Starting phenix.real_space_refine on Tue Dec 31 17:44:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iro_35681/12_2024/8iro_35681_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iro_35681/12_2024/8iro_35681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iro_35681/12_2024/8iro_35681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iro_35681/12_2024/8iro_35681.map" model { file = "/net/cci-nas-00/data/ceres_data/8iro_35681/12_2024/8iro_35681_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iro_35681/12_2024/8iro_35681_trim.cif" } resolution = 2.7 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= 0.007 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 52 5.16 5 C 5300 2.51 5 N 1316 2.21 5 O 1474 1.98 5 H 8208 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16350 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.90, per 1000 atoms: 0.48 Number of scatterers: 16350 At special positions: 0 Unit cell: (94.461, 108.077, 101.269, 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 52 16.00 O 1474 8.00 N 1316 7.00 C 5300 6.00 H 8208 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.04 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.04 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 4.70 Conformation dependent library (CDL) restraints added in 1.7 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 68.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 31 through 37 Processing helix chain 'B' and resid 39 through 43 Processing helix chain 'B' and resid 46 through 61 Processing helix chain 'B' and resid 62 through 74 removed outlier: 4.779A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 117 through 150 Processing helix chain 'B' and resid 159 through 169 removed outlier: 3.952A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 201 Processing helix chain 'B' and resid 203 through 209 removed outlier: 3.574A pdb=" N LEU B 207 " --> pdb=" O PHE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 232 removed outlier: 4.400A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 294 through 313 Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 355 removed outlier: 3.906A pdb=" N LYS B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 375 removed outlier: 4.341A pdb=" N ASN B 375 " --> pdb=" O SER B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 376 through 405 removed outlier: 3.718A pdb=" N TRP B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 435 Processing helix chain 'B' and resid 444 through 451 removed outlier: 4.049A pdb=" N GLY B 448 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 470 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 480 through 496 Proline residue: B 486 - end of helix Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.659A pdb=" N THR B 500 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 523 Proline residue: B 512 - end of helix removed outlier: 3.771A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 525 through 541 Processing helix chain 'B' and resid 541 through 554 Processing helix chain 'A' and resid 19 through 30 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 39 through 43 Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 62 through 74 removed outlier: 4.779A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 93 through 97 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 117 through 150 Processing helix chain 'A' and resid 159 through 169 removed outlier: 3.953A pdb=" N ALA A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.574A pdb=" N LEU A 207 " --> pdb=" O PHE A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 232 removed outlier: 4.399A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 294 through 313 Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.907A pdb=" N LYS A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 removed outlier: 4.340A pdb=" N ASN A 375 " --> pdb=" O SER A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 405 removed outlier: 3.717A pdb=" N TRP A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 435 Processing helix chain 'A' and resid 444 through 451 removed outlier: 4.049A pdb=" N GLY A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 480 through 496 Proline residue: A 486 - end of helix Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.659A pdb=" N THR A 500 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 523 Proline