Starting phenix.real_space_refine on Thu Jul 2 18:51:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7psm_13614/07_2026/7psm_13614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7psm_13614/07_2026/7psm_13614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7psm_13614/07_2026/7psm_13614.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7psm_13614/07_2026/7psm_13614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7psm_13614/07_2026/7psm_13614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7psm_13614/07_2026/7psm_13614.map" model { file = "/net/cci-nas-00/data/ceres_data/7psm_13614/07_2026/7psm_13614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7psm_13614/07_2026/7psm_13614.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.096 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 8 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 6038 2.51 5 N 1602 2.21 5 O 1710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9394 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "B" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 75 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 1.86, per 1000 atoms: 0.20 Number of scatterers: 9394 At special positions: 0 Unit cell: (82.467, 77.469, 141.61, 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 34 16.00 P 8 15.00 Mg 2 11.99 O 1710 8.00 N 1602 7.00 C 6038 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: 2.54 Conformation dependent library (CDL) restraints added in 307.8 milliseconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 68.0% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 93 through 100 Processing helix chain 'A' and resid 104 through 140 removed outlier: 3.878A pdb=" N ARG A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Proline residue: A 129 - end of helix removed outlier: 3.598A pdb=" N MET A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 201 removed outlier: 3.996A pdb=" N THR A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 208 removed outlier: 3.680A pdb=" N HIS A 206 " --> pdb=" O ASP A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 235 Processing helix chain 'A' and resid 235 through 254 removed outlier: 3.828A pdb=" N PHE A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 304 removed outlier: 5.370A pdb=" N HIS A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE A 283 " --> pdb=" O TRP A 279 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 284 " --> pdb=" O ARG A 280 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 313 through 367 removed outlier: 4.052A pdb=" N SER A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 367 " --> pdb=" O THR A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 396 removed outlier: 3.508A pdb=" N LEU A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Proline residue: A 388 - end of helix removed outlier: 3.635A pdb=" N TYR A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'A' and resid 538 through 547 Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.962A pdb=" N GLY A 570 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 604 through 617 Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.756A pdb=" N GLU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 104 through 140 removed outlier: 3.819A pdb=" N ARG B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Proline residue: B 129 - end of helix removed outlier: 3.593A pdb=" N MET B 139 " --> pdb=" O THR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 201 removed outlier: 4.022A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 201 " --> pdb=" O HIS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 208 removed outlier: 3.681A pdb=" N HIS B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 235 Processing helix chain 'B' and resid 235 through 254 removed outlier: 3.811A pdb=" N PHE B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 304 removed outlier: 5.371A pdb=" N HIS B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE B 283 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 313 through 367 removed outlier: 4.052A pdb=" N SER B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 367 " --> pdb=" O THR B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 396 removed outlier: 3.502A pdb=" N LEU B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Proline residue: B 388 - end of helix removed outlier: 3.620A pdb=" N TYR B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 414 Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'B' and resid 538 through 547 Processing helix chain 'B' and resid 551 through 558 Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.958A pdb=" N GLY B 570 " --> pdb=" O GLY B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 590 Processing helix chain 'B' and resid 604 through 617 Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 665 through 676 removed outlier: 3.791A pdb=" N GLU B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 455 through 459 removed outlier: 5.533A pdb=" N ALA A 455 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL A 441 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N SER A 490 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 514 through 515 removed outlier: 6.010A pdb=" N VAL A 515 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N PHE A 596 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR A 465 " --> pdb=" O TYR A 628 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 455 through 459 removed outlier: 5.548A pdb=" N ALA B 455 " --> pdb=" O ASN B 440 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL B 441 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER B 490 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 514 through 515 removed outlier: 6.019A pdb=" N VAL B 515 " --> pdb=" O ASP B 597 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE B 596 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR B 465 " --> pdb=" O TYR B 628 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1824 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: 1.32 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 1496 1.29 - 1.42: 2402 1.42 - 1.55: 5589 1.55 - 1.68: 13 1.68 - 1.81: 68 Bond restraints: 9568 Sorted by residual: bond pdb=" C3' ANP B 701 " pdb=" C4' ANP B 701 " ideal model delta sigma weight residual 1.532 1.308 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C3' ANP A 701 " pdb=" C4' ANP A 701 " ideal model delta sigma weight residual 1.532 1.309 0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C4' ANP A 701 " pdb=" O4' ANP A 701 " ideal model delta sigma weight residual 1.431 1.623 -0.192 2.00e-02 2.50e+03 9.21e+01 bond pdb=" C4' ANP B 701 " pdb=" O4' ANP B 701 " ideal model delta sigma weight residual 1.431 1.623 -0.192 2.00e-02 2.50e+03 9.19e+01 bond pdb=" C6 ANP B 701 " pdb=" N6 ANP B 701 " ideal model delta sigma weight residual 1.340 1.474 -0.134 2.00e-02 2.50e+03 4.51e+01 ... (remaining 9563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 12644 2.86 - 5.72: 220 5.72 - 8.57: 52 8.57 - 11.43: 22 11.43 - 14.29: 4 Bond angle restraints: 12942 Sorted by residual: angle pdb=" C1' ANP A 701 " pdb=" N9 ANP A 701 " pdb=" C4 ANP A 701 " ideal model delta sigma weight residual 125.38 111.09 14.29 3.00e+00 1.11e-01 2.27e+01 angle pdb=" C1' ANP B 701 " pdb=" N9 ANP B 701 " pdb=" C4 ANP B 701 " ideal model delta sigma weight residual 125.38 111.10 14.28 3.00e+00 1.11e-01 2.27e+01 angle pdb=" O3 LOP A 703 " pdb=" P1 LOP A 703 " pdb=" O4 LOP A 703 " ideal model delta sigma weight residual 120.67 108.32 12.35 3.00e+00 1.11e-01 1.69e+01 angle pdb=" O3 LOP B 703 " pdb=" P1 LOP B 703 " pdb=" O4 LOP B 703 " ideal model delta sigma weight residual 120.67 108.34 12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C ARG B 188 " pdb=" CA ARG B 188 " pdb=" CB ARG B 188 " ideal model delta sigma weight residual 110.88 104.55 6.33 1.57e+00 4.06e-01 1.63e+01 ... (remaining 12937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.22: 5393 26.22 - 52.44: 280 52.44 - 78.66: 39 78.66 - 104.89: 0 104.89 - 131.11: 2 Dihedral angle restraints: 5714 sinusoidal: 2330 harmonic: 3384 Sorted by residual: dihedral pdb=" O1A ANP A 701 " pdb=" O3A ANP A 701 " pdb=" PA ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sinusoidal sigma weight residual 83.11 -48.00 131.11 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" O1A ANP B 701 " pdb=" O3A ANP B 701 " pdb=" PA ANP B 701 " pdb=" PB ANP B 701 " ideal model delta sinusoidal sigma weight residual 83.11 -47.95 131.06 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" C VAL B 128 " pdb=" N VAL B 128 " pdb=" CA VAL B 128 " pdb=" CB VAL B 128 " ideal model delta harmonic sigma