Starting phenix.real_space_refine on Sun Jul 27 22:30:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7psm_13614/07_2025/7psm_13614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7psm_13614/07_2025/7psm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7psm_13614/07_2025/7psm_13614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7psm_13614/07_2025/7psm_13614.map" model { file = "/net/cci-nas-00/data/ceres_data/7psm_13614/07_2025/7psm_13614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7psm_13614/07_2025/7psm_13614.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.096 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.24, per 1000 atoms: 0.66 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: 2.26 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.82 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: 2.60 Time building geometry restraints manager: 2.65 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: 5401 26.22 - 52.44: 318 52.44 - 78.66: 61 78.66 - 104.89: 8 104.89 - 131.11: 2 Dihedral angle restraints: 5790 sinusoidal: 2406 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 5787 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: 0.04 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.500 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 17.189 131.107 3606 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (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 TRP 0.004 0.001 TRP B 100 HIS 0.005 0.001 HIS B 235 PHE 0.016 0.002 PHE A 179 TYR 0.011 0.002 TYR B 321 ARG 0.002 0.000 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.11054 ( 612) hydrogen bonds : angle 5.33065 ( 1824) covalent geometry : bond 0.00762 ( 9568) covalent geometry : angle 1.04402 (12942) *********************** 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 : 0.841 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: 0.7646 (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: 0.8182 (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: 0.3053 time to fit residues: 74.1009 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 : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3544 r_free = 0.3544 target = 0.121977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098090 restraints weight = 13254.855| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.69 r_work: 0.3097 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1195 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= 0.141 Angle : 0.545 6.808 12942 Z= 0.284 Chirality : 0.039 0.146 1494 Planarity : 0.004 0.032 1616 Dihedral : 12.934 156.376 1408 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.90 % Allowed : 15.37 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1166 helix: 0.51 (0.18), residues: 790 sheet: -2.55 (0.60), residues: 48 loop : -2.90 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 463 HIS 0.003 0.001 HIS B 197 PHE 0.013 0.001 PHE B 195 TYR 0.007 0.001 TYR B 316 ARG 0.004 0.000 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.05114 ( 612) hydrogen bonds : angle 3.99400 ( 1824) covalent geometry : bond 0.00312 ( 9568) covalent geometry : angle 0.54465 (12942) *********************** 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 174 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 1.193 Fit side-chains REVERT: A 199 MET cc_start: 0.8728 (tpp) cc_final: 0.8376 (mpp) REVERT: A 284 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7711 (ttp80) REVERT: A 350 PHE cc_start: 0.8112 (t80) cc_final: 0.7552 (t80) REVERT: A 383 PHE cc_start: 0.8546 (t80) cc_final: 0.8312 (t80) REVERT: A 572 MET cc_start: 0.8846 (mmm) cc_final: 0.8503 (mmm) REVERT: A 616 ARG cc_start: 0.8215 (ttp-110) cc_final: 0.7960 (ttp80) REVERT: A 628 TYR cc_start: 0.8853 (m-80) cc_final: 0.8545 (m-10) REVERT: B 199 MET cc_start: 0.8723 (tpp) cc_final: 0.8363 (mpp) REVERT: B 284 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7770 (ttp80) REVERT: B 350 PHE cc_start: 0.8115 (t80) cc_final: 0.7540 (t80) REVERT: B 359 TYR cc_start: 0.8596 (t80) cc_final: 0.8365 (t80) REVERT: B 383 PHE cc_start: 0.8549 (t80) cc_final: 0.8306 (t80) REVERT: B 396 TYR cc_start: 0.7517 (m-80) cc_final: 0.7229 (m-80) REVERT: B 616 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7915 (ttp80) REVERT: B 628 TYR cc_start: 0.8880 (m-80) cc_final: 0.8574 (m-10) outliers start: 19 outliers final: 12 residues processed: 165 average time/residue: 0.3026 time to fit residues: 68.7097 Evaluate side-chains 159 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.428 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3587 