residue: A 512 - end of helix removed outlier: 3.770A pdb=" N MET A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 525 through 541 Processing helix chain 'A' and resid 541 through 554 Processing sheet with id=AA1, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AA3, first strand: chain 'B' and resid 241 through 242 Processing sheet with id=AA4, first strand: chain 'B' and resid 274 through 275 removed outlier: 3.692A pdb=" N SER B 274 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 274 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 287 removed outlier: 3.933A pdb=" N SER B 261 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 261 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 158 Processing sheet with id=AA8, first strand: chain 'A' and resid 241 through 242 512 hydrogen bonds defined for protein. 1452 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: 6.32 Time building geometry restraints manager: 5.49 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: 8204 1.03 - 1.23: 39 1.23 - 1.42: 3387 1.42 - 1.62: 4822 1.62 - 1.82: 84 Bond restraints: 16536 Sorted by residual: bond pdb=" C6 ZEA B 701 " pdb=" N10 ZEA B 701 " ideal model delta sigma weight residual 1.336 1.464 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C6 ZEA A 701 " pdb=" N10 ZEA A 701 " ideal model delta sigma weight residual 1.336 1.464 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 1.502 1.589 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 1.502 1.588 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.73e+00 ... (remaining 16531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.22: 29910 8.22 - 16.45: 6 16.45 - 24.67: 0 24.67 - 32.90: 0 32.90 - 41.12: 6 Bond angle restraints: 29922 Sorted by residual: angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C15 ZEA B 701 " ideal model delta sigma weight residual 125.58 166.70 -41.12 3.00e+00 1.11e-01 1.88e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 125.58 166.66 -41.08 3.00e+00 1.11e-01 1.88e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 121.92 87.45 34.47 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 121.92 87.48 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C14 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 112.50 79.23 33.27 3.00e+00 1.11e-01 1.23e+02 ... (remaining 29917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.96: 7423 24.96 - 49.93: 328 49.93 - 74.89: 123 74.89 - 99.86: 6 99.86 - 124.82: 2 Dihedral angle restraints: 7882 sinusoidal: 4248 harmonic: 3634 Sorted by residual: dihedral pdb=" CA VAL A 484 " pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta harmonic sigma weight residual 180.00 141.09 38.91 0 5.00e+00 4.00e-02 6.05e+01 dihedral pdb=" CA VAL B 484 " pdb=" C VAL B 484 " pdb=" N GLY B 485 " pdb=" CA GLY B 485 " ideal model delta harmonic sigma weight residual 180.00 141.10 38.90 0 5.00e+00 4.00e-02 6.05e+01 dihedral pdb=" CA PHE A 332 " pdb=" C PHE A 332 " pdb=" N ARG A 333 " pdb=" CA ARG A 333 " ideal model delta harmonic sigma weight residual 180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 7879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1303 0.097 - 0.194: 49 0.194 - 0.291: 3 0.291 - 0.388: 0 0.388 - 0.486: 1 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 270 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.89 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 270 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR A 250 " pdb=" CA THR A 250 " pdb=" OG1 THR A 250 " pdb=" CG2 THR A 250 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1353 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 270 " -0.091 2.00e-02 2.50e+03 6.88e-02 7.09e+01 pdb=" CG ASN A 270 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 270 " 0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN A 270 " 0.073 2.00e-02 2.50e+03 pdb="HD21 ASN A 270 " 0.045 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO A 487 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO B 487 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.035 5.00e-02 4.00e+02 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 440 2.13 - 2.74: 30686 2.74 - 3.36: 50422 3.36 - 3.98: 64783 3.98 - 4.60: 101898 Nonbonded interactions: 248229 Sorted by model distance: nonbonded pdb="HD22 ASN B 67 " pdb=" OG1 THR B 135 " model vdw 1.507 2.450 nonbonded pdb="HD22 ASN A 67 " pdb=" OG1 THR A 135 " model vdw 1.507 2.450 nonbonded pdb="HH22 ARG B 333 " pdb=" OD1 ASP B 347 " model vdw 1.550 2.450 nonbonded pdb="HH22 ARG A 333 " pdb=" OD1 ASP A 347 " model vdw 1.550 2.450 nonbonded pdb=" O PHE B 419 " pdb=" HG SER B 423 " model vdw 1.553 2.450 ... (remaining 248224 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' 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: 0.790 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: 0.290 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.260 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:12.