weight residual -122.00 -131.14 9.14 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 5711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1127 0.054 - 0.109: 300 0.109 - 0.163: 57 0.163 - 0.217: 6 0.217 - 0.272: 4 Chirality restraints: 1494 Sorted by residual: chirality pdb=" CB ILE B 419 " pdb=" CA ILE B 419 " pdb=" CG1 ILE B 419 " pdb=" CG2 ILE B 419 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB ILE A 419 " pdb=" CA ILE A 419 " pdb=" CG1 ILE A 419 " pdb=" CG2 ILE A 419 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL B 128 " pdb=" CA VAL B 128 " pdb=" CG1 VAL B 128 " pdb=" CG2 VAL B 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1491 not shown) Planarity restraints: 1616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET B 594 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C MET B 594 " 0.034 2.00e-02 2.50e+03 pdb=" O MET B 594 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE B 595 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 594 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00 pdb=" C MET A 594 " -0.034 2.00e-02 2.50e+03 pdb=" O MET A 594 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE A 595 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 376 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C VAL A 376 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL A 376 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU A 377 " 0.011 2.00e-02 2.50e+03 ... (remaining 1613 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 104 2.64 - 3.21: 8213 3.21 - 3.77: 14658 3.77 - 4.34: 18956 4.34 - 4.90: 32089 Nonbonded interactions: 74020 Sorted by model distance: nonbonded pdb=" O2B ANP A 701 " pdb="MG MG A 702 " model vdw 2.078 2.170 nonbonded pdb=" O2B ANP B 701 " pdb="MG MG B 702 " model vdw 2.079 2.170 nonbonded pdb=" O3G ANP A 701 " pdb="MG MG A 702 " model vdw 2.093 2.170 nonbonded pdb=" O3G ANP B 701 " pdb="MG MG B 702 " model vdw 2.095 2.170 nonbonded pdb=" OE1 GLN B 517 " pdb="MG MG B 702 " model vdw 2.117 2.170 ... (remaining 74015 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.00 max=1.00 mean=0.95 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: 2.670 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.330 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.008 0.224 9568 Z= 0.384 Angle : 1.044 14.289 12942 Z= 0.511 Chirality : 0.052 0.272 1494 Planarity : 0.006 0.045 1616 Dihedral : 15.591 131.107 3530 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.20), residues: 1166 helix: -1.52 (0.14), residues: 788 sheet: -3.68 (0.43), residues: 82 loop : -3.03 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 534 TYR 0.011 0.002 TYR B 321 PHE 0.016 0.002 PHE A 179 TRP 0.004 0.001 TRP B 100 HIS 0.005 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00762 / 0.38 ( 9568) covalent geometry : angle 1.04402 / 0.51 (12942) hydrogen bonds : bond 0.11054 / 6.87 ( 612) hydrogen bonds : angle 5.33065 / 3.80 ( 1824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.241 Fit side-chains REVERT: A 202 ASP cc_start: 0.7765 (p0) cc_final: 0.7452 (p0) REVERT: A 284 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7570 (ttp80) REVERT: A 350 PHE cc_start: 0.7901 (t80) cc_final: 0.7439 (t80) REVERT: A 383 PHE cc_start: 0.8428 (t80) cc_final: 0.8197 (t80) REVERT: A 628 TYR cc_start: 0.8668 (m-80) cc_final: 0.8279 (m-10) REVERT: B 100 TRP cc_start: 0.7942 (t-100) cc_final: 0.7645 (t60) REVERT: B 202 ASP cc_start: 0.7785 (p0) cc_final: 0.7464 (p0) REVERT: B 284 ARG cc_start: 0.7827 (ttp80) cc_final: 0.7575 (ttp80) REVERT: B 350 PHE cc_start: 0.7915 (t80) cc_final: 0.7448 (t80) REVERT: B 383 PHE cc_start: 0.8424 (t80) cc_final: 0.8181 (t80) REVERT: B 628 TYR cc_start: 0.8673 (m-80) cc_final: 0.8284 (m-10) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.0985 time to fit residues: 24.0660 Evaluate side-chains 135 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.0070 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN A 235 HIS A 347 ASN B 127 GLN B 235 HIS B 347 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.096264 restraints weight = 13389.293| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.68 r_work: 0.3074 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9568 Z= 0.175 Angle : 0.565 6.937 12942 Z= 0.298 Chirality : 0.040 0.149 1494 Planarity : 0.004 