Starting phenix.real_space_refine on Thu Feb 15 19:02:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyf_29572/02_2024/8fyf_29572.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyf_29572/02_2024/8fyf_29572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyf_29572/02_2024/8fyf_29572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyf_29572/02_2024/8fyf_29572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyf_29572/02_2024/8fyf_29572.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyf_29572/02_2024/8fyf_29572.pdb" } resolution = 3.4 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= 0.003 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 C 4244 2.51 5 N 1086 2.21 5 O 1080 1.98 5 H 6754 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 251": "OD1" <-> "OD2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 415": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13202 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6163 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 16, 'TRANS': 370} Chain breaks: 1 Chain: "B" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6163 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 16, 'TRANS': 370} Chain breaks: 1 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 438 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 438 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Time building chain proxies: 6.23, per 1000 atoms: 0.47 Number of scatterers: 13202 At special positions: 0 Unit cell: (105.25, 73.254, 82.516, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 O 1080 8.00 N 1086 7.00 C 4244 6.00 H 6754 1.00 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: 11.45 Conformation dependent library (CDL) restraints added in 1.4 seconds 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 89.4% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 33 through 50 Processing helix chain 'A' and resid 51 through 57 removed outlier: 4.354A pdb=" N VAL A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 102 removed outlier: 5.521A pdb=" N ARG A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 136 through 164 removed outlier: 4.447A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.882A pdb=" N ARG A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 274 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.977A pdb=" N LEU A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 306 through 332 removed outlier: 3.701A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 353 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 368 through 399 removed outlier: 3.881A pdb=" N GLU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 4.910A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 3.566A pdb=" N THR A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'B' and resid 33 through 50 Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.354A pdb=" N VAL B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 102 removed outlier: 5.521A pdb=" N ARG B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.500A pdb=" N LEU B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 136 through 164 removed outlier: 4.447A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 175 Processing helix chain 'B' and resid 177 through 190 removed outlier: 3.886A pdb=" N ARG B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 274 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.977A pdb=" N LEU B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.699A pdb=" N PHE B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 368 through 399 removed outlier: 3.856A pdb=" N GLU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 4.911A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 3.567A pdb=" N THR B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 461 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'C' and resid 384 through 410 Processing helix chain 'D' and resid 384 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 256 removed outlier: 4.266A pdb=" N ALA A 337 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 31 through 32 Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 256 removed outlier: 4.287A pdb=" N ALA B 337 " --> pdb=" O LEU B 256 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1545 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: 4.79 Time building geometry restraints manager: 11.