Starting phenix.real_space_refine on Mon Mar 11 06:09:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fex_29033/03_2024/8fex_29033_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fex_29033/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fex_29033/03_2024/8fex_29033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fex_29033/03_2024/8fex_29033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fex_29033/03_2024/8fex_29033_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fex_29033/03_2024/8fex_29033_neut.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.28, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.3 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: 0.83 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: 2.10 Time building geometry restraints manager: 2.96 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: 99.49 - 106.40: 178 106.40 - 113.32: 4024 113.32 - 120.23: 2650 120.23 - 127.15: 3166 127.15 - 134.06: 95 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 2.440 nonbonded pdb=" O TRP B 269 " pdb=" OH TYR B 467 " model vdw 2.183 2.440 nonbonded pdb=" O PHE B 365 " pdb=" NZ LYS B 447 " model vdw 2.201 2.520 nonbonded pdb=" OD1 ASN A 270 " pdb=" OG SER A 327 " model vdw 2.206 2.440 nonbonded pdb=" OD2 ASP B 22 " pdb=" NZ LYS B 428 " model vdw 2.230 2.520 ... (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 ========== 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: 0.010 Normalize map: mean=0, sd=1: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 17.520 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 23.230 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.490 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2641 time to fit residues: 36.2119 Evaluate side-chains 89 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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: 2.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 68 optimal weight: 0.0020 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 ASN B 349 GLN B 446 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1028 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= 0.226 Angle : 0.520 7.728 10113 Z= 0.273 Chirality : 0.041 0.161 1086 Planarity : 0.004 0.033 1279 Dihedral : 4.229 18.529 962 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.51 % Allowed : 6.78 % Favored : 91.72 % 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: 1.16 (0.31), residues: 304 sheet: -1.02 (0.43), residues: 149 loop : -1.50 (0.28), residues: 432 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 0.021 0.002 PHE A 332 TYR 0.007 0.001 TYR A 154 ARG 0.007 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 107 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 387 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6811 (p0) outliers start: 12 outliers final: 11 residues processed: 101 average time/residue: 0.2349 time to fit residues: 31.1178 Evaluate side-chains 99 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 184 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 327 SER 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 96 VAL Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 474 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 80 optimal weight: 0.0060 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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: 0.7106 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7485 Z= 0.192 Angle : 0.483 6.881 10113 Z= 0.254 Chirality : 0.040 0.137 1086 Planarity : 0.004 0.036 1279 Dihedral : 4.159 18.163 962 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.76 % Allowed : 9.54 % Favored : 88.71 % 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: -0.57 (0.28), residues: 885 helix: 1.34 (0.31), residues: 304 sheet: -1.01 (0.43), residues: 149 loop : -1.42 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 370 HIS 0.006 0.001 HIS B 207 PHE 0.020 0.002 PHE A 158 TYR 0.009 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 100 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.851 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 92 average time/residue: 0.2447 time to fit residues: 29.4793 Evaluate side-chains 94 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 A residue 327 SER 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 380 GLU Chi-restraints excluded: chain B residue 474 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 80 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7167 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7485 Z= 0.255 Angle : 0.528 7.815 10113 Z= 0.275 Chirality : 0.042 0.152 1086 Planarity : 0.004 0.041 1279 Dihedral : 4.294 18.243 962 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.63 % Allowed : 11.04 % Favored : 86.32 % 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: -0.88 (0.28), residues: 885 helix: 1.03 (0.30), residues: 310 sheet: -1.19 (0.42), residues: 157 loop : -1.59 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 370 HIS 0.007 0.001 HIS B 207 PHE 0.025 0.002 PHE A 342 TYR 0.008 0.001 TYR A 154 ARG 0.008 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 108 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 87 time to evaluate : 0.883 Fit side-chains REVERT: A 189 GLU cc_start: 0.7054 (tp30) cc_final: 0.6817 (tp30) REVERT: B 55 ASP cc_start: 0.6300 (m-30) cc_final: 0.6082 (m-30) REVERT: B 59 HIS cc_start: 0.6781 (m170) cc_final: 0.6484 (m170) REVERT: B 503 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6885 (m-80) outliers start: 21 outliers final: 16 residues processed: 100 average time/residue: 0.2230 time to fit residues: 29.7171 Evaluate side-chains 99 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 A residue 327 SER 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 44 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 143 VAL Chi-restraints excluded: chain B residue 342 SER Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 503 PHE 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: 3.9990 chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7485 Z= 0.206 Angle : 0.503 7.682 10113 Z= 0.260 Chirality : 0.041 0.220 1086 Planarity : 0.004 0.038 1279 Dihedral : 4.201 18.295 962 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.76 % Allowed : 11.92 % Favored : 85.32 % 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: -0.77 (0.28), residues: 885 helix: 1.18 (0.31), residues: 310 sheet: -1.23 (0.42), residues: 157 loop : -1.53 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 PHE 0.017 0.002 PHE A 342 TYR 0.007 0.001 TYR A 154 ARG 0.008 0.000 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 fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.846 Fit side-chains REVERT: A 328 LYS cc_start: 0.7795 (tttt) cc_final: 0.7361 (ttpt) REVERT: A 394 GLU cc_start: 0.6251 (mt-10) cc_final: 0.6035 (mm-30) REVERT: B 55 ASP cc_start: 0.6311 (m-30) cc_final: 0.6074 (m-30) REVERT: B 59 HIS cc_start: 0.6713 (m170) cc_final: 0.6438 (m170) outliers start: 22 outliers final: 15 residues processed: 104 average time/residue: 0.2287 time to fit residues: 32.0006 Evaluate side-chains 100 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 A residue 327 SER 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 87 GLU Chi-restraints excluded: chain B residue 96 VAL 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 474 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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: 0.7156 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7485 Z= 0.227 Angle : 0.517 7.891 10113 Z= 0.266 Chirality : 0.041 0.184 1086 Planarity : 0.004 0.039 1279 Dihedral : 4.238 18.010 962 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.51 % Allowed : 13.30 % Favored : 84.19 % 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: -0.84 (0.28), residues: 885 helix: 1.14 (0.30), residues: 310 sheet: -1.33 (0.42), residues: 157 loop : -1.56 (0.28), residues: 418 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 0.019 0.002 PHE A 342 TYR 0.009 0.001 TYR A 154 ARG 0.007 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 105 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.947 Fit side-chains REVERT: A 328 LYS cc_start: 0.7799 (tttt) cc_final: 0.7355 (ttpt) REVERT: A 394 GLU cc_start: 0.6303 (mt-10) cc_final: 0.6086 (mm-30) REVERT: B 55 ASP cc_start: 0.6317 (m-30) cc_final: 0.6045 (m-30) REVERT: B 59 HIS cc_start: 0.6741 (m170) cc_final: 0.6452 (m170) REVERT: B 285 TYR cc_start: 0.6709 (t80) cc_final: 0.5369 (t80) outliers start: 20 outliers final: 17 residues processed: 97 average time/residue: 0.2178 time to fit residues: 28.2859 Evaluate side-chains 101 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 327 SER 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 71 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL 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 474 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7141 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7485 Z= 0.209 Angle : 0.497 7.951 10113 Z= 0.259 Chirality : 0.041 0.170 1086 Planarity : 0.004 0.039 1279 Dihedral : 4.220 18.231 962 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.26 % Allowed : 12.67 % Favored : 84.07 % 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: -0.80 (0.28), residues: 885 helix: 1.20 (0.31), residues: 310 sheet: -1.32 (0.42), residues: 157 loop : -1.55 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 320 HIS 0.008 0.001 HIS B 207 PHE 0.017 0.002 PHE A 342 TYR 0.011 0.001 TYR B 56 ARG 0.008 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 114 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 0.858 Fit side-chains REVERT: A 328 LYS cc_start: 0.7812 (tttt) cc_final: 0.7340 (ttpt) REVERT: A 394 GLU cc_start: 0.6277 (mt-10) cc_final: 0.6050 (mm-30) REVERT: B 55 ASP cc_start: 0.6337 (m-30) cc_final: 0.6046 (m-30) REVERT: B 59 HIS cc_start: 0.6739 (m170) cc_final: 0.6471 (m170) REVERT: B 285 TYR cc_start: 0.6738 (t80) cc_final: 0.5371 (t80) outliers start: 26 outliers final: 18 residues processed: 104 average time/residue: 0.2249 time to fit residues: 30.7821 Evaluate side-chains 103 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 327 SER 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 71 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 101 ILE 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 474 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 57 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.7151 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7485 Z= 0.224 Angle : 0.507 7.997 10113 Z= 0.264 Chirality : 0.041 0.154 1086 Planarity : 0.004 0.039 1279 Dihedral : 4.250 17.940 962 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.76 % Allowed : 13.80 % Favored : 83.44 % 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: -0.83 (0.28), residues: 885 helix: 1.15 (0.30), residues: 310 sheet: -1.31 (0.42), residues: 157 loop : -1.56 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 320 HIS 0.008 0.001 HIS B 207 PHE 0.017 0.002 PHE A 342 TYR 0.010 0.001 TYR A 213 ARG 0.008 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 107 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 0.836 Fit side-chains REVERT: A 328 LYS cc_start: 0.7802 (tttt) cc_final: 0.7316 (ttpt) REVERT: A 394 GLU cc_start: 0.6314 (mt-10) cc_final: 0.6096 (mm-30) REVERT: B 285 TYR cc_start: 0.6760 (t80) cc_final: 0.5412 (t80) outliers start: 22 outliers final: 18 residues processed: 99 average time/residue: 0.2240 time to fit residues: 29.4640 Evaluate side-chains 102 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 327 SER 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 71 THR Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 101 ILE 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 474 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 34 optimal weight: 0.4980 chunk 62 optimal weight: 0.0980 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 0.0670 chunk 83 optimal weight: 0.3980 overall best weight: 0.4120 ------------------------------------------------------------------------------- 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: 0.7071 moved from start: 0.2035 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 : 0.489 12.001 10113 Z= 0.250 Chirality : 0.040 0.153 1086 Planarity : 0.004 0.039 1279 Dihedral : 4.060 18.078 962 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.42 % Favored : 94.46 % Rotamer: Outliers : 2.26 % Allowed : 14.93 % Favored : 82.81 % 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: -0.70 (0.28), residues: 885 helix: 1.33 (0.31), residues: 311 sheet: -1.43 (0.43), residues: 150 loop : -1.47 (0.27), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 PHE 0.013 0.001 PHE A 332 TYR 0.009 0.001 TYR B 56 ARG 0.010 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 105 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.858 Fit side-chains REVERT: A 285 TYR cc_start: 0.6992 (t80) cc_final: 0.6751 (t80) REVERT: A 395 MET cc_start: 0.5197 (mmm) cc_final: 0.4431 (mmm) REVERT: B 285 TYR cc_start: 0.6718 (t80) cc_final: 0.5425 (t80) outliers start: 18 outliers final: 13 residues processed: 97 average time/residue: 0.2283 time to fit residues: 29.4328 Evaluate side-chains 99 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 327 SER 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 71 THR Chi-restraints excluded: chain B residue 96 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 0.0470 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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: 0.7093 moved from start: 0.2070 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= 0.172 Angle : 0.490 10.030 10113 Z= 0.251 Chirality : 0.040 0.148 1086 Planarity : 0.004 0.040 1279 Dihedral : 4.030 17.440 962 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.65 % Favored : 94.24 % Rotamer: Outliers : 2.13 % Allowed : 15.18 % Favored : 82.69 % 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: 1.36 (0.31), residues: 311 sheet: -1.24 (0.43), residues: 147 loop : -1.42 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 PHE 0.013 0.001 PHE A 332 TYR 0.011 0.001 TYR B 56 ARG 0.009 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 100 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.850 Fit side-chains REVERT: A 285 TYR cc_start: 0.6979 (t80) cc_final: 0.6738 (t80) REVERT: A 395 MET cc_start: 0.5425 (mmm) cc_final: 0.4794 (mmm) REVERT: B 285 TYR cc_start: 0.6710 (t80) cc_final: 0.5391 (t80) outliers start: 17 outliers final: 15 residues processed: 91 average time/residue: 0.2098 time to fit residues: 25.7045 Evaluate side-chains 95 residues out of total 797 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASN Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 327 SER 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 44 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 0.0470 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 0.0870 chunk 29 optimal weight: 0.0010 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.3862 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.206733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.168645 restraints weight = 7883.626| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.34 r_work: 0.3882 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2176 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= 0.141 Angle : 0.472 9.883 10113 Z= 0.242 Chirality : 0.040 0.146 1086 Planarity : 0.004 0.040 1279 Dihedral : 3.930 17.718 962 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.69 % Rotamer: Outliers : 1.88 % Allowed : 15.93 % 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: -0.54 (0.28), residues: 885 helix: 1.47 (0.31), residues: 311 sheet: -1.38 (0.42), residues: 150 loop : -1.37 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 320 HIS 0.007 0.001 HIS B 207 PHE 0.012 0.001 PHE A 332 TYR 0.008 0.001 TYR B 56 ARG 0.009 0.000 ARG A 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2066.78 seconds wall clock time: 38 minutes 25.28 seconds (2305.28 seconds total)