0.032 1616 Dihedral : 10.101 154.239 1332 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.10 % Allowed : 15.67 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.23), residues: 1166 helix: 0.44 (0.18), residues: 788 sheet: -2.61 (0.59), residues: 48 loop : -2.94 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 165 TYR 0.008 0.001 TYR B 321 PHE 0.010 0.001 PHE B 195 TRP 0.004 0.001 TRP B 463 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 9568) covalent geometry : angle 0.56547 / 0.30 (12942) hydrogen bonds : bond 0.05410 / 3.54 ( 612) hydrogen bonds : angle 4.08089 / 2.91 ( 1824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.296 Fit side-chains REVERT: A 284 ARG cc_start: 0.7975 (ttp80) cc_final: 0.7731 (ttp80) REVERT: A 350 PHE cc_start: 0.8146 (t80) cc_final: 0.7574 (t80) REVERT: A 383 PHE cc_start: 0.8583 (t80) cc_final: 0.8346 (t80) REVERT: A 396 TYR cc_start: 0.7529 (m-80) cc_final: 0.7244 (m-80) REVERT: A 616 ARG cc_start: 0.8222 (ttp-110) cc_final: 0.7965 (ttp80) REVERT: A 628 TYR cc_start: 0.8860 (m-80) cc_final: 0.8516 (m-10) REVERT: B 284 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7724 (ttp80) REVERT: B 350 PHE cc_start: 0.8131 (t80) cc_final: 0.7555 (t80) REVERT: B 359 TYR cc_start: 0.8627 (t80) cc_final: 0.8412 (t80) REVERT: B 383 PHE cc_start: 0.8575 (t80) cc_final: 0.8313 (t80) REVERT: B 396 TYR cc_start: 0.7559 (m-80) cc_final: 0.7266 (m-80) REVERT: B 616 ARG cc_start: 0.8172 (ttp-110) cc_final: 0.7914 (ttp80) REVERT: B 628 TYR cc_start: 0.8880 (m-80) cc_final: 0.8594 (m-10) outliers start: 21 outliers final: 14 residues processed: 164 average time/residue: 0.0867 time to fit residues: 19.8755 Evaluate side-chains 156 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 565 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 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 = 0.3566 r_free = 0.3566 target = 0.123648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.099798 restraints weight = 13304.813| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.68 r_work: 0.3122 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9568 Z= 0.130 Angle : 0.506 6.690 12942 Z= 0.267 Chirality : 0.039 0.145 1494 Planarity : 0.003 0.033 1616 Dihedral : 9.555 153.839 1332 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.70 % Allowed : 18.56 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.25), residues: 1166 helix: 1.36 (0.18), residues: 784 sheet: -2.48 (0.60), residues: 48 loop : -2.82 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 280 TYR 0.012 0.001 TYR A 269 PHE 0.027 0.001 PHE A 234 TRP 0.004 0.001 TRP A 463 HIS 0.003 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 9568) covalent geometry : angle 0.50593 / 0.27 (12942) hydrogen bonds : bond 0.04874 / 3.16 ( 612) hydrogen bonds : angle 3.85942 / 2.74 ( 1824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 0.292 Fit side-chains REVERT: A 284 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7656 (ttp80) REVERT: A 326 MET cc_start: 0.7888 (mmt) cc_final: 0.7581 (mmt) REVERT: A 350 PHE cc_start: 0.8029 (t80) cc_final: 0.7475 (t80) REVERT: A 383 PHE cc_start: 0.8525 (t80) cc_final: 0.8275 (t80) REVERT: A 616 ARG cc_start: 0.8175 (ttp-110) cc_final: 0.7913 (ttp80) REVERT: A 628 TYR cc_start: 0.8806 (m-80) cc_final: 0.8525 (m-10) REVERT: A 632 ARG cc_start: 0.7480 (mtp180) cc_final: 0.7255 (mtm-85) REVERT: B 232 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7381 (mmm) REVERT: B 284 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7671 (ttp80) REVERT: B 326 MET cc_start: 0.7874 (mmt) cc_final: 0.7565 (mmt) REVERT: B 350 PHE cc_start: 0.8080 (t80) cc_final: 0.7524 (t80) REVERT: B 359 TYR cc_start: 0.8520 (t80) cc_final: 0.8245 (t80) REVERT: B 383 PHE cc_start: 0.8508 (t80) cc_final: 0.8256 (t80) REVERT: B 628 TYR cc_start: 0.8843 (m-80) cc_final: 0.8554 (m-10) outliers start: 17 outliers final: 12 residues processed: 166 average time/residue: 0.0859 time to fit residues: 19.5859 Evaluate side-chains 149 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 60 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 0.0050 chunk 114 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 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 = 0.3550 r_free = 0.3550 target = 0.122085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098356 