Starting phenix.real_space_refine on Sat Dec 28 12:03:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uvc_42615/12_2024/8uvc_42615.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uvc_42615/12_2024/8uvc_42615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uvc_42615/12_2024/8uvc_42615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uvc_42615/12_2024/8uvc_42615.map" model { file = "/net/cci-nas-00/data/ceres_data/8uvc_42615/12_2024/8uvc_42615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uvc_42615/12_2024/8uvc_42615.cif" } resolution = 2.09 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= 0.050 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 52 5.16 5 Na 2 4.78 5 C 5838 2.51 5 N 1272 2.21 5 O 1390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8558 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4011 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 34, 'TRANS': 478} Chain breaks: 2 Chain: "B" Number of atoms: 4011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4011 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 34, 'TRANS': 478} Chain breaks: 2 Chain: "A" Number of atoms: 282 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 12, 272 Unusual residues: {' NA': 1, '3PE': 2, 'AKG': 1, 'C14': 4, 'CLR': 4} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Conformer: "B" Number of residues, atoms: 12, 272 Unusual residues: {' NA': 1, '3PE': 2, 'AKG': 1, 'C14': 4, 'CLR': 4} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 bond proxies already assigned to first conformer: 267 Chain: "B" Number of atoms: 254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 10, 244 Unusual residues: {' NA': 1, '3PE': 2, 'AKG': 1, 'C14': 2, 'CLR': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Conformer: "B" Number of residues, atoms: 10, 244 Unusual residues: {' NA': 1, '3PE': 2, 'AKG': 1, 'C14': 2, 'CLR': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 bond proxies already assigned to first conformer: 241 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 AAKG A 702 " occ=0.50 ... (18 atoms not shown) pdb=" O5 BAKG A 702 " occ=0.50 residue: pdb=" C1 AAKG B 702 " occ=0.50 ... (18 atoms not shown) pdb=" O5 BAKG B 702 " occ=0.50 Time building chain proxies: 6.37, per 1000 atoms: 0.74 Number of scatterers: 8558 At special positions: 0 Unit cell: (85.8, 106.425, 82.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 P 4 15.00 Na 2 11.00 O 1390 8.00 N 1272 7.00 C 5838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.0 seconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 84.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 removed outlier: 3.831A pdb=" N ALA A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 34 Proline residue: A 24 - end of helix Proline residue: A 29 - end of helix removed outlier: 3.692A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 55 Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.805A pdb=" N VAL A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 106 removed outlier: 3.794A pdb=" N PHE A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.566A pdb=" N GLY A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 143 through 164 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 220 through 247 removed outlier: 3.782A pdb=" N ILE A 238 " --> pdb=" O PHE A 234 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.869A pdb=" N THR A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 7.059A pdb=" N THR A 251 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.924A pdb=" N LEU A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 301 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 320 through 334 Processing helix chain 'A' and resid 339 through 358 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 377 through 389 removed outlier: 3.897A pdb=" N ILE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.816A pdb=" N PHE A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 426 through 446 Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 457 through 462 removed outlier: 4.257A pdb=" N ASN A 461 " --> pdb=" O PRO