Starting phenix.real_space_refine on Sat Dec 28 01:33:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fex_29033/12_2024/8fex_29033_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fex_29033/12_2024/8fex_29033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fex_29033/12_2024/8fex_29033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fex_29033/12_2024/8fex_29033.map" model { file = "/net/cci-nas-00/data/ceres_data/8fex_29033/12_2024/8fex_29033_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fex_29033/12_2024/8fex_29033_neut.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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 22 5.16 5 C 4730 2.51 5 N 1208 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7302 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3604 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 420} Chain: "B" Number of atoms: 3698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3698 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 434} Chain breaks: 1 Time building chain proxies: 5.88, per 1000 atoms: 0.81 Number of scatterers: 7302 At special positions: 0 Unit cell: (75.3927, 84.4826, 129.932, 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 22 16.00 O 1342 8.00 N 1208 7.00 C 4730 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: 1.92 Conformation dependent library (CDL) restraints added in 1.0 seconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 8 sheets defined 38.7% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 14 through 29 Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.960A pdb=" N ASN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.540A pdb=" N ASN A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 Processing helix chain 'A' and resid 123 through 138 Processing helix chain 'A' and resid 146 through 159 removed outlier: 4.381A pdb=" N SER A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.749A pdb=" N LYS A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 308 removed outlier: 3.565A pdb=" N ASP A 303 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 304 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N PHE A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N GLU A 306 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 368 removed outlier: 3.628A pdb=" N ASN A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 385 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.738A pdb=" N ALA A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 46 through 62 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 109 through 132 removed outlier: 3.736A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 248 through 264 removed outlier: 3.546A pdb=" N ALA B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 351 Processing helix chain 'B' and resid 366 through 374 removed outlier: 3.601A pdb=" N TRP B 370 " --> pdb=" O ASN B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 477 through 482 removed outlier: 4.195A pdb=" N PHE B 482 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 493 Processing helix chain 'B' and resid 504 through 506 No H-bonds generated for 'chain 'B' and resid 504 through 506' Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 3.691A pdb=" N TRP A 33 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS A 4 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU A 61 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE A 6 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL A 63 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER A 8 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N ILE A 95 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE A 60 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU A 97 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 62 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 180 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 170 through 180 current: chain 'A' and resid 291 through 294 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 291 through 294 current: chain 'A' and resid 317 through 328 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 334 through 337 current: chain 'A' and resid 400 through 411 removed outlier: 9.761A pdb=" N LYS B 2 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LYS A 409 " --> pdb=" O LYS B 2 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 214 through 216 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 6 removed outlier: 6.467A pdb=" N SER B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ILE B 443 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N SER B 389 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE B 445 