restraints weight = 13563.083| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.66 r_work: 0.3088 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9568 Z= 0.154 Angle : 0.524 6.635 12942 Z= 0.276 Chirality : 0.040 0.147 1494 Planarity : 0.003 0.032 1616 Dihedral : 9.149 148.309 1332 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.89 % Allowed : 19.46 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.25), residues: 1166 helix: 1.69 (0.19), residues: 784 sheet: -2.54 (0.61), residues: 48 loop : -2.74 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 616 TYR 0.013 0.001 TYR A 269 PHE 0.016 0.001 PHE B 234 TRP 0.004 0.001 TRP A 463 HIS 0.011 0.002 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 9568) covalent geometry : angle 0.52403 / 0.28 (12942) hydrogen bonds : bond 0.04948 / 3.24 ( 612) hydrogen bonds : angle 3.81874 / 2.72 ( 1824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.347 Fit side-chains REVERT: A 235 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.6651 (m170) REVERT: A 284 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7380 (tpp-160) REVERT: A 350 PHE cc_start: 0.8098 (t80) cc_final: 0.7554 (t80) REVERT: A 383 PHE cc_start: 0.8532 (t80) cc_final: 0.8287 (t80) REVERT: A 396 TYR cc_start: 0.7680 (m-80) cc_final: 0.6799 (m-80) REVERT: A 572 MET cc_start: 0.8673 (mmm) cc_final: 0.8164 (mmt) REVERT: A 616 ARG cc_start: 0.8221 (ttp-110) cc_final: 0.7970 (ttp80) REVERT: A 628 TYR cc_start: 0.8821 (m-80) cc_final: 0.8504 (m-10) REVERT: A 632 ARG cc_start: 0.7577 (mtp180) cc_final: 0.7370 (mtm-85) REVERT: B 199 MET cc_start: 0.8564 (tpp) cc_final: 0.8231 (mpp) REVERT: B 232 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7462 (mmm) REVERT: B 284 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7366 (tpp-160) REVERT: B 347 ASN cc_start: 0.8395 (t0) cc_final: 0.8189 (t0) REVERT: B 350 PHE cc_start: 0.8118 (t80) cc_final: 0.7569 (t80) REVERT: B 383 PHE cc_start: 0.8534 (t80) cc_final: 0.8266 (t80) outliers start: 29 outliers final: 19 residues processed: 167 average time/residue: 0.0884 time to fit residues: 20.5594 Evaluate side-chains 155 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 0.0170 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 347 ASN B 347 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098806 restraints weight = 13496.173| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.61 r_work: 0.3101 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9568 Z= 0.149 Angle : 0.521 6.576 12942 Z= 0.275 Chirality : 0.040 0.145 1494 Planarity : 0.003 0.031 1616 Dihedral : 8.853 146.108 1332 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.29 % Allowed : 20.46 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.25), residues: 1166 helix: 1.88 (0.19), residues: 784 sheet: -2.53 (0.61), residues: 48 loop : -2.67 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 616 TYR 0.013 0.001 TYR A 316 PHE 0.021 0.001 PHE A 234 TRP 0.004 0.001 TRP B 463 HIS 0.010 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9568) covalent geometry : angle 0.52134 / 0.27 (12942) hydrogen bonds : bond 0.04872 / 3.18 ( 612) hydrogen bonds : angle 3.80360 / 2.71 ( 1824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 0.361 Fit side-chains REVERT: A 199 MET cc_start: 0.8610 (tpp) cc_final: 0.8265 (mpp) REVERT: A 235 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6612 (m170) REVERT: A 284 ARG cc_start: 0.7921 (ttp80) cc_final: 0.7692 (ttp80) REVERT: A 359 TYR cc_start: 0.8512 (t80) cc_final: 0.8241 (t80) REVERT: A 383 PHE cc_start: 0.8517 (t80) cc_final: 0.8244 (t80) REVERT: A 396 TYR cc_start: 0.7771 (m-80) cc_final: 0.6830 (m-80) REVERT: A 616 ARG cc_start: 0.8231 (ttp-110) cc_final: 0.7982 (ttp80) REVERT: A 628 TYR cc_start: 0.8816 (m-80) cc_final: 0.8506 (m-10) REVERT: A 632 ARG cc_start: 0.7590 (mtp180) cc_final: 0.7385 (mtm-85) REVERT: B 232 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7517 (mmm) REVERT: B 235 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.6600 (m170) REVERT: B 284 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7688 (ttp80) REVERT: B 347 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.8210 (t0) REVERT: B 350 PHE cc_start: 0.8125 (t80) cc_final: 0.7554 (t80) REVERT: B 383 PHE cc_start: 0.8512 (t80) cc_final: 0.8245 (t80) REVERT: B 396 TYR