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 : 0.006 0.128 8328 Z= 0.369 Angle : 1.088 41.124 11334 Z= 0.454 Chirality : 0.045 0.486 1356 Planarity : 0.005 0.062 1400 Dihedral : 13.581 124.823 2938 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1076 helix: 1.28 (0.21), residues: 664 sheet: -4.84 (0.53), residues: 20 loop : -0.47 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.002 0.001 HIS B 350 PHE 0.012 0.002 PHE A 414 TYR 0.013 0.002 TYR B 524 ARG 0.002 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7851 (m-30) cc_final: 0.7624 (m-30) REVERT: B 440 THR cc_start: 0.8584 (p) cc_final: 0.8325 (t) REVERT: A 390 ASP cc_start: 0.7851 (m-30) cc_final: 0.7631 (m-30) REVERT: A 440 THR cc_start: 0.8581 (p) cc_final: 0.8315 (t) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 2.1037 time to fit residues: 207.4937 Evaluate side-chains 75 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8344 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8328 Z= 0.203 Angle : 1.004 37.108 11334 Z= 0.409 Chirality : 0.040 0.156 1356 Planarity : 0.005 0.061 1400 Dihedral : 8.513 108.479 1236 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.58 % Allowed : 5.71 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1076 helix: 1.45 (0.20), residues: 670 sheet: -4.47 (0.64), residues: 20 loop : -0.64 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.003 0.001 HIS B 360 PHE 0.011 0.001 PHE B 414 TYR 0.009 0.001 TYR B 399 ARG 0.002 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7789 (m-30) cc_final: 0.7556 (m-30) REVERT: B 440 THR cc_start: 0.8588 (p) cc_final: 0.8147 (t) REVERT: B 494 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7273 (mtp) REVERT: A 390 ASP cc_start: 0.7765 (m-30) cc_final: 0.7550 (m-30) REVERT: A 440 THR cc_start: 0.8606 (p) cc_final: 0.8127 (t) REVERT: A 494 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7283 (mtp) outliers start: 5 outliers final: 2 residues processed: 82 average time/residue: 2.3088 time to fit residues: 204.5443 Evaluate side-chains 84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 78 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8333 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8328 Z= 0.194 Angle : 0.987 36.854 11334 Z= 0.392 Chirality : 0.039 0.166 1356 Planarity : 0.005 0.060 1400 Dihedral : 7.615 96.409 1236 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.65 % Rotamer: Outliers : 0.82 % Allowed : 6.64 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.05 (0.26), residues: 1076 helix: 1.65 (0.20), residues: 670 sheet: -4.49 (0.62), residues: 20 loop : -0.68 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 482 HIS 0.001 0.001 HIS B 350 PHE 0.010 0.001 PHE B 414 TYR 0.008 0.001 TYR B 388 ARG 0.002 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7780 (m-30) cc_final: 0.7538 (m-30) REVERT: B 440 THR cc_start: 0.8584 (p) cc_final: 0.8097 (t) REVERT: A 390 ASP cc_start: 0.7761 (m-30) cc_final: 0.7518 (m-30) REVERT: A 440 THR cc_start: 0.8576 (p) cc_final: 0.8087 (t) outliers start: 7 outliers final: 0 residues processed: 88 average time/residue: 2.1862 time to fit residues: 208.0462 Evaluate side-chains 81 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8328 Z= 0.211 Angle : 0.990 37.063 11334 Z= 0.395 Chirality : 0.039 0.165 1356 Planarity : 0.005 0.060 1400 Dihedral : 7.168 85.909 1236 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.35 % Favored : 96.47 % Rotamer: Outliers : 1.05 % Allowed : 7.81 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.03 (0.26), residues: 1076 helix: 1.64 (0.20), residues: 670 sheet: -4.46 (0.66), residues: 20 loop : -0.70 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.002 0.001 HIS A 360 PHE 0.010 0.001 PHE B 414 TYR 0.009 0.001 TYR B 388 ARG 0.001 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7764 (m-30) cc_final: 0.7514 (m-30) REVERT: B 440 THR cc_start: 0.8564 (p) cc_final: 0.8062 (t) REVERT: B 494 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7112 (mtp) REVERT: A 390 ASP cc_start: 0.7751 (m-30) cc_final: 0.7512 (m-30) REVERT: A 440 THR cc_start: 0.8565 (p) cc_final: 0.8055 (t) REVERT: A 494 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7117 (mtp) outliers start: 9 outliers final: 2 residues processed: 87 average time/residue: 2.2106 time to fit residues: 207.7002 Evaluate side-chains 84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.1980 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8328 Z= 0.292 Angle : 1.015 37.459 11334 Z= 0.412 Chirality : 0.041 0.159 1356 Planarity : 0.005 0.060 1400 Dihedral : 6.540 63.933 1236 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.44 % Favored : 96.38 % Rotamer: Outliers : 1.63 % Allowed : 8.62 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.25), residues: 1076 helix: 1.47 (0.20), residues: 670 sheet: -4.41 (0.64), residues: 20 loop : -0.79 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 298 HIS 0.003 0.001 HIS B 360 PHE 0.011 0.002 PHE A 414 TYR 0.010 0.002 TYR B 388 ARG 0.002 0.000 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7770 (m-30) cc_final: 0.7551 (m-30) REVERT: B 440 THR cc_start: 0.8627 (p) cc_final: 0.8070 (t) REVERT: B 451 GLU cc_start: 0.7901 (tp30) cc_final: 0.7408 (mp0) REVERT: B 494 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7048 (mtp) REVERT: A 390 ASP cc_start: 0.7753 (m-30) cc_final: 0.7529 (m-30) REVERT: A 440 THR cc_start: 0.8611 (p) cc_final: 0.8053 (t) REVERT: A 494 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7065 (mtp) outliers start: 14 outliers final: 6 residues processed: 87 average time/residue: 2.1387 time to fit residues: 201.5974 Evaluate side-chains 85 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8328 Z= 0.267 Angle : 1.002 37.407 11334 Z= 0.404 Chirality : 0.040 0.158 1356 Planarity : 0.005 0.060 1400 Dihedral : 5.811 41.155 1236 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.72 % Favored : 96.10 % Rotamer: Outliers : 1.75 % Allowed : 8.74 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1076 helix: 1.48 (0.20), residues: 670 sheet: -4.52 (0.60), residues: 20 loop : -0.75 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 380 HIS 0.003 0.001 HIS B 360 PHE 0.011 0.002 PHE B 414 TYR 0.010 0.002 TYR B 388 ARG 0.002 0.000 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7754 (m-30) cc_final: 0.7523 (m-30) REVERT: B 440 THR cc_start: 0.8608 (p) cc_final: 0.8040 (t) REVERT: B 494 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7057 (mtp) REVERT: A 390 ASP cc_start: 0.7748 (m-30) cc_final: 0.7528 (m-30) REVERT: A 440 THR cc_start: 0.8609 (p) cc_final: 0.8031 (t) REVERT: A 494 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7045 (mtp) outliers start: 15 outliers final: 6 residues processed: 88 average time/residue: 2.1690 time to fit residues: 207.1144 Evaluate side-chains 83 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8328 Z= 0.180 Angle : 0.983 37.152 11334 Z= 0.392 Chirality : 0.039 0.173 1356 Planarity : 0.005 0.060 1400 Dihedral : 5.420 39.301 1236 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.81 % Favored : 96.00 % Rotamer: Outliers : 0.58 % Allowed : 10.84 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.07 (0.26), residues: 1076 helix: 1.66 (0.20), residues: 670 sheet: -4.49 (0.63), residues: 20 loop : -0.66 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 380 HIS 0.001 0.001 HIS A 350 PHE 0.011 0.001 PHE A 414 TYR 0.008 0.001 TYR B 388 ARG 0.001 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 1.274 Fit side-chains REVERT: B 390 ASP cc_start: 0.7759 (m-30) cc_final: 0.7528 (m-30) REVERT: B 440 THR cc_start: 0.8575 (p) cc_final: 0.7993 (t) REVERT: B 494 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.6902 (mtp) REVERT: A 390 ASP cc_start: 0.7739 (m-30) cc_final: 0.7507 (m-30) REVERT: A 440 THR cc_start: 0.8560 (p) cc_final: 0.7981 (t) REVERT: A 494 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.6906 (mtp) outliers start: 5 outliers final: 0 residues processed: 84 average time/residue: 2.2704 time to fit residues: 205.8942 Evaluate side-chains 80 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8328 Z= 0.297 Angle : 1.007 37.454 11334 Z= 0.410 Chirality : 0.041 0.174 1356 Planarity : 0.005 