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR B 387 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 357 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL B 386 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 359 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ILE B 388 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA B 361 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B 281 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 501 " --> pdb=" O VAL B 312 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 18 through 20 Processing sheet with id=AA6, first strand: chain 'B' and resid 94 through 95 removed outlier: 5.999A pdb=" N TRP B 139 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N PHE B 224 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL B 141 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 285 through 287 Processing sheet with id=AA8, first strand: chain 'B' and resid 425 through 426 removed outlier: 3.795A pdb=" N THR B 431 " --> pdb=" O VAL B 426 " (cutoff:3.500A) 255 hydrogen bonds defined for protein. 702 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: 2.42 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2293 1.34 - 1.46: 1639 1.46 - 1.58: 3520 1.58 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 7485 Sorted by residual: bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" CB VAL A 334 " pdb=" CG1 VAL A 334 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.88e-01 bond pdb=" C GLY A 412 " pdb=" N ASN A 413 " ideal model delta sigma weight residual 1.332 1.321 0.012 1.40e-02 5.10e+03 6.80e-01 bond pdb=" CA PHE B 14 " pdb=" C PHE B 14 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.34e-02 5.57e+03 4.15e-01 bond pdb=" N PRO A 333 " pdb=" CA PRO A 333 " ideal model delta sigma weight residual 1.468 1.475 -0.007 1.20e-02 6.94e+03 3.84e-01 ... (remaining 7480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 9551 0.88 - 1.76: 464 1.76 - 2.64: 65 2.64 - 3.52: 21 3.52 - 4.40: 12 Bond angle restraints: 10113 Sorted by residual: angle pdb=" N ASN B 446 " pdb=" CA ASN B 446 " pdb=" CB ASN B 446 " ideal model delta sigma weight residual 110.07 112.31 -2.24 1.45e+00 4.76e-01 2.38e+00 angle pdb=" N ARG B 24 " pdb=" CA ARG B 24 " pdb=" CB ARG B 24 " ideal model delta sigma weight residual 110.91 108.52 2.39 1.58e+00 4.01e-01 2.28e+00 angle pdb=" C GLN B 205 " pdb=" N PHE B 206 " pdb=" CA PHE B 206 " ideal model delta sigma weight residual 120.82 123.01 -2.19 1.50e+00 4.44e-01 2.13e+00 angle pdb=" C ALA B 212 " pdb=" N ARG B 213 " pdb=" CA ARG B 213 " ideal model delta sigma weight residual 122.27 119.63 2.64 1.85e+00 2.92e-01 2.03e+00 angle pdb=" N THR A 389 " pdb=" CA THR A 389 " pdb=" C THR A 389 " ideal model delta sigma weight residual 110.80 113.77 -2.97 2.13e+00 2.20e-01 1.95e+00 ... (remaining 10108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 4028 17.17 - 34.35: 375 34.35 - 51.52: 60 51.52 - 68.69: 12 68.69 - 85.87: 5 Dihedral angle restraints: 4480 sinusoidal: 1856 harmonic: 2624 Sorted by residual: dihedral pdb=" CA LEU B 36 " pdb=" C LEU B 36 " pdb=" N TYR B 37 " pdb=" CA TYR B 37 " ideal model delta harmonic sigma weight residual -180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PHE B 304 " pdb=" C PHE B 304 " pdb=" N LEU B 305 " pdb=" CA LEU B 305 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA LYS B 392 " pdb=" C LYS B 392 " pdb=" N PRO B 393 " pdb=" CA PRO B 393 " ideal model delta harmonic sigma weight residual -180.00 -163.28 -16.72 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 4477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 665 0.027 - 0.055: 271 0.055 - 0.082: 72 0.082 - 0.110: 52 0.110 - 0.137: 26 Chirality restraints: 1086 Sorted by residual: chirality pdb=" CA ILE A 418 " pdb=" N ILE A 418 " pdb=" C ILE A 418 " pdb=" CB ILE A 418 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE A 5 " pdb=" N ILE A 5 " pdb=" C ILE A 5 " pdb=" CB ILE A 5 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CA VAL A 140 " pdb=" N VAL A 140 " pdb=" C VAL A 140 " pdb=" CB VAL A 140 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1083 not shown) Planarity restraints: 1279 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 11 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO A 12 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 12 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 12 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 332 " 0.009 2.00e-02 2.50e+03 1.23e-02 2.67e+00 pdb=" CG PHE A 332 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 332 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 332 