cc_start: 0.7746 (m-80) cc_final: 0.6824 (m-80) outliers start: 33 outliers final: 23 residues processed: 170 average time/residue: 0.0873 time to fit residues: 20.9241 Evaluate side-chains 160 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 565 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 3.9990 chunk 101 optimal weight: 0.0570 chunk 111 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.124234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100665 restraints weight = 13464.123| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.63 r_work: 0.3126 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9568 Z= 0.121 Angle : 0.503 6.593 12942 Z= 0.265 Chirality : 0.039 0.142 1494 Planarity : 0.003 0.030 1616 Dihedral : 8.626 147.520 1332 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.40 % Allowed : 21.76 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.25), residues: 1166 helix: 2.07 (0.19), residues: 784 sheet: -2.44 (0.61), residues: 48 loop : -2.57 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 280 TYR 0.013 0.001 TYR A 316 PHE 0.020 0.001 PHE A 234 TRP 0.004 0.001 TRP A 463 HIS 0.009 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 9568) covalent geometry : angle 0.50304 / 0.27 (12942) hydrogen bonds : bond 0.04629 / 3.02 ( 612) hydrogen bonds : angle 3.72604 / 2.65 ( 1824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.313 Fit side-chains REVERT: A 199 MET cc_start: 0.8489 (tpp) cc_final: 0.8233 (mpp) REVERT: A 235 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6621 (m170) REVERT: A 284 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7676 (ttp80) REVERT: A 396 TYR cc_start: 0.7825 (m-80) cc_final: 0.6979 (m-80) REVERT: A 572 MET cc_start: 0.8669 (mmm) cc_final: 0.8174 (mmt) REVERT: A 616 ARG cc_start: 0.8214 (ttp-110) cc_final: 0.7969 (ttp80) REVERT: A 628 TYR cc_start: 0.8827 (m-80) cc_final: 0.8557 (m-10) REVERT: A 632 ARG cc_start: 0.7475 (mtp180) cc_final: 0.7261 (mtm-85) REVERT: B 199 MET cc_start: 0.8586 (tpp) cc_final: 0.8177 (mpp) REVERT: B 232 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7519 (mmm) REVERT: B 235 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.6707 (m170) REVERT: B 284 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7665 (ttp80) REVERT: B 347 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8246 (t0) REVERT: B 350 PHE cc_start: 0.8097 (t80) cc_final: 0.7631 (t80) REVERT: B 396 TYR cc_start: 0.7762 (m-80) cc_final: 0.7001 (m-80) REVERT: B 572 MET cc_start: 0.8704 (mmm) cc_final: 0.8189 (mmt) outliers start: 24 outliers final: 15 residues processed: 161 average time/residue: 0.0945 time to fit residues: 20.9964 Evaluate side-chains 150 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 85 optimal weight: 0.0970 chunk 3 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 104 optimal weight: 0.0870 chunk 107 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 95 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.101841 restraints weight = 13264.471| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.68 r_work: 0.3166 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9568 Z= 0.107 Angle : 0.489 7.308 12942 Z= 0.258 Chirality : 0.039 0.142 1494 Planarity : 0.003 0.030 1616 Dihedral : 8.209 145.320 1332 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.89 % Allowed : 21.56 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1166 helix: 2.30 (0.18), residues: 780 sheet: -2.16 (0.61), residues: 48 loop : -2.39 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 424 TYR 0.014 0.001 TYR B 316 PHE 0.017 0.001 PHE A 234 TRP 0.004 0.000 TRP B 463 HIS 0.009 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 ( 9568) covalent geometry : angle 0.48856 / 0.26 (12942) hydrogen bonds : bond 0.04310 / 2.80 ( 612) hydrogen bonds : angle 3.63643 / 2.59 ( 1824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.348 Fit side-chains REVERT: A 199 MET cc_start: 0.8446 (tpp) cc_final: 0.8243 (mpp) REVERT: A 235 HIS cc_start: 0.7067 (OUTLIER) cc_final: 0.6668 (m170) REVERT: A 284 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7632 (ttp80) REVERT: A 396 TYR cc_start: 0.7857 (m-80) cc_final: 0.7087 (m-80) REVERT: A 572 MET cc_start: 0.8619 (mmm) cc_final: 0.8063 (mmt) REVERT: A 616 ARG cc_start: 0.8200 (ttp-110) cc_final: 0.7953 (ttp80) REVERT: A 628 TYR