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6736 1.03 - 1.23: 20 1.23 - 1.42: 2680 1.42 - 1.61: 3852 1.61 - 1.81: 58 Bond restraints: 13346 Sorted by residual: bond pdb=" C THR B 306 " pdb=" N GLY B 307 " ideal model delta sigma weight residual 1.340 1.328 0.012 6.60e-03 2.30e+04 3.27e+00 bond pdb=" C THR A 306 " pdb=" N GLY A 307 " ideal model delta sigma weight residual 1.340 1.328 0.012 6.60e-03 2.30e+04 3.12e+00 bond pdb=" N LEU C 383 " pdb=" CA LEU C 383 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N LEU D 383 " pdb=" CA LEU D 383 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N ILE A 30 " pdb=" CA ILE A 30 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 ... (remaining 13341 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.07: 274 107.07 - 113.80: 16048 113.80 - 120.53: 4628 120.53 - 127.26: 3175 127.26 - 133.99: 77 Bond angle restraints: 24202 Sorted by residual: angle pdb=" N GLU A 403 " pdb=" CA GLU A 403 " pdb=" C GLU A 403 " ideal model delta sigma weight residual 114.56 111.34 3.22 1.27e+00 6.20e-01 6.45e+00 angle pdb=" N GLU B 403 " pdb=" CA GLU B 403 " pdb=" C GLU B 403 " ideal model delta sigma weight residual 114.56 111.36 3.20 1.27e+00 6.20e-01 6.35e+00 angle pdb=" C ILE A 60 " pdb=" N SER A 61 " pdb=" CA SER A 61 " ideal model delta sigma weight residual 122.00 119.39 2.61 1.08e+00 8.57e-01 5.86e+00 angle pdb=" N SER B 61 " pdb=" CA SER B 61 " pdb=" C SER B 61 " ideal model delta sigma weight residual 108.55 112.86 -4.31 1.79e+00 3.12e-01 5.81e+00 angle pdb=" C ILE B 60 " pdb=" N SER B 61 " pdb=" CA SER B 61 " ideal model delta sigma weight residual 122.00 119.43 2.57 1.08e+00 8.57e-01 5.66e+00 ... (remaining 24197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 5611 17.62 - 35.23: 459 35.23 - 52.85: 127 52.85 - 70.47: 43 70.47 - 88.09: 8 Dihedral angle restraints: 6248 sinusoidal: 3352 harmonic: 2896 Sorted by residual: dihedral pdb=" CA GLU A 59 " pdb=" C GLU A 59 " pdb=" N ILE A 60 " pdb=" CA ILE A 60 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLU B 59 " pdb=" C GLU B 59 " pdb=" N ILE B 60 " pdb=" CA ILE B 60 " ideal model delta harmonic sigma weight residual 180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA LEU A 276 " pdb=" C LEU A 276 " pdb=" N ILE A 277 " pdb=" CA ILE A 277 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 6245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 716 0.028 - 0.055: 235 0.055 - 0.083: 109 0.083 - 0.111: 36 0.111 - 0.138: 10 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA ILE A 30 " pdb=" N ILE A 30 " pdb=" C ILE A 30 " pdb=" CB ILE A 30 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE B 30 " pdb=" N ILE B 30 " pdb=" C ILE B 30 " pdb=" CB ILE B 30 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA VAL B 136 " pdb=" N VAL B 136 " pdb=" C VAL B 136 " pdb=" CB VAL B 136 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1103 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 254 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.87e+00 pdb=" N PRO B 255 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 255 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 255 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 287 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO B 288 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 288 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 288 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 287 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 288 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.019 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 203 2.08 - 2.71: 21938 2.71 - 3.34: 39930 3.34 - 3.97: 47602 3.97 - 4.60: 76240 Nonbonded interactions: 185913 Sorted by model distance: nonbonded pdb=" OE1 GLU A 259 " pdb=" H GLU A 259 " model vdw 1.451 1.850 nonbonded pdb=" OE1 GLU B 259 " pdb=" H GLU B 259 " model vdw 1.452 1.850 nonbonded pdb=" OE1 GLN A 171 " pdb=" H GLN A 171 " model vdw 1.633 1.850 nonbonded pdb=" OE1 GLN B 171 " pdb=" H GLN B 171 " model vdw 1.637 1.850 nonbonded pdb=" HE2 HIS A 95 " pdb=" OD1 ASN A 113 " model vdw 1.666 1.850 ... (remaining 185908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.200 Extract box with map and model: 5.800 Check model and map are aligned: 0.180 Set scattering table: 0.140 Process input model: 46.440 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 0.033 6592 Z= 0.188 Angle : 0.582 6.706 8974 Z= 0.331 Chirality : 0.036 0.138 1106 Planarity : 0.004 0.034 1098 Dihedral : 14.089 88.087 2318 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.14 % Allowed : 10.34 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.30), residues: 818 helix: 2.32 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.24 (0.63), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 324 HIS 0.003 0.001 HIS B 328 PHE 0.011 0.001 PHE B 314 TYR 0.008 0.001 TYR A 313 ARG 0.002 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 1.170 Fit side-chains REVERT: B 426 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.7217 (t80) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.3820 time to fit residues: 39.5753 Evaluate side-chains 72 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6592 Z= 0.218 Angle : 0.544 4.905 8974 Z= 0.293 Chirality : 0.037 0.113 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.894 49.005 892 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.86 % Allowed : 10.92 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.30), residues: 818 helix: 2.39 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -1.00 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 324 HIS 0.004 0.001 HIS A 449 PHE 0.010 0.001 PHE B 99 TYR 0.010 0.001 TYR A 160 