A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 483 through 502 Proline residue: A 493 - end of helix Processing helix chain 'A' and resid 505 through 517 removed outlier: 3.916A pdb=" N LEU A 509 " --> pdb=" O HIS A 505 " (cutoff:3.500A) Proline residue: A 512 - end of helix Processing helix chain 'A' and resid 527 through 535 Processing helix chain 'A' and resid 540 through 566 removed outlier: 4.149A pdb=" N LEU A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 14 through 34 Proline residue: B 24 - end of helix Proline residue: B 29 - end of helix removed outlier: 3.693A pdb=" N PHE B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 55 Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.805A pdb=" N VAL B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 87 through 106 removed outlier: 3.794A pdb=" N PHE B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.567A pdb=" N GLY B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 143 through 164 Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 220 through 247 removed outlier: 3.782A pdb=" N ILE B 238 " --> pdb=" O PHE B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.869A pdb=" N THR B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 252 removed outlier: 7.059A pdb=" N THR B 251 " --> pdb=" O ALA B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 267 removed outlier: 3.924A pdb=" N LEU B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 301 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 320 through 334 Processing helix chain 'B' and resid 339 through 358 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 377 through 389 removed outlier: 3.897A pdb=" N ILE B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.815A pdb=" N PHE B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 425 Processing helix chain 'B' and resid 426 through 446 Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 457 through 462 removed outlier: 4.257A pdb=" N ASN B 461 " --> pdb=" O PRO B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 483 through 502 Proline residue: B 493 - end of helix Processing helix chain 'B' and resid 505 through 517 removed outlier: 3.916A pdb=" N LEU B 509 " --> pdb=" O HIS B 505 " (cutoff:3.500A) Proline residue: B 512 - end of helix Processing helix chain 'B' and resid 527 through 535 Processing helix chain 'B' and resid 540 through 566 removed outlier: 4.149A pdb=" N LEU B 550 " --> pdb=" O ARG B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 572 550 hydrogen bonds defined for protein. 1608 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: 2.41 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1228 1.30 - 1.43: 2188 1.43 - 1.55: 5266 1.55 - 1.68: 26 1.68 - 1.81: 90 Bond restraints: 8798 Sorted by residual: bond pdb=" C ARG B 126 " pdb=" O ARG B 126 " ideal model delta sigma weight residual 1.236 1.173 0.064 1.25e-02 6.40e+03 2.60e+01 bond pdb=" C ARG A 126 " pdb=" O ARG A 126 " ideal model delta sigma weight residual 1.236 1.173 0.064 1.25e-02 6.40e+03 2.59e+01 bond pdb=" C LEU B 129 " pdb=" O LEU B 129 " ideal model delta sigma weight residual 1.236 1.194 0.043 1.15e-02 7.56e+03 1.39e+01 bond pdb=" C LEU A 129 " pdb=" O LEU A 129 " ideal model delta sigma weight residual 1.236 1.194 0.043 1.15e-02 7.56e+03 1.39e+01 bond pdb=" C GLN A 84 " pdb=" O GLN A 84 " ideal model delta sigma weight residual 1.236 1.193 0.043 1.28e-02 6.10e+03 1.11e+01 ... (remaining 8793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 11503 1.71 - 3.43: 370 3.43 - 5.14: 65 5.14 - 6.85: 18 6.85 - 8.57: 8 Bond angle restraints: 11964 Sorted by residual: angle pdb=" C LEU B 87 " pdb=" N ASP B 88 " pdb=" CA ASP B 88 " ideal model delta sigma weight residual 120.60 129.17 -8.57 1.60e+00 3.91e-01 2.87e+01 angle pdb=" C LEU A 87 " pdb=" N ASP A 88 " pdb=" CA ASP A 88 " ideal model delta sigma weight residual 120.60 129.16 -8.56 1.60e+00 3.91e-01 2.86e+01 angle pdb=" CA LEU B 87 " pdb=" C LEU B 87 " pdb=" O LEU B 87 " ideal model delta sigma weight residual 121.87 116.15 5.72 1.10e+00 8.26e-01 2.70e+01 angle pdb=" CA LEU A 87 " pdb=" C LEU A 87 " pdb=" O