cc_start: 0.8813 (m-80) cc_final: 0.8539 (m-10) REVERT: A 632 ARG cc_start: 0.7378 (mtp180) cc_final: 0.7172 (mtm-85) REVERT: B 199 MET cc_start: 0.8448 (tpp) cc_final: 0.8146 (mpp) REVERT: B 232 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7437 (mmm) REVERT: B 235 HIS cc_start: 0.7249 (OUTLIER) cc_final: 0.6707 (m170) REVERT: B 284 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7635 (ttp80) REVERT: B 396 TYR cc_start: 0.7684 (m-80) cc_final: 0.7003 (m-80) REVERT: B 628 TYR cc_start: 0.8837 (m-80) cc_final: 0.8555 (m-10) outliers start: 29 outliers final: 20 residues processed: 164 average time/residue: 0.0923 time to fit residues: 21.0580 Evaluate side-chains 160 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 538 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 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 = 0.3556 r_free = 0.3556 target = 0.123215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.099281 restraints weight = 13504.302| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.68 r_work: 0.3122 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9568 Z= 0.146 Angle : 0.534 11.648 12942 Z= 0.279 Chirality : 0.040 0.148 1494 Planarity : 0.003 0.030 1616 Dihedral : 7.893 139.575 1332 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.19 % Allowed : 22.16 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.25), residues: 1166 helix: 2.23 (0.19), residues: 780 sheet: -1.81 (0.61), residues: 48 loop : -2.34 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 424 TYR 0.013 0.001 TYR A 316 PHE 0.017 0.001 PHE A 234 TRP 0.006 0.000 TRP A 463 HIS 0.009 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 9568) covalent geometry : angle 0.53412 / 0.28 (12942) hydrogen bonds : bond 0.04743 / 3.12 ( 612) hydrogen bonds : angle 3.78642 / 2.70 ( 1824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.313 Fit side-chains REVERT: A 235 HIS cc_start: 0.7208 (OUTLIER) cc_final: 0.6744 (m170) REVERT: A 284 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7656 (ttp80) REVERT: A 359 TYR cc_start: 0.8485 (t80) cc_final: 0.8266 (t80) REVERT: A 616 ARG cc_start: 0.8208 (ttp-110) cc_final: 0.7962 (ttp80) REVERT: A 628 TYR cc_start: 0.8833 (m-80) cc_final: 0.8571 (m-10) REVERT: A 632 ARG cc_start: 0.7528 (mtp180) cc_final: 0.7295 (mtm-85) REVERT: B 199 MET cc_start: 0.8513 (tpp) cc_final: 0.8198 (mpp) REVERT: B 232 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7524 (mmm) REVERT: B 235 HIS cc_start: 0.7249 (OUTLIER) cc_final: 0.6696 (m170) REVERT: B 284 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7649 (ttp80) REVERT: B 628 TYR cc_start: 0.8843 (m-80) cc_final: 0.8583 (m-10) outliers start: 32 outliers final: 25 residues processed: 162 average time/residue: 0.0879 time to fit residues: 19.8490 Evaluate side-chains 158 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 30 optimal weight: 0.0870 chunk 70 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 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 = 0.3592 r_free = 0.3592 target = 0.125685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101807 restraints weight = 13368.809| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.69 r_work: 0.3167 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 9568 Z= 0.114 Angle : 0.521 12.131 12942 Z= 0.270 Chirality : 0.039 0.142 1494 Planarity : 0.003 0.031 1616 Dihedral : 7.708 139.397 1332 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.69 % Allowed : 22.46 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.25), residues: 1166 helix: 2.33 (0.19), residues: 786 sheet: -1.53 (0.62), residues: 48 loop : -2.52 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 424 TYR 0.017 0.001 TYR A 316 PHE 0.018 0.001 PHE A 234 TRP 0.004 0.000 TRP B 463 HIS 0.009 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 9568) covalent geometry : angle 0.52116 / 0.27 (12942) hydrogen bonds : bond 0.04419 / 2.90 ( 612) hydrogen bonds : angle 3.67814 / 2.63 ( 1824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.219 Fit side-chains REVERT: A 235 HIS cc_start: 0.6911 (OUTLIER) cc_final: 0.6688 (m170) REVERT: A 284 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7631 (ttp80) REVERT: A 616 ARG cc_start: 0.8198 (ttp-110) cc_final: 0.7954 (ttp80) REVERT: A 628 TYR cc_start: 0.8801 (m-80) cc_final: 0.8515 (m-10) REVERT: B 199 MET cc_start: 0.8466 (tpp) cc_final: 0.8211 (mpp) REVERT: B 232 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7468 (mmm) REVERT: B 235 HIS cc_start: 0.7046 (OUTLIER) cc_final: 0.6631 (m170) REVERT: B 284 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7644 (ttp80) REVERT: B 396 TYR cc_start: 0.7696 (m-80) cc_final: 0.7088 (m-80) REVERT: B 628 TYR cc_start: 0.8824 (m-80) cc_final: 0.8548 (m-10) outliers start: 27 outliers final: 24 residues processed: 163 average time/residue: 0.0959 time to fit residues: 21.6354 Evaluate side-chains 160 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 51 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 0.2980 chunk 84 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 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 = 0.3576 r_free = 0.3576 target = 0.124316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100423 restraints weight = 13355.993| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.68 r_work: 0.3147 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9568 Z= 0.131 Angle : 0.551 11.795 12942 Z= 0.286 Chirality : 0.040 0.145 1494 Planarity : 0.003 0.031 1616 Dihedral : 7.551 135.571 1332 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.99 % Allowed : 22.85 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.25), residues: 1166 helix: 2.38 (0.19), residues: 780 sheet: -1.46 (0.63), residues: 48 loop : -2.18 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 424 TYR 0.016 0.001 TYR B 316 PHE 0.020 0.001 PHE A 234 TRP 0.005 0.000 TRP B 463 HIS 0.008 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9568) covalent geometry : angle 0.55073 / 0.29 (12942) hydrogen bonds : bond 0.04553 / 3.00 ( 612) hydrogen bonds : angle 3.73464 / 2.67 ( 1824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.347 Fit side-chains REVERT: A 235 HIS cc_start: 0.6913 (OUTLIER) cc_final: 0.6672 (m170) REVERT: A 284 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7646 (ttp80) REVERT: A 396 TYR cc_start: 0.7631 (m-80) cc_final: 0.6857 (m-80) REVERT: A 616 ARG cc_start: 0.8199 (ttp-110) cc_final: 0.7952 (ttp80) REVERT: A 628 TYR cc_start: 0.8808 (m-80) cc_final: 0.8529 (m-10) REVERT: B 199 MET cc_start: 0.8489 (tpp) cc_final: 0.8231 (mpp) REVERT: B 232 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7495 (mmm) REVERT: B 235 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6661 (m170) REVERT: B 284 ARG cc_start: 0.7904 (ttp80) cc_final: 0.7657 (ttp80) REVERT: B 350 PHE cc_start: 0.7744 (t80) cc_final: 0.7496 (t80) REVERT: B 396 TYR cc_start: 0.7654 (m-80) cc_final: 0.7027 (m-80) REVERT: B 628 TYR cc_start: 0.8835 (m-80) cc_final: 0.8557 (m-10) outliers start: 30 outliers final: 25 residues processed: 161 average time/residue: 0.0886 time to fit residues: 20.1661 Evaluate side-chains 165 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 232 MET Chi-restraints excluded: chain B residue 235 HIS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 653 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 78 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 90 optimal weight: 0.0570 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 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 = 0.3592 r_free = 0.3592 target = 0.125716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101879 restraints weight = 13302.599| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.69 r_work: 0.3164 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9568 Z= 0.118 Angle : 0.538 12.157 12942 Z= 0.280 Chirality : 0.039 0.142 1494 Planarity : 0.003 0.030 1616 Dihedral : 7.493 135.464 1332 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.99 % Allowed : 23.15 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.25), residues: 1166 helix: 2.38 (0.19), residues: 786 sheet: -1.31 (0.64), residues: 48 loop : -2.40 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 424 TYR 0.011 0.001 TYR B 269 PHE 0.017 0.001 PHE A 234 TRP 0.004 0.000 TRP B 463 HIS 0.008 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9568) covalent geometry : angle 0.53786 / 0.28 (12942) hydrogen bonds : bond 0.04421 / 2.91 ( 612) hydrogen bonds : angle 3.68974 / 2.64 ( 1824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1654.61 seconds wall clock time: 29 minutes 10.36 seconds (1750.36 seconds total)