ARG 0.001 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 1.004 Fit side-chains REVERT: A 65 GLN cc_start: 0.3323 (OUTLIER) cc_final: 0.2594 (tm-30) REVERT: A 293 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: A 426 TYR cc_start: 0.9114 (OUTLIER) cc_final: 0.7340 (t80) REVERT: B 65 GLN cc_start: 0.3309 (OUTLIER) cc_final: 0.2575 (tm-30) REVERT: B 293 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: B 426 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.7312 (t80) outliers start: 6 outliers final: 0 residues processed: 81 average time/residue: 0.3543 time to fit residues: 39.7566 Evaluate side-chains 74 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6592 Z= 0.225 Angle : 0.532 4.978 8974 Z= 0.284 Chirality : 0.036 0.113 1106 Planarity : 0.004 0.031 1098 Dihedral : 4.841 49.486 892 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.58 % Allowed : 10.34 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.30), residues: 818 helix: 2.37 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.68 (0.66), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 324 HIS 0.004 0.001 HIS B 328 PHE 0.010 0.001 PHE B 99 TYR 0.007 0.001 TYR B 160 ARG 0.001 0.000 ARG B 442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 1.140 Fit side-chains REVERT: A 65 GLN cc_start: 0.3388 (OUTLIER) cc_final: 0.2664 (tm-30) REVERT: A 293 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: A 426 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.7359 (t80) REVERT: B 65 GLN cc_start: 0.3374 (OUTLIER) cc_final: 0.2646 (tm-30) REVERT: B 293 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7234 (mp0) outliers start: 11 outliers final: 6 residues processed: 87 average time/residue: 0.3466 time to fit residues: 42.1491 Evaluate side-chains 84 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN B 177 HIS B 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6592 Z= 0.292 Angle : 0.551 4.956 8974 Z= 0.297 Chirality : 0.037 0.112 1106 Planarity : 0.004 0.030 1098 Dihedral : 4.913 49.616 892 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.59 % Allowed : 10.34 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.30), residues: 818 helix: 2.27 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.82 (0.65), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.011 0.002 PHE A 99 TYR 0.008 0.001 TYR B 160 ARG 0.002 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 GLN cc_start: 0.3295 (OUTLIER) cc_final: 0.2363 (tm-30) REVERT: A 293 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: B 65 GLN cc_start: 0.3238 (OUTLIER) cc_final: 0.2398 (tm-30) REVERT: B 293 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7239 (mp0) outliers start: 18 outliers final: 11 residues processed: 94 average time/residue: 0.3413 time to fit residues: 45.0873 Evaluate side-chains 89 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 395 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6592 Z= 0.244 Angle : 0.543 4.934 8974 Z= 0.296 Chirality : 0.037 0.132 1106 Planarity : 0.004 0.029 1098 Dihedral : 4.926 50.892 892 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.44 % Allowed : 10.78 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.30), residues: 818 helix: 2.39 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -1.01 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.027 0.002 HIS B 177 PHE 0.010 0.001 PHE A 99 TYR 0.007 0.001 TYR B 160 ARG 0.002 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 GLN cc_start: 0.3153 (OUTLIER) cc_final: 0.2430 (tm-30) REVERT: A 293 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: A 426 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.7402 (t80) REVERT: B 65 GLN cc_start: 0.3144 (OUTLIER) cc_final: 0.2421 (tm-30) REVERT: B 293 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: B 426 TYR cc_start: 0.9173 (OUTLIER) cc_final: 0.7274 (t80) outliers start: 17 outliers final: 7 residues processed: 91 average time/residue: 0.3350 time to fit residues: 42.5393 Evaluate side-chains 87 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 0.0970 chunk 77 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6592 Z= 0.208 Angle : 0.521 4.918 8974 Z= 0.281 Chirality : 0.036 0.121 1106 Planarity : 0.004 0.028 1098 Dihedral : 4.842 51.812 892 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.16 % Allowed : 11.35 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.30), residues: 818 helix: 2.47 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -1.02 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.020 0.002 HIS A 177 PHE 0.010 0.001 PHE A 99 TYR 0.007 0.001 TYR B 160 ARG 0.003 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: A 426 TYR cc_start: 0.9168 (OUTLIER) cc_final: 0.7428 (t80) REVERT: B 293 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: B 426 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.7311 (t80) outliers start: 15 outliers final: 7 residues processed: 86 average time/residue: 0.4102 time to fit residues: 46.9928 Evaluate side-chains 84 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6592 