LEU A 87 " ideal model delta sigma weight residual 121.87 116.17 5.70 1.10e+00 8.26e-01 2.69e+01 angle pdb=" CA LEU B 87 " pdb=" C LEU B 87 " pdb=" N ASP B 88 " ideal model delta sigma weight residual 115.30 121.61 -6.31 1.33e+00 5.65e-01 2.25e+01 ... (remaining 11959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.25: 5330 24.25 - 48.50: 202 48.50 - 72.75: 48 72.75 - 96.99: 6 96.99 - 121.24: 12 Dihedral angle restraints: 5598 sinusoidal: 2640 harmonic: 2958 Sorted by residual: dihedral pdb=" C PHE B 86 " pdb=" N PHE B 86 " pdb=" CA PHE B 86 " pdb=" CB PHE B 86 " ideal model delta harmonic sigma weight residual -122.60 -135.30 12.70 0 2.50e+00 1.60e-01 2.58e+01 dihedral pdb=" C PHE A 86 " pdb=" N PHE A 86 " pdb=" CA PHE A 86 " pdb=" CB PHE A 86 " ideal model delta harmonic sigma weight residual -122.60 -135.28 12.68 0 2.50e+00 1.60e-01 2.57e+01 dihedral pdb=" N PHE B 86 " pdb=" C PHE B 86 " pdb=" CA PHE B 86 " pdb=" CB PHE B 86 " ideal model delta harmonic sigma weight residual 122.80 134.02 -11.22 0 2.50e+00 1.60e-01 2.01e+01 ... (remaining 5595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1321 0.093 - 0.187: 64 0.187 - 0.280: 3 0.280 - 0.374: 0 0.374 - 0.467: 2 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA PHE B 86 " pdb=" N PHE B 86 " pdb=" C PHE B 86 " pdb=" CB PHE B 86 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA PHE A 86 " pdb=" N PHE A 86 " pdb=" C PHE A 86 " pdb=" CB PHE A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA LEU B 87 " pdb=" N LEU B 87 " pdb=" C LEU B 87 " pdb=" CB LEU B 87 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1387 not shown) Planarity restraints: 1396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 133 " 0.014 2.00e-02 2.50e+03 2.95e-02 8.72e+00 pdb=" C VAL B 133 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL B 133 " 0.019 2.00e-02 2.50e+03 pdb=" N THR B 134 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 133 " -0.014 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C VAL A 133 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL A 133 " -0.019 2.00e-02 2.50e+03 pdb=" N THR A 134 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 132 " 0.014 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C MET B 132 " -0.050 2.00e-02 2.50e+03 pdb=" O MET B 132 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL B 133 " 0.017 2.00e-02 2.50e+03 ... (remaining 1393 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1943 2.79 - 3.32: 8603 3.32 - 3.84: 14966 3.84 - 4.37: 17900 4.37 - 4.90: 30108 Nonbonded interactions: 73520 Sorted by model distance: nonbonded pdb=" OG SER B 139 " pdb=" OD1 ASN B 144 " model vdw 2.262 3.040 nonbonded pdb=" OG SER A 139 " pdb=" OD1 ASN A 144 " model vdw 2.262 3.040 nonbonded pdb=" O LEU A 561 " pdb=" OG1 THR A 565 " model vdw 2.269 3.040 nonbonded pdb=" O LEU B 561 " pdb=" OG1 THR B 565 " model vdw 2.270 3.040 nonbonded pdb=" OH TYR B 240 " pdb=" O PHE B 521 " model vdw 2.339 3.040 ... (remaining 73515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 581 or resid 701 or resid 703 or resid 706 throu \ gh 707)) selection = (chain 'B' and (resid 1 through 581 or resid 701 or resid 703 or resid 706 throu \ gh 707)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.440 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 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 : 0.005 0.064 8798 Z= 0.330 Angle : 0.732 8.567 11964 Z= 0.414 Chirality : 0.047 0.467 1390 Planarity : 0.005 0.037 1396 Dihedral : 14.953 121.241 3674 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.47 % Allowed : 1.40 % Favored : 98.14 % Cbeta Deviations : 0.21 % 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: 2.48 (0.27), residues: 1014 helix: 1.95 (0.19), residues: 776 sheet: None (None), residues: 0 loop : 0.79 (0.43), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 418 HIS 0.002 0.001 HIS A 109 PHE 0.023 0.002 PHE B 72 TYR 0.021 0.003 TYR A 301 ARG 0.008 0.001 ARG B 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 1.074 Fit side-chains REVERT: A 123 GLN cc_start: 0.6894 (mp10) cc_final: 0.6486 (mp10) REVERT: A 223 