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 332 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 332 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 332 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 418 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 419 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 419 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 419 " 0.020 5.00e-02 4.00e+02 ... (remaining 1276 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 50 2.51 - 3.11: 5542 3.11 - 3.70: 10926 3.70 - 4.30: 16234 4.30 - 4.90: 27214 Nonbonded interactions: 59966 Sorted by model distance: nonbonded pdb=" OH TYR A 154 " pdb=" OD2 ASP B 25 " model vdw 1.911 3.040 nonbonded pdb=" O TRP B 269 " pdb=" OH TYR B 467 " model vdw 2.183 3.040 nonbonded pdb=" O PHE B 365 " pdb=" NZ LYS B 447 " model vdw 2.201 3.120 nonbonded pdb=" OD1 ASN A 270 " pdb=" OG SER A 327 " model vdw 2.206 3.040 nonbonded pdb=" OD2 ASP B 22 " pdb=" NZ LYS B 428 " model vdw 2.230 3.120 ... (remaining 59961 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: 6.160 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.530 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 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 0.032 7485 Z= 0.166 Angle : 0.459 4.396 10113 Z= 0.243 Chirality : 0.040 0.137 1086 Planarity : 0.003 0.042 1279 Dihedral : 13.443 85.868 2784 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.28), residues: 885 helix: 0.94 (0.32), residues: 300 sheet: -0.92 (0.43), residues: 158 loop : -1.65 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 269 HIS 0.005 0.001 HIS B 207 PHE 0.026 0.001 PHE A 332 TYR 0.010 0.001 TYR B 115 ARG 0.003 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2690 time to fit residues: 37.2554 Evaluate side-chains 89 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 68 optimal weight: 0.0870 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 0.0970 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 322 ASN B 349 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7485 Z= 0.173 Angle : 0.501 6.997 10113 Z= 0.265 Chirality : 0.041 0.142 1086 Planarity : 0.004 0.032 1279 Dihedral : 4.163 18.478 962 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.88 % Allowed : 6.90 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.55 (0.28), residues: 885 helix: 1.35 (0.31), residues: 304 sheet: -1.15 (0.42), residues: 161 loop : -1.32 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 370 HIS 0.006 0.001 HIS B 207 PHE 0.020 0.002 PHE A 332 TYR 0.008 0.001 TYR B 115 ARG 0.006 0.001 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.895 Fit side-chains revert: symmetry clash REVERT: A 313 LYS cc_start: 0.7520 (ptpt) cc_final: 0.7186 (tttt) outliers start: 7 outliers final: 7 residues processed: 104 average time/residue: 0.2455 time to fit residues: 33.6999 Evaluate side-chains 98 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 380 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN B 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7485 Z= 0.231 Angle : 0.511 6.876 10113 Z= 0.269 Chirality : 0.042 0.137 1086 Planarity : 0.004 0.035 1279 Dihedral : 4.232 18.035 962 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.63 % Allowed : 10.04 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.65 (0.28), residues: 885 helix: 1.21 (0.31), residues: 304 sheet: -1.12 (0.43), residues: 161 loop : -1.37 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 370 HIS 0.007 0.001 HIS B 207 PHE 0.021 0.002 PHE A 342 TYR 0.007 0.001 TYR A 293 ARG 0.008 0.001 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.872 Fit side-chains REVERT: A 313 LYS cc_start: 0.7545 (ptpt) cc_final: 0.7219 (tttt) outliers start: 13 outliers final: 10 residues processed: 98 average time/residue: 0.2557 time to fit residues: 32.4833 Evaluate side-chains 102 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 380 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.0060 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 53 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 0.0980 chunk 76 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7485 Z= 0.148 Angle : 0.462 6.104 10113 Z= 0.244 Chirality : 0.040 0.142 1086 Planarity : 0.003 0.038 1279 Dihedral : 4.060 18.095 962 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.31 % Favored : 94.58 % Rotamer: Outliers : 1.63 % Allowed : 12.30 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.53 (0.28), residues: 885 helix: 1.35 (0.31), residues: 309 sheet: -1.16 (0.42), residues: 161 loop : -1.32 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 320 HIS 0.006 0.001 HIS B 207 PHE 0.021 0.001 PHE A 342 