r_free = 0.3587 target = 0.126086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102609 restraints weight = 13389.190| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.65 r_work: 0.3132 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9568 Z= 0.128 Angle : 0.503 6.674 12942 Z= 0.264 Chirality : 0.039 0.146 1494 Planarity : 0.003 0.033 1616 Dihedral : 11.002 159.944 1408 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.50 % Allowed : 19.26 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.25), residues: 1166 helix: 1.43 (0.18), residues: 784 sheet: -2.37 (0.61), residues: 48 loop : -2.81 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 463 HIS 0.002 0.001 HIS A 197 PHE 0.027 0.001 PHE A 234 TYR 0.012 0.001 TYR A 269 ARG 0.003 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.04774 ( 612) hydrogen bonds : angle 3.78802 ( 1824) covalent geometry : bond 0.00276 ( 9568) covalent geometry : angle 0.50336 (12942) *********************** 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 162 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.943 Fit side-chains REVERT: A 199 MET cc_start: 0.8677 (tpp) cc_final: 0.8406 (mpp) REVERT: A 284 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7721 (ttp80) REVERT: A 326 MET cc_start: 0.8005 (mmt) cc_final: 0.7713 (mmt) REVERT: A 350 PHE cc_start: 0.8114 (t80) cc_final: 0.7608 (t80) REVERT: A 572 MET cc_start: 0.8756 (mmm) cc_final: 0.8311 (mmm) REVERT: A 616 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7969 (ttp80) REVERT: A 628 TYR cc_start: 0.8843 (m-80) cc_final: 0.8554 (m-10) REVERT: B 199 MET cc_start: 0.8645 (tpp) cc_final: 0.8400 (mpp) REVERT: B 232 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7446 (mmm) REVERT: B 284 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7715 (ttp80) REVERT: B 326 MET cc_start: 0.8008 (mmt) cc_final: 0.7717 (mmt) REVERT: B 350 PHE cc_start: 0.8113 (t80) cc_final: 0.7598 (t80) REVERT: B 359 TYR cc_start: 0.8547 (t80) cc_final: 0.8271 (t80) REVERT: B 572 MET cc_start: 0.8810 (mmm) cc_final: 0.8507 (mmm) REVERT: B 616 ARG cc_start: 0.8176 (ttp-110) cc_final: 0.7916 (ttp80) REVERT: B 628 TYR cc_start: 0.8878 (m-80) cc_final: 0.8583 (m-10) outliers start: 15 outliers final: 12 residues processed: 156 average time/residue: 0.2467 time to fit residues: 53.2298 Evaluate side-chains 148 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 0 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 92 optimal weight: 0.0000 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.125429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.101955 restraints weight = 13476.821| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.64 r_work: 0.3123 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1651 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= 0.134 Angle : 0.499 6.590 12942 Z= 0.263 Chirality : 0.039 0.146 1494 Planarity : 0.003 0.032 1616 Dihedral : 10.646 160.140 1408 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.40 % Allowed : 20.06 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1166 helix: 1.83 (0.19), residues: 780 sheet: -2.44 (0.61), residues: 48 loop : -2.69 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 463 HIS 0.009 0.001 HIS A 235 PHE 0.014 0.001 PHE B 234 TYR 0.010 0.001 TYR B 269 ARG 0.003 0.000 ARG B 424 Details of bonding type rmsd hydrogen bonds : bond 0.04701 ( 612) hydrogen bonds : angle 3.72158 ( 1824) covalent geometry : bond 0.00298 ( 9568) covalent geometry : angle 0.49857 (12942) *********************** 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 174 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.948 Fit side-chains REVERT: A 199 MET cc_start: 0.8652 (tpp) cc_final: 0.8393 (mpp) REVERT: A 235 HIS cc_start: 0.7321 (OUTLIER) cc_final: 0.6672 (m170) REVERT: A 284 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7710 (ttp80) REVERT: A 350 PHE cc_start: 0.8114 (t80) cc_final: 0.7612 (t80) REVERT: A 396 TYR cc_start: 0.7738 (m-80) cc_final: 0.6802 (m-80) REVERT: A 445 TYR cc_start: 0.8398 (m-80) cc_final: 0.8165 (m-80) REVERT: A 572 MET cc_start: 0.8685 (mmm) cc_final: 0.8307 (tpt) REVERT: A 616 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7967 (ttp80) REVERT: A 628 TYR cc_start: 0.8847 (m-80) cc_final: 0.8519 (m-10) REVERT: B 199 MET cc_start: 0.8604 (tpp) cc_final: 0.8352 (mpp) REVERT: B 232 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7482 (mmm) REVERT: B 284 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7705 (ttp80) REVERT: B 350 PHE cc_start: 0.8104 (t80) cc_final: 