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7265 (tp30) REVERT: B 223 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7303 (tp30) outliers start: 4 outliers final: 2 residues processed: 138 average time/residue: 1.1207 time to fit residues: 166.6494 Evaluate side-chains 113 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain B residue 86 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8798 Z= 0.223 Angle : 0.589 7.655 11964 Z= 0.284 Chirality : 0.041 0.136 1390 Planarity : 0.005 0.040 1396 Dihedral : 11.279 88.364 1852 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.51 % Allowed : 5.47 % Favored : 93.02 % 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: 2.56 (0.27), residues: 1014 helix: 2.00 (0.19), residues: 784 sheet: None (None), residues: 0 loop : 0.82 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 418 HIS 0.004 0.001 HIS B 109 PHE 0.019 0.002 PHE B 363 TYR 0.014 0.001 TYR A 226 ARG 0.002 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.977 Fit side-chains REVERT: A 223 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7384 (tp30) REVERT: B 1 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.4888 (mmt) REVERT: B 223 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7307 (tp30) outliers start: 13 outliers final: 5 residues processed: 117 average time/residue: 0.9225 time to fit residues: 117.7448 Evaluate side-chains 120 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8798 Z= 0.260 Angle : 0.571 5.749 11964 Z= 0.282 Chirality : 0.043 0.155 1390 Planarity : 0.005 0.042 1396 Dihedral : 11.134 87.976 1852 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.74 % Allowed : 6.86 % Favored : 91.40 % 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: 2.66 (0.27), residues: 1014 helix: 2.03 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 1.06 (0.44), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 418 HIS 0.005 0.001 HIS A 109 PHE 0.017 0.002 PHE A 477 TYR 0.015 0.001 TYR B 226 ARG 0.003 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.906 Fit side-chains REVERT: A 1 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.4058 (mmt) REVERT: A 223 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7410 (tp30) REVERT: A 478 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7674 (t80) REVERT: B 1 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.4844 (mmt) REVERT: B 223 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7325 (tp30) REVERT: B 404 ASP cc_start: 0.7973 (t0) cc_final: 0.7665 (t70) outliers start: 15 outliers final: 8 residues processed: 119 average time/residue: 0.9595 time to fit residues: 124.2662 Evaluate side-chains 120 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 9 LYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.0170 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN A 552 ASN B 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8798 Z= 0.183 Angle : 0.524 5.410 11964 Z= 0.258 Chirality : 0.040 0.144 1390 Planarity : 0.005 0.040 1396 Dihedral : 11.049 89.883 1852 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.63 % Allowed : 7.33 % Favored : 91.05 % 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: 2.78 (0.27), residues: 1014 helix: 2.15 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 1.01 (0.43), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 418 HIS 0.007 0.001 HIS B 109 PHE 0.015 0.001 PHE A 352 TYR 0.016 0.001 TYR B 226 ARG 0.003 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.957 Fit side-chains REVERT: A 223 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7414 (tp30) REVERT: A 478 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7714 (t80) REVERT: B 1 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.4834 (mmt) REVERT: B 223 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7303 (tp30) REVERT: B 404 ASP cc_start: 0.7993 (t0) cc_final: 0.7788 (t0) outliers start: 14 outliers final: 6 residues processed: 119 average time/residue: 0.9102 time to fit residues: 118.6866 Evaluate side-chains 118 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 527 