 3.040 nonbonded pdb=" O LEU A 463 " pdb=" OG1 THR A 467 " model vdw 2.195 3.040 nonbonded pdb=" O PHE A 304 " pdb=" OG1 THR A 308 " model vdw 2.237 3.040 nonbonded pdb=" O CYS C 57 " pdb=" NH2 ARG D 145 " model vdw 2.247 3.120 ... (remaining 65067 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: 6.700 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.510 Find NCS groups from input model: 0.030 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 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 0.054 8256 Z= 0.149 Angle : 0.578 8.181 11196 Z= 0.294 Chirality : 0.044 0.394 1250 Planarity : 0.005 0.107 1440 Dihedral : 18.075 90.060 3100 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.73 % Allowed : 23.41 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: -0.14 (0.26), residues: 1004 helix: 0.45 (0.22), residues: 541 sheet: 0.02 (0.49), residues: 106 loop : -0.81 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 73 TYR 0.010 0.001 TYR A 495 PHE 0.012 0.001 PHE B 340 TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8256) covalent geometry : angle 0.57785 (11196) hydrogen bonds : bond 0.21237 ( 431) hydrogen bonds : angle 6.76002 ( 1317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.7001 (mtm) cc_final: 0.6752 (mtt) outliers start: 24 outliers final: 19 residues processed: 126 average time/residue: 0.4941 time to fit residues: 66.6678 Evaluate side-chains 121 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 29 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN A 395 ASN A 418 ASN A 487 GLN A 534 HIS A 551 ASN ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** 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 = 0.4050 r_free = 0.4050 target = 0.169424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143886 restraints weight = 10201.120| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.79 r_work: 0.3705 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8256 Z= 0.141 Angle : 0.573 6.945 11196 Z= 0.298 Chirality : 0.042 0.177 1250 Planarity : 0.005 0.056 1440 Dihedral : 6.441 42.067 1202 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.43 % Allowed : 20.80 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 0.23 (0.26), residues: 1004 helix: 0.84 (0.22), residues: 554 sheet: 0.15 (0.50), residues: 108 loop : -0.88 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 73 TYR 0.018 0.002 TYR A 495 PHE 0.012 0.001 PHE B 340 TRP 0.009 0.001 TRP B 21 HIS 0.004 0.001 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8256) covalent geometry : angle 0.57319 (11196) hydrogen bonds : bond 0.05080 ( 431) hydrogen bonds : angle 4.60017 ( 1317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 107 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6834 (mm-30) REVERT: B 36 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.6130 (mtp180) REVERT: C 102 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6703 (mpt-90) outliers start: 39 outliers final: 15 residues processed: 132 average time/residue: 0.5064 time to fit residues: 71.4116 Evaluate side-chains 120 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 294 HIS A 335 GLN A 424 HIS A 542 GLN B 214 ASN ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** 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 = 0.4014 r_free = 0.4014 target = 0.166107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140697 restraints weight = 10139.671| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.77 r_work: 0.3678 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8256 Z= 0.222 Angle : 0.654 8.086 11196 Z= 0.338 Chirality : 0.046 0.175 1250 Planarity : 0.005 0.048 1440 Dihedral : 6.236 40.162 1187 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.89 % Allowed : 21.14 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: -0.11 (0.26), residues: 1004 helix: 0.50 (0.21), residues: 556 sheet: 0.29 (0.49), residues: 114 loop : -1.03 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 73 TYR 0.016 0.002 TYR A 495 PHE 0.016 0.002 PHE B 340 TRP 0.015 0.002 TRP B 21 HIS 0.007 0.001 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 8256) covalent geometry : angle 0.65426 (11196) hydrogen bonds : bond 0.05879 ( 431) hydrogen bonds : angle 4.67772 ( 1317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 103 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.7069 (mtm) cc_final: 0.6744 (mtt) REVERT: A 406 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6928 (mm-30) REVERT: B 36 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6361 (mtp180) REVERT: C 102 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6761 (mpt-90) REVERT: D 102 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.6984 (mp) outliers start: 43 outliers final: 18 residues processed: 135 average time/residue: 0.5146 time to fit residues: 74.1969 Evaluate side-chains 118 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN C 63 HIS C 67 GLN D 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.169096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.143647 restraints weight = 10316.361| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.80 r_work: 0.3714 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8256 Z= 0.124 Angle : 0.540 7.235 11196 Z= 0.281 Chirality : 0.041 0.164 1250 Planarity : 0.004 0.045 1440 Dihedral : 5.705 41.962 1187 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.41 % Allowed : 23.52 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 0.35 (0.26), residues: 1004 helix: 0.92 (0.22), residues: 559 sheet: 0.47 (0.50), residues: 106 loop : -0.92 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 73 TYR 0.016 0.002 TYR A 495 PHE 0.011 0.001 PHE B 340 TRP 0.010 0.001 TRP B 21 HIS 0.004 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8256) covalent geometry : angle 0.54045 (11196) hydrogen bonds : bond 0.04361 ( 431) hydrogen bonds : angle 4.30915 ( 1317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 211 LEU cc_start: 0.7800 (mp) cc_final: 0.7370 (mp) REVERT: A 271 ARG cc_start: 0.7569 (ptm160) cc_final: 0.6745 (ptp-170) REVERT: A 406 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6859 (mm-30) REVERT: A 491 MET cc_start: 0.7808 (mmm) cc_final: 0.7532 (mmp) REVERT: A 513 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8292 (mm-30) REVERT: B 36 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.6311 (mtp180) REVERT: C 102 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6698 (mpt-90) REVERT: D 102 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.6957 (mp) outliers start: 30 outliers final: 15 residues processed: 127 average time/residue: 0.5466 time to fit residues: 73.9881 Evaluate side-chains 121 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 8.9990 chunk 73 optimal weight: 0.0170 chunk 94 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 0.0070 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 0.0980 chunk 46 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 overall best weight: 0.2836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN B 214 ASN D 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.172495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.147203 restraints weight = 10234.020| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.80 r_work: 0.3754 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8256 Z= 0.096 Angle : 0.478 6.271 11196 Z= 0.250 Chirality : 0.039 0.135 1250 Planarity : 0.004 0.042 1440 Dihedral : 4.817 42.651 1182 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.07 % Allowed : 23.52 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 0.84 (0.27), residues: 1004 helix: 1.37 (0.22), residues: 559 sheet: 0.54 (0.50), residues: 108 loop : -0.74 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 73 TYR 0.013 0.001 TYR A 495 PHE 0.011 0.001 PHE A 304 TRP 0.009 0.001 TRP C 72 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 8256) covalent geometry : angle 0.47848 (11196) hydrogen bonds : bond 0.03501 ( 431) hydrogen bonds : angle 4.03851 ( 1317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LEU cc_start: 0.7596 (mp) cc_final: 0.7050 (mp) REVERT: A 271 ARG cc_start: 0.7402 (ptm160) cc_final: 0.6569 (ptp-170) REVERT: A 365 ASN cc_start: 0.2733 (OUTLIER) cc_final: 0.2317 (m-40) REVERT: A 406 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6836 (mm-30) REVERT: A 491 MET cc_start: 0.7740 (mmm) cc_final: 0.7463 (mmp) REVERT: B 36 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.6207 (mtp180) REVERT: B 73 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7610 (mpp-170) REVERT: B 95 LEU cc_start: 0.5581 (OUTLIER) cc_final: 0.4638 (tt) REVERT: D 102 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.6886 (mp) REVERT: D 143 GLU cc_start: 0.6795 (mp0) cc_final: 0.6445 (mm-30) outliers start: 27 outliers final: 9 residues processed: 128 average time/residue: 0.6021 time to fit residues: 81.6985 Evaluate side-chains 115 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 332 ASN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.170478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145110 restraints weight = 10143.105| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.79 r_work: 0.3729 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8256 Z= 0.123 Angle : 0.522 6.537 11196 Z= 0.270 Chirality : 0.041 0.186 1250 Planarity : 0.004 0.040 1440 Dihedral : 4.727 41.484 1178 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.30 % Allowed : 23.64 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 0.79 (0.27), residues: 1004 helix: 1.31 (0.22), residues: 559 sheet: 0.56 (0.49), residues: 108 loop : -0.75 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 73 TYR 0.012 0.001 TYR A 495 PHE 0.012 0.001 PHE B 340 TRP 0.008 0.001 TRP B 21 HIS 0.003 0.001 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8256) covalent geometry : angle 0.52233 (11196) hydrogen bonds : bond 0.04025 ( 431) hydrogen bonds : angle 4.08554 ( 1317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 211 LEU cc_start: 0.7654 (mp) cc_final: 0.7061 (mp) REVERT: A 258 MET cc_start: 0.6119 (OUTLIER) cc_final: 0.5707 (mmm) REVERT: A 271 ARG cc_start: 0.7336 (ptm160) cc_final: 0.6510 (ptp-170) REVERT: A 365 ASN cc_start: 0.2877 (OUTLIER) cc_final: 0.2455 (m-40) REVERT: A 406 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6786 (mm-30) REVERT: A 491 MET cc_start: 0.7742 (mmm) cc_final: 0.7459 (mmp) REVERT: A 513 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: B 36 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6340 (mtp180) REVERT: B 73 