TYR 0.009 0.001 TYR A 293 ARG 0.007 0.001 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6853 (t80) cc_final: 0.6625 (t80) REVERT: A 328 LYS cc_start: 0.7809 (tttt) cc_final: 0.7401 (ttpt) REVERT: B 39 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7813 (mt) outliers start: 13 outliers final: 8 residues processed: 102 average time/residue: 0.2210 time to fit residues: 30.1937 Evaluate side-chains 93 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 380 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7485 Z= 0.321 Angle : 0.577 8.105 10113 Z= 0.300 Chirality : 0.044 0.189 1086 Planarity : 0.004 0.043 1279 Dihedral : 4.461 17.560 962 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.14 % Allowed : 11.79 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.27), residues: 885 helix: 0.83 (0.30), residues: 310 sheet: -1.24 (0.42), residues: 157 loop : -1.56 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 320 HIS 0.009 0.001 HIS B 207 PHE 0.023 0.002 PHE A 342 TYR 0.010 0.001 TYR B 505 ARG 0.008 0.001 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 189 GLU cc_start: 0.7090 (tp30) cc_final: 0.6814 (tp30) REVERT: B 39 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8152 (mt) REVERT: B 134 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5648 (pm20) REVERT: B 503 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6993 (m-80) outliers start: 25 outliers final: 16 residues processed: 103 average time/residue: 0.2456 time to fit residues: 32.8342 Evaluate side-chains 103 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 387 ASP Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 503 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 49 optimal weight: 0.2980 chunk 20 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 70 optimal weight: 0.0570 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7485 Z= 0.160 Angle : 0.487 8.999 10113 Z= 0.254 Chirality : 0.040 0.135 1086 Planarity : 0.004 0.037 1279 Dihedral : 4.178 18.074 962 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.38 % Allowed : 13.80 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.72 (0.28), residues: 885 helix: 1.24 (0.31), residues: 309 sheet: -1.40 (0.40), residues: 169 loop : -1.40 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 PHE 0.016 0.001 PHE A 342 TYR 0.006 0.001 TYR A 293 ARG 0.008 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.880 Fit side-chains REVERT: A 189 GLU cc_start: 0.7099 (tp30) cc_final: 0.6819 (tp30) REVERT: B 39 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7942 (mt) REVERT: B 134 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5644 (pm20) REVERT: B 285 TYR cc_start: 0.6612 (t80) cc_final: 0.5272 (t80) REVERT: B 503 PHE cc_start: 0.7332 (OUTLIER) cc_final: 0.6892 (m-80) outliers start: 19 outliers final: 10 residues processed: 101 average time/residue: 0.2168 time to fit residues: 29.4168 Evaluate side-chains 99 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 503 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.0040 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7485 Z= 0.181 Angle : 0.482 7.859 10113 Z= 0.252 Chirality : 0.040 0.133 1086 Planarity : 0.004 0.039 1279 Dihedral : 4.121 17.471 962 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.26 % Allowed : 14.55 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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 (0.28), residues: 885 helix: 1.23 (0.31), residues: 310 sheet: -1.38 (0.39), residues: 169 loop : -1.34 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 PHE 0.016 0.001 PHE A 342 TYR 0.007 0.001 TYR A 154 ARG 0.009 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.728 Fit side-chains REVERT: A 285 TYR cc_start: 0.6820 (t80) cc_final: 0.6592 (t80) REVERT: B 39 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7942 (mt) REVERT: B 134 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5637 (pm20) REVERT: B 285 TYR cc_start: 0.6650 (t80) cc_final: 0.5339 (t80) REVERT: B 503 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6925 (m-80) outliers start: 18 outliers final: 13 residues processed: 95 average time/residue: 0.2109 time to fit residues: 26.9979 Evaluate side-chains 98 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 503 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.0170 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7485 Z= 0.190 Angle : 0.486 8.004 10113 Z= 0.254 Chirality : 0.041 0.134 1086 Planarity : 0.004 0.033 1279 Dihedral : 4.146 17.992 962 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.38 % Allowed : 15.06 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.68 (0.28), residues: 885 