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 333 GLN B 552 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8798 Z= 0.239 Angle : 0.551 5.936 11964 Z= 0.271 Chirality : 0.042 0.168 1390 Planarity : 0.005 0.040 1396 Dihedral : 11.205 89.540 1852 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.51 % Allowed : 8.14 % Favored : 90.35 % 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: 2.72 (0.27), residues: 1014 helix: 2.10 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 1.00 (0.43), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 418 HIS 0.008 0.002 HIS B 109 PHE 0.016 0.002 PHE A 352 TYR 0.016 0.001 TYR B 226 ARG 0.002 0.000 ARG B 503 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.158 Fit side-chains REVERT: A 223 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7360 (tp30) REVERT: A 478 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7710 (t80) REVERT: B 1 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.4858 (mmt) REVERT: B 404 ASP cc_start: 0.7993 (t0) cc_final: 0.7777 (t0) outliers start: 13 outliers final: 6 residues processed: 117 average time/residue: 0.9713 time to fit residues: 123.6298 Evaluate side-chains 115 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8798 Z= 0.239 Angle : 0.553 5.948 11964 Z= 0.272 Chirality : 0.042 0.180 1390 Planarity : 0.005 0.040 1396 Dihedral : 11.276 89.612 1852 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.40 % Allowed : 8.49 % Favored : 90.12 % 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: 2.72 (0.27), residues: 1014 helix: 2.12 (0.19), residues: 772 sheet: None (None), residues: 0 loop : 0.92 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 418 HIS 0.005 0.001 HIS B 109 PHE 0.016 0.001 PHE A 352 TYR 0.017 0.001 TYR B 226 ARG 0.002 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 1.155 Fit side-chains REVERT: A 224 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8382 (m-30) REVERT: A 478 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7711 (t80) REVERT: B 1 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.4820 (mmt) REVERT: B 150 MET cc_start: 0.9171 (tmm) cc_final: 0.8799 (ttt) REVERT: B 404 ASP cc_start: 0.8023 (t0) cc_final: 0.7774 (t0) outliers start: 12 outliers final: 5 residues processed: 113 average time/residue: 0.8812 time to fit residues: 109.7221 Evaluate side-chains 115 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8798 Z= 0.190 Angle : 0.533 5.714 11964 Z= 0.261 Chirality : 0.041 0.182 1390 Planarity : 0.005 0.040 1396 Dihedral : 11.164 89.863 1852 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.40 % Allowed : 8.95 % Favored : 89.65 % 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: 2.80 (0.27), residues: 1014 helix: 2.15 (0.19), residues: 778 sheet: None (None), residues: 0 loop : 1.03 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 418 HIS 0.004 0.001 HIS B 109 PHE 0.015 0.001 PHE A 352 TYR 0.018 0.001 TYR B 226 ARG 0.002 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.932 Fit side-chains REVERT: A 223 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7328 (tp30) REVERT: A 478 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7730 (t80) REVERT: B 1 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.4815 (mmt) REVERT: B 150 MET cc_start: 0.9162 (tmm) cc_final: 0.8783 (ttt) REVERT: B 404 ASP cc_start: 0.8022 (t0) cc_final: 0.7774 (t0) outliers start: 12 outliers final: 6 residues processed: 114 average time/residue: 0.8923 time to fit residues: 111.5918 Evaluate side-chains 121 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8798 Z= 0.201 Angle : 0.542 6.590 11964 Z= 0.265 Chirality : 0.042 0.191 1390 Planarity : 0.005 0.040 1396 Dihedral : 11.156 89.907 1852 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.28 % Allowed : 9.07 % Favored : 89.65 % 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: 2.79 (0.27), residues: 1014 helix: 2.13 (0.19), residues: 780 sheet: None (None), residues: 0 loop : 1.05 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 418 HIS 0.004 0.001 HIS B 109 PHE 0.016 0.001 PHE A 352 TYR 0.019 0.001 TYR A 226 ARG 0.002 