0.061 1400 Dihedral : 5.509 41.437 1236 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.62 % Favored : 96.19 % Rotamer: Outliers : 1.40 % Allowed : 10.02 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1076 helix: 1.47 (0.20), residues: 670 sheet: -4.34 (0.67), residues: 20 loop : -0.66 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.003 0.001 HIS B 350 PHE 0.012 0.002 PHE B 414 TYR 0.010 0.002 TYR B 388 ARG 0.002 0.000 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7743 (m-30) cc_final: 0.7513 (m-30) REVERT: B 440 THR cc_start: 0.8597 (p) cc_final: 0.8007 (t) REVERT: B 494 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7014 (mtp) REVERT: A 162 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8252 (m) REVERT: A 390 ASP cc_start: 0.7736 (m-30) cc_final: 0.7504 (m-30) REVERT: A 440 THR cc_start: 0.8595 (p) cc_final: 0.8008 (t) REVERT: A 494 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7013 (mtp) outliers start: 12 outliers final: 5 residues processed: 82 average time/residue: 2.2749 time to fit residues: 201.5725 Evaluate side-chains 87 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 63 optimal weight: 0.0770 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8328 Z= 0.234 Angle : 0.993 37.275 11334 Z= 0.400 Chirality : 0.040 0.179 1356 Planarity : 0.005 0.061 1400 Dihedral : 5.425 40.249 1236 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.00 % Favored : 95.82 % Rotamer: Outliers : 0.58 % Allowed : 11.19 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1076 helix: 1.53 (0.20), residues: 670 sheet: -4.48 (0.63), residues: 20 loop : -0.63 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 380 HIS 0.002 0.001 HIS B 350 PHE 0.011 0.001 PHE A 414 TYR 0.009 0.001 TYR B 388 ARG 0.001 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 1.304 Fit side-chains REVERT: B 390 ASP cc_start: 0.7731 (m-30) cc_final: 0.7509 (m-30) REVERT: B 440 THR cc_start: 0.8581 (p) cc_final: 0.7983 (t) REVERT: A 160 MET cc_start: 0.8796 (tpt) cc_final: 0.8572 (tpt) REVERT: A 162 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8242 (m) REVERT: A 390 ASP cc_start: 0.7725 (m-30) cc_final: 0.7492 (m-30) REVERT: A 440 THR cc_start: 0.8571 (p) cc_final: 0.7998 (t) outliers start: 5 outliers final: 1 residues processed: 82 average time/residue: 2.2793 time to fit residues: 201.8976 Evaluate side-chains 80 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8328 Z= 0.189 Angle : 0.980 37.172 11334 Z= 0.390 Chirality : 0.039 0.184 1356 Planarity : 0.005 0.060 1400 Dihedral : 5.299 39.332 1236 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.00 % Favored : 95.82 % Rotamer: Outliers : 0.47 % Allowed : 11.42 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.11 (0.26), residues: 1076 helix: 1.65 (0.20), residues: 670 sheet: -4.39 (0.68), residues: 20 loop : -0.54 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 298 HIS 0.001 0.001 HIS A 350 PHE 0.011 0.001 PHE B 414 TYR 0.009 0.001 TYR B 418 ARG 0.001 0.000 ARG A 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 1.202 Fit side-chains REVERT: B 160 MET cc_start: 0.8820 (tpt) cc_final: 0.8575 (tpt) REVERT: B 390 ASP cc_start: 0.7753 (m-30) cc_final: 0.7525 (m-30) REVERT: A 390 ASP cc_start: 0.7741 (m-30) cc_final: 0.7508 (m-30) outliers start: 4 outliers final: 1 residues processed: 83 average time/residue: 2.2645 time to fit residues: 202.9718 Evaluate side-chains 81 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.120992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.098605 restraints weight = 25929.796| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.42 r_work: 0.2956 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8328 Z= 0.236 Angle : 0.989 37.203 11334 Z= 0.397 Chirality : 0.040 0.177 1356 Planarity : 0.005 0.060 1400 Dihedral : 5.359 40.509 1236 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.72 % Favored : 96.10 % Rotamer: Outliers : 0.70 % Allowed : 10.96 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.07 (0.26), residues: 1076 helix: 1.59 (0.20), residues: 670 sheet: -4.41 (0.67), residues: 20 loop : -0.52 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 482 HIS 0.002 0.001 HIS B 350 PHE 0.011 0.001 PHE A 414 TYR 0.009 0.001 TYR B 388 ARG 0.001 0.000 ARG A 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4930.65 seconds wall clock time: 88 minutes 7.95 seconds (5287.95 seconds total)