0.7595 (t80) REVERT: B 359 TYR cc_start: 0.8541 (t80) cc_final: 0.8288 (t80) REVERT: B 572 MET cc_start: 0.8723 (mmm) cc_final: 0.8522 (mmt) REVERT: B 628 TYR cc_start: 0.8863 (m-80) cc_final: 0.8586 (m-10) outliers start: 24 outliers final: 16 residues processed: 167 average time/residue: 0.2345 time to fit residues: 53.3695 Evaluate side-chains 152 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 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 653 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 26 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3575 r_free = 0.3575 target = 0.124090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.099978 restraints weight = 13271.963| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.67 r_work: 0.3143 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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= 0.123 Angle : 0.501 8.210 12942 Z= 0.263 Chirality : 0.039 0.143 1494 Planarity : 0.003 0.031 1616 Dihedral : 10.216 160.496 1408 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.89 % Allowed : 20.46 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.25), residues: 1166 helix: 2.09 (0.19), residues: 780 sheet: -2.40 (0.61), residues: 48 loop : -2.58 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 463 HIS 0.009 0.001 HIS B 235 PHE 0.017 0.001 PHE A 234 TYR 0.010 0.001 TYR B 269 ARG 0.006 0.000 ARG B 616 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 612) hydrogen bonds : angle 3.67593 ( 1824) covalent geometry : bond 0.00267 ( 9568) covalent geometry : angle 0.50100 (12942) *********************** 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 176 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.942 Fit side-chains REVERT: A 235 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6580 (m170) REVERT: A 284 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7661 (ttp80) REVERT: A 350 PHE cc_start: 0.8006 (t80) cc_final: 0.7521 (t80) REVERT: A 396 TYR cc_start: 0.7798 (m-80) cc_final: 0.6863 (m-80) REVERT: A 445 TYR cc_start: 0.8319 (m-80) cc_final: 0.8102 (m-80) REVERT: A 572 MET cc_start: 0.8600 (mmm) cc_final: 0.8328 (mmm) REVERT: A 616 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7971 (ttp80) REVERT: A 628 TYR cc_start: 0.8811 (m-80) cc_final: 0.8504 (m-10) REVERT: B 232 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7436 (mmm) REVERT: B 235 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6519 (m170) REVERT: B 284 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7658 (ttp80) REVERT: B 350 PHE cc_start: 0.8021 (t80) cc_final: 0.7512 (t80) REVERT: B 359 TYR cc_start: 0.8494 (t80) cc_final: 0.8254 (t80) REVERT: B 396 TYR cc_start: 0.7700 (m-80) cc_final: 0.6769 (m-80) REVERT: B 445 TYR cc_start: 0.8330 (m-80) cc_final: 0.8078 (m-80) REVERT: B 628 TYR cc_start: 0.8842 (m-80) cc_final: 0.8521 (m-10) outliers start: 29 outliers final: 17 residues processed: 168 average time/residue: 0.2229 time to fit residues: 51.7606 Evaluate side-chains 154 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 A residue 538 THR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 72 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 0.0670 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3570 r_free = 0.3570 target = 0.123740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.099758 restraints weight = 13315.109| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.66 r_work: 0.3140 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1907 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= 0.129 Angle : 0.509 7.382 12942 Z= 0.267 Chirality : 0.039 0.144 1494 Planarity : 0.003 0.030 1616 Dihedral : 9.881 158.902 1408 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.79 % Allowed : 20.76 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1166 helix: 2.19 (0.19), residues: 780 sheet: -2.19 (0.61), residues: 48 loop : -2.49 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 100 HIS 0.009 0.001 HIS B 235 PHE 0.019 0.001 PHE A 234 TYR 0.011 0.001 TYR A 269 ARG 0.005 0.000 ARG B 616 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 612) hydrogen bonds : angle 3.71815 ( 1824) covalent geometry : bond 0.00287 ( 9568) covalent geometry : angle 0.50903 (12942) *********************** 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 174 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 1.119 Fit side-chains REVERT: A 235 HIS cc_start: 0.7080 (OUTLIER) cc_final: 0.6556 (m170) REVERT: A 284 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7664 (ttp80) REVERT: A 396 TYR cc_start: 