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.937 Fit side-chains REVERT: A 1 MET cc_start: 0.5861 (OUTLIER) cc_final: 0.3852 (mmm) REVERT: A 478 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7720 (t80) REVERT: B 1 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.4816 (mmt) REVERT: B 150 MET cc_start: 0.9156 (tmm) cc_final: 0.8816 (ttt) REVERT: B 404 ASP cc_start: 0.8023 (t0) cc_final: 0.7774 (t0) outliers start: 11 outliers final: 6 residues processed: 118 average time/residue: 0.8464 time to fit residues: 109.8921 Evaluate side-chains 119 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 0.0870 chunk 86 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 0.0000 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 0.0470 overall best weight: 0.2260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8798 Z= 0.137 Angle : 0.507 6.004 11964 Z= 0.247 Chirality : 0.039 0.191 1390 Planarity : 0.005 0.041 1396 Dihedral : 10.766 87.293 1852 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.93 % Allowed : 9.88 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.27), residues: 1014 helix: 2.30 (0.19), residues: 780 sheet: None (None), residues: 0 loop : 1.11 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 566 HIS 0.003 0.001 HIS B 109 PHE 0.014 0.001 PHE B 352 TYR 0.020 0.001 TYR A 226 ARG 0.002 0.000 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.934 Fit side-chains REVERT: A 1 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.3834 (mmm) REVERT: B 1 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.4705 (mmt) REVERT: B 150 MET cc_start: 0.9164 (tmm) cc_final: 0.8891 (ttt) REVERT: B 404 ASP cc_start: 0.8017 (t0) cc_final: 0.7773 (t0) REVERT: B 510 MET cc_start: 0.9037 (mtp) cc_final: 0.8713 (mtp) outliers start: 8 outliers final: 3 residues processed: 116 average time/residue: 0.8649 time to fit residues: 110.0931 Evaluate side-chains 111 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 80 optimal weight: 0.0870 chunk 8 optimal weight: 0.0570 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8798 Z= 0.166 Angle : 0.531 6.926 11964 Z= 0.257 Chirality : 0.041 0.180 1390 Planarity : 0.005 0.040 1396 Dihedral : 10.774 88.057 1852 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.70 % Allowed : 10.81 % Favored : 88.49 % 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: 3.02 (0.27), residues: 1014 helix: 2.30 (0.19), residues: 780 sheet: None (None), residues: 0 loop : 1.12 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 418 HIS 0.003 0.001 HIS B 109 PHE 0.015 0.001 PHE A 352 TYR 0.019 0.001 TYR A 226 ARG 0.001 0.000 ARG B 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.908 Fit side-chains REVERT: A 1 MET cc_start: 0.5886 (OUTLIER) cc_final: 0.3832 (mmm) REVERT: B 1 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.4650 (mmt) REVERT: B 150 MET cc_start: 0.9173 (tmm) cc_final: 0.8836 (ttt) REVERT: B 404 ASP cc_start: 0.8054 (t0) cc_final: 0.7808 (t0) outliers start: 6 outliers final: 4 residues processed: 113 average time/residue: 0.8462 time to fit residues: 105.0640 Evaluate side-chains 114 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 527 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.106896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.075273 restraints weight = 14813.408| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.03 r_work: 0.2824 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8798 Z= 0.191 Angle : 0.540 6.450 11964 Z= 0.264 Chirality : 0.041 0.182 1390 Planarity : 0.005 0.039 1396 Dihedral : 10.848 88.784 1852 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.81 % Allowed : 10.47 % Favored : 88.72 % 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: 2.93 (0.27), residues: 1014 helix: 2.23 (0.19), residues: 780 sheet: None (None), residues: 0 loop : 1.10 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 418 HIS 0.004 0.001 HIS B 109 PHE 0.015 0.001 PHE A 352 TYR 0.019 0.001 TYR B 226 ARG 0.001 0.000 ARG B 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3045.38 seconds wall clock time: 55 minutes 39.11 seconds (3339.11 seconds total)