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.7629 (mpp-170) REVERT: D 102 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.6958 (mp) REVERT: D 143 GLU cc_start: 0.6841 (mp0) cc_final: 0.6504 (mm-30) outliers start: 29 outliers final: 13 residues processed: 121 average time/residue: 0.5371 time to fit residues: 69.3983 Evaluate side-chains 117 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 0.0770 chunk 78 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 ASN ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.171150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.145674 restraints weight = 10224.503| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.80 r_work: 0.3734 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8256 Z= 0.107 Angle : 0.495 6.185 11196 Z= 0.257 Chirality : 0.040 0.137 1250 Planarity : 0.004 0.042 1440 Dihedral : 4.389 18.503 1176 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.64 % Allowed : 23.64 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 0.92 (0.27), residues: 1004 helix: 1.42 (0.22), residues: 559 sheet: 0.59 (0.49), residues: 108 loop : -0.70 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 73 TYR 0.013 0.001 TYR A 495 PHE 0.010 0.001 PHE B 340 TRP 0.008 0.001 TRP A 336 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8256) covalent geometry : angle 0.49452 (11196) hydrogen bonds : bond 0.03759 ( 431) hydrogen bonds : angle 4.02308 ( 1317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6880 (mtm) cc_final: 0.6638 (mtt) REVERT: A 211 LEU cc_start: 0.7748 (mp) cc_final: 0.7233 (mp) REVERT: A 258 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5715 (mmm) REVERT: A 271 ARG cc_start: 0.7299 (ptm160) cc_final: 0.6537 (ptp-170) REVERT: A 365 ASN cc_start: 0.2797 (OUTLIER) cc_final: 0.2372 (m-40) REVERT: A 406 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6865 (mm-30) REVERT: A 491 MET cc_start: 0.7763 (mmm) cc_final: 0.7488 (mmp) REVERT: A 513 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: B 36 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6290 (mtp180) REVERT: B 73 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7495 (mpp-170) REVERT: B 95 LEU cc_start: 0.5600 (OUTLIER) cc_final: 0.4613 (tt) REVERT: D 102 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.6961 (mp) REVERT: D 143 GLU cc_start: 0.6822 (mp0) cc_final: 0.6495 (mm-30) outliers start: 32 outliers final: 14 residues processed: 126 average time/residue: 0.5504 time to fit residues: 74.1519 Evaluate side-chains 121 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 48 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 ASN B 332 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.170364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.144965 restraints weight = 10204.176| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.78 r_work: 0.3724 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8256 Z= 0.122 Angle : 0.514 6.236 11196 Z= 0.267 Chirality : 0.041 0.127 1250 Planarity : 0.004 0.041 1440 Dihedral : 4.432 18.659 1176 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.09 % Allowed : 23.18 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 0.85 (0.27), residues: 1004 helix: 1.37 (0.22), residues: 556 sheet: 0.58 (0.49), residues: 108 loop : -0.74 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 73 TYR 0.013 0.001 TYR A 495 PHE 0.012 0.001 PHE B 340 TRP 0.008 0.001 TRP B 21 HIS 0.003 0.001 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8256) covalent geometry : angle 0.51379 (11196) hydrogen bonds : bond 0.03982 ( 431) hydrogen bonds : angle 4.07536 ( 1317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6917 (mtm) cc_final: 0.6682 (mtt) REVERT: A 211 LEU cc_start: 0.7702 (mp) cc_final: 0.7162 (mp) REVERT: A 271 ARG cc_start: 0.7305 (ptm160) cc_final: 0.6535 (ptp-170) REVERT: A 365 ASN cc_start: 0.2885 (OUTLIER) cc_final: 0.2435 (m-40) REVERT: A 406 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6882 (mm-30) REVERT: A 453 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7030 (mt0) REVERT: A 491 MET cc_start: 0.7775 (mmm) cc_final: 0.7497 (mmp) REVERT: A 513 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8063 (mm-30) REVERT: B 36 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6329 (mtp180) REVERT: B 73 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7493 (mpp-170) REVERT: C 74 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5856 (mp) REVERT: D 102 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.6976 (mp) REVERT: D 143 GLU cc_start: 0.6861 (mp0) cc_final: 0.6522 (mm-30) outliers start: 36 outliers final: 23 residues processed: 125 average time/residue: 0.5787 time to fit residues: 77.0444 Evaluate side-chains 129 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN B 214 ASN B 332 ASN C 89 GLN 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 = 0.170671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.145185 restraints weight = 10172.449| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.79 r_work: 0.3727 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8256 Z= 0.112 Angle : 0.501 6.106 11196 Z= 0.261 Chirality : 0.040 0.127 1250 Planarity : 0.004 0.042 1440 Dihedral : 4.388 18.482 1176 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.30 % Allowed : 23.86 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 0.91 (0.27), residues: 1004 helix: 1.42 (0.22), residues: 559 sheet: 0.59 (0.49), residues: 108 loop : -0.72 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 73 TYR 0.013 0.001 TYR A 495 PHE 0.011 0.001 PHE B 340 TRP 0.008 0.001 TRP A 336 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8256) covalent geometry : angle 0.50062 (11196) hydrogen bonds : bond 0.03869 ( 431) hydrogen bonds : angle 4.04026 ( 1317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6894 (mtm) cc_final: 0.6661 (mtt) REVERT: A 211 LEU cc_start: 0.7716 (mp) cc_final: 0.7194 (mp) REVERT: A 271 ARG cc_start: 0.7268 (ptm160) cc_final: 0.6520 (ptp-170) REVERT: A 365 ASN cc_start: 0.2774 (OUTLIER) cc_final: 0.2342 (m-40) REVERT: A 406 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6884 (mm-30) REVERT: A 491 MET cc_start: 0.7754 (mmm) cc_final: 0.7478 (mmp) REVERT: A 513 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: B 36 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.6366 (mtp180) REVERT: B 73 ARG cc_start: 0.7815 (mtm-85) cc_final: 0.7499 (mpp-170) REVERT: B 214 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7772 (m-40) REVERT: C 74 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5923 (mp) REVERT: D 102 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.6944 (mp) REVERT: D 143 GLU cc_start: 0.6829 (mp0) cc_final: 0.6477 (mm-30) outliers start: 29 outliers final: 21 residues processed: 120 average time/residue: 0.5698 time to fit residues: 72.7137 Evaluate side-chains 126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 52 optimal weight: 0.0470 chunk 76 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN B 214 ASN B 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.171086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.145637 restraints weight = 10160.953| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.79 r_work: 0.3732 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8256 Z= 0.112 Angle : 0.505 6.046 11196 Z= 0.263 Chirality : 0.040 0.127 1250 Planarity : 0.004 0.042 1440 Dihedral : 4.380 18.275 1176 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.18 % Allowed : 24.09 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 0.91 (0.27), residues: 1004 helix: 1.43 (0.22), residues: 559 sheet: 0.58 (0.49), residues: 108 loop : -0.74 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 73 TYR 0.013 0.001 TYR A 495 PHE 0.011 0.001 PHE B 340 TRP 0.008 0.001 TRP B 21 HIS 0.003 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8256) covalent geometry : angle 0.50462 (11196) hydrogen bonds : bond 0.03844 ( 431) hydrogen bonds : angle 4.02873 ( 1317) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 MET cc_start: 0.6843 (mtm) cc_final: 0.6627 (mtt) REVERT: A 211 LEU cc_start: 0.7717 (mp) cc_final: 0.7196 (mp) REVERT: A 271 ARG cc_start: 0.7252 (ptm160) cc_final: 0.6505 (ptp-170) REVERT: A 365 ASN cc_start: 0.2791 (OUTLIER) cc_final: 0.2353 (m-40) REVERT: A 406 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6887 (mm-30) REVERT: A 453 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.7021 (mt0) REVERT: A 491 MET cc_start: 0.7749 (mmm) cc_final: 0.7475 (mmp) REVERT: A 513 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8060 (mm-30) REVERT: B 36 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6390 (mtp180) REVERT: B 73 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7518 (mpp-170) REVERT: C 74 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5911 (mp) REVERT: D 102 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.6937 (mp) REVERT: D 143 GLU cc_start: 0.6843 (mp0) cc_final: 0.6492 (mm-30) outliers start: 28 outliers final: 21 residues processed: 117 average time/residue: 0.5820 time to fit residues: 72.3883 Evaluate side-chains 126 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 258 MET Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 513 GLU Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 214 ASN Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 81 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN B 214 ASN B 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.169563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144000 restraints weight = 10231.906| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.80 r_work: 0.3710 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8256 Z= 0.145 Angle : 0.538 6.367 11196 Z= 0.280 Chirality : 0.042 0.128 1250 Planarity : 0.004 0.040 1440 Dihedral : 4.546 18.637 1176 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.41 % Allowed : 24.09 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 aren not related in a simple way. whole: 0.71 (0.27), residues: 1004 helix: 1.26 (0.22), residues: 556 sheet: 0.69 (0.50), residues: 106 loop : -0.86 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 73 TYR 0.014 0.002 TYR A 495 PHE 0.014 0.001 PHE B 340 TRP 0.009 0.001 TRP B 21 HIS 0.004 0.001 HIS C 79 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8256) covalent geometry : angle 0.53800 (11196) hydrogen bonds : bond 0.04336 ( 431) hydrogen bonds : angle 4.13439 ( 1317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2932.78 seconds wall clock time: 50 minutes 44.17 seconds (3044.17 seconds total)