helix: 1.22 (0.31), residues: 310 sheet: -1.42 (0.39), residues: 169 loop : -1.32 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 PHE 0.016 0.001 PHE A 342 TYR 0.007 0.001 TYR A 154 ARG 0.006 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.871 Fit side-chains REVERT: A 189 GLU cc_start: 0.7057 (tp30) cc_final: 0.6835 (tp30) REVERT: B 39 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7964 (mt) REVERT: B 134 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5625 (pm20) REVERT: B 285 TYR cc_start: 0.6689 (t80) cc_final: 0.5347 (t80) REVERT: B 503 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.6948 (m-80) outliers start: 19 outliers final: 13 residues processed: 98 average time/residue: 0.2346 time to fit residues: 30.9495 Evaluate side-chains 102 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 503 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 74 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN B 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7485 Z= 0.188 Angle : 0.501 11.249 10113 Z= 0.258 Chirality : 0.041 0.133 1086 Planarity : 0.004 0.032 1279 Dihedral : 4.122 17.537 962 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.13 % Allowed : 15.68 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.69 (0.28), residues: 885 helix: 1.24 (0.31), residues: 310 sheet: -1.50 (0.39), residues: 171 loop : -1.30 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 PHE 0.014 0.001 PHE A 342 TYR 0.007 0.001 TYR A 154 ARG 0.006 0.000 ARG A 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.935 Fit side-chains REVERT: A 395 MET cc_start: 0.5417 (mmm) cc_final: 0.4544 (mmm) REVERT: B 39 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7928 (mt) REVERT: B 134 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5636 (pm20) REVERT: B 285 TYR cc_start: 0.6705 (t80) cc_final: 0.5374 (t80) REVERT: B 503 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.6965 (m-80) outliers start: 17 outliers final: 12 residues processed: 99 average time/residue: 0.2259 time to fit residues: 30.0290 Evaluate side-chains 102 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 503 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 80 optimal weight: 0.0050 chunk 69 optimal weight: 0.0870 chunk 7 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7485 Z= 0.153 Angle : 0.482 10.551 10113 Z= 0.250 Chirality : 0.040 0.134 1086 Planarity : 0.003 0.031 1279 Dihedral : 4.034 17.824 962 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.01 % Allowed : 16.06 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.60 (0.28), residues: 885 helix: 1.33 (0.31), residues: 310 sheet: -1.45 (0.40), residues: 160 loop : -1.28 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 320 HIS 0.005 0.001 HIS B 207 PHE 0.013 0.001 PHE A 342 TYR 0.008 0.001 TYR A 213 ARG 0.006 0.000 ARG A 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.902 Fit side-chains REVERT: A 328 LYS cc_start: 0.7844 (tttt) cc_final: 0.7379 (ttpt) REVERT: A 395 MET cc_start: 0.5370 (mmm) cc_final: 0.4507 (mmm) REVERT: B 39 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7823 (mt) REVERT: B 134 GLU cc_start: 0.6000 (OUTLIER) cc_final: 0.5616 (pm20) REVERT: B 211 LYS cc_start: 0.7637 (tppp) cc_final: 0.7416 (tptp) REVERT: B 285 TYR cc_start: 0.6688 (t80) cc_final: 0.5379 (t80) REVERT: B 503 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6883 (m-80) outliers start: 16 outliers final: 11 residues processed: 97 average time/residue: 0.2216 time to fit residues: 29.1091 Evaluate side-chains 100 residues out of total 797 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 503 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 349 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.207239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.170593 restraints weight = 7809.287| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.12 r_work: 0.3905 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7485 Z= 0.157 Angle : 0.486 10.170 10113 Z= 0.251 Chirality : 0.040 0.132 1086 Planarity : 0.003 0.031 1279 Dihedral : 4.002 17.248 962 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.65 % Favored : 94.24 % Rotamer: Outliers : 2.26 % Allowed : 16.06 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -0.51 (0.28), residues: 885 helix: 1.40 (0.31), residues: 309 sheet: -1.37 (0.40), residues: 169 loop : -1.22 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 320 HIS 0.006 0.001 HIS B 207 PHE 0.013 0.001 PHE B 503 TYR 0.007 0.001 TYR A 154 ARG 0.006 0.000 ARG A 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2017.50 seconds wall clock time: 39 minutes 57.04 seconds (2397.04 seconds total)