Z= 0.167 Angle : 0.497 4.887 8974 Z= 0.264 Chirality : 0.036 0.115 1106 Planarity : 0.004 0.029 1098 Dihedral : 4.731 52.405 892 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.58 % Allowed : 10.78 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.30), residues: 818 helix: 2.63 (0.20), residues: 690 sheet: None (None), residues: 0 loop : -0.90 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS B 328 PHE 0.009 0.001 PHE A 99 TYR 0.006 0.001 TYR B 160 ARG 0.001 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.6489 (mp0) cc_final: 0.6233 (mp0) REVERT: A 293 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: A 426 TYR cc_start: 0.9135 (OUTLIER) cc_final: 0.7418 (t80) REVERT: B 293 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: B 426 TYR cc_start: 0.9116 (OUTLIER) cc_final: 0.7392 (t80) outliers start: 11 outliers final: 5 residues processed: 81 average time/residue: 0.3592 time to fit residues: 40.3179 Evaluate side-chains 82 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6592 Z= 0.251 Angle : 0.519 4.932 8974 Z= 0.279 Chirality : 0.037 0.117 1106 Planarity : 0.004 0.029 1098 Dihedral : 4.785 51.984 892 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.58 % Allowed : 10.34 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.30), residues: 818 helix: 2.51 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.94 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 324 HIS 0.004 0.001 HIS A 328 PHE 0.011 0.001 PHE A 99 TYR 0.007 0.001 TYR B 160 ARG 0.001 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: A 426 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.7426 (t80) REVERT: B 293 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: B 426 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.7398 (t80) outliers start: 11 outliers final: 6 residues processed: 82 average time/residue: 0.3631 time to fit residues: 41.4886 Evaluate side-chains 83 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6592 Z= 0.169 Angle : 0.496 4.876 8974 Z= 0.261 Chirality : 0.036 0.116 1106 Planarity : 0.004 0.029 1098 Dihedral : 4.683 53.047 892 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.58 % Allowed : 10.49 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.30), residues: 818 helix: 2.68 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.90 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 324 HIS 0.003 0.001 HIS B 328 PHE 0.009 0.001 PHE A 99 TYR 0.006 0.001 TYR B 160 ARG 0.001 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.6469 (mp0) cc_final: 0.6204 (mp0) REVERT: A 293 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: A 426 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.7393 (t80) REVERT: B 293 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: B 426 TYR cc_start: 0.9125 (OUTLIER) cc_final: 0.7445 (t80) outliers start: 11 outliers final: 6 residues processed: 81 average time/residue: 0.3581 time to fit residues: 40.2208 Evaluate side-chains 83 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.2980 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6592 Z= 0.225 Angle : 0.510 4.938 8974 Z= 0.271 Chirality : 0.036 0.115 1106 Planarity : 0.004 0.030 1098 Dihedral : 4.701 52.653 892 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.44 % Allowed : 10.63 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.30), residues: 818 helix: 2.62 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.92 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 324 HIS 0.004 0.001 HIS A 328 PHE 0.011 0.001 PHE A 99 TYR 0.006 0.001 TYR B 160 ARG 0.001 0.000 ARG B 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.6495 (mp0) cc_final: 0.6213 (mp0) REVERT: A 293 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: A 426 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.7407 (t80) REVERT: B 293 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7161 (mp0) REVERT: B 426 TYR cc_start: 0.9156 (OUTLIER) cc_final: 0.7311 (t80) outliers start: 10 outliers final: 6 residues processed: 81 average time/residue: 0.3567 time to fit residues: 40.1915 Evaluate side-chains 82 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.126305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.096150 restraints weight = 32150.366| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.44 r_work: 0.2963 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6592 Z= 0.168 Angle : 0.490 4.882 8974 Z= 0.258 Chirality : 0.036 0.114 1106 Planarity : 0.004 0.030 1098 Dihedral : 4.624 53.284 892 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.44 % Allowed : 10.78 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.30), residues: 818 helix: 2.77 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.85 (0.65), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 324 HIS 0.003 0.001 HIS B 328 PHE 0.009 0.001 PHE B 314 TYR 0.006 0.001 TYR B 160 ARG 0.001 0.000 ARG B 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2913.44 seconds wall clock time: 52 minutes 13.53 seconds (3133.53 seconds total)