0.7756 (m-80) cc_final: 0.6878 (m-80) REVERT: A 572 MET cc_start: 0.8585 (mmm) cc_final: 0.8283 (mmm) REVERT: A 616 ARG cc_start: 0.8199 (ttp-110) cc_final: 0.7951 (ttp80) REVERT: A 628 TYR cc_start: 0.8809 (m-80) cc_final: 0.8506 (m-10) REVERT: A 659 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7962 (mm) REVERT: B 232 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7470 (mmm) REVERT: B 235 HIS cc_start: 0.7315 (OUTLIER) cc_final: 0.6621 (m170) REVERT: B 284 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7645 (ttp80) REVERT: B 359 TYR cc_start: 0.8494 (t80) cc_final: 0.8260 (t80) REVERT: B 396 TYR cc_start: 0.7769 (m-80) cc_final: 0.6929 (m-80) REVERT: B 572 MET cc_start: 0.8753 (mmt) cc_final: 0.8473 (mmt) REVERT: B 628 TYR cc_start: 0.8829 (m-80) cc_final: 0.8525 (m-10) outliers start: 28 outliers final: 20 residues processed: 167 average time/residue: 0.2330 time to fit residues: 53.7044 Evaluate side-chains 157 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 A residue 458 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 659 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 110 optimal weight: 0.0770 chunk 17 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3591 r_free = 0.3591 target = 0.125583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101515 restraints weight = 13297.784| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.68 r_work: 0.3163 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9568 Z= 0.114 Angle : 0.500 7.823 12942 Z= 0.264 Chirality : 0.039 0.142 1494 Planarity : 0.003 0.030 1616 Dihedral : 9.434 157.957 1408 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.69 % Allowed : 21.16 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.31 (0.25), residues: 1166 helix: 2.33 (0.19), residues: 780 sheet: -1.95 (0.62), residues: 48 loop : -2.39 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 463 HIS 0.009 0.001 HIS A 235 PHE 0.017 0.001 PHE A 234 TYR 0.010 0.001 TYR A 269 ARG 0.006 0.000 ARG B 424 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 612) hydrogen bonds : angle 3.65706 ( 1824) covalent geometry : bond 0.00246 ( 9568) covalent geometry : angle 0.50018 (12942) *********************** 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 164 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.029 Fit side-chains REVERT: A 199 MET cc_start: 0.8555 (tpp) cc_final: 0.8116 (mpp) REVERT: A 235 HIS cc_start: 0.7090 (OUTLIER) cc_final: 0.6687 (m170) REVERT: A 284 ARG cc_start: 0.7870 (ttp80) cc_final: 0.7637 (ttp80) REVERT: A 396 TYR cc_start: 0.7842 (m-80) cc_final: 0.7069 (m-80) REVERT: A 572 MET cc_start: 0.8543 (mmm) cc_final: 0.8247 (mmm) REVERT: A 616 ARG cc_start: 0.8201 (ttp-110) cc_final: 0.7958 (ttp80) REVERT: A 628 TYR cc_start: 0.8800 (m-80) cc_final: 0.8491 (m-10) REVERT: A 659 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7965 (mm) REVERT: B 199 MET cc_start: 0.8542 (tpp) cc_final: 0.8104 (mpp) REVERT: B 232 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7501 (mmm) REVERT: B 235 HIS cc_start: 0.7167 (OUTLIER) cc_final: 0.6667 (m170) REVERT: B 284 ARG cc_start: 0.7879 (ttp80) cc_final: 0.7638 (ttp80) REVERT: B 359 TYR cc_start: 0.8457 (t80) cc_final: 0.8202 (t80) REVERT: B 572 MET cc_start: 0.8766 (mmt) cc_final: 0.8478 (mmt) REVERT: B 628 TYR cc_start: 0.8828 (m-80) cc_final: 0.8566 (m-10) outliers start: 27 outliers final: 22 residues processed: 157 average time/residue: 0.2413 time to fit residues: 52.2877 Evaluate side-chains 156 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 653 GLU Chi-restraints excluded: chain A residue 659 LEU 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 239 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3575 r_free = 0.3575 target = 0.124412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.100166 restraints weight = 13609.884| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.72 r_work: 0.3144 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9568 Z= 0.128 Angle : 0.508 6.823 12942 Z= 0.268 Chirality : 0.040 0.144 1494 Planarity : 0.003 0.029 1616 Dihedral : 9.327 156.551 1408 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.79 % Allowed : 21.16 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.25), residues: 1166 helix: 2.33 (0.18), residues: 780 sheet: -1.90 (0.62), residues: 48 loop : -2.27 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 463 HIS 0.008 0.001 HIS B 235 PHE 0.018 0.001 PHE A 234 TYR 0.009 0.001 TYR A 269 ARG 0.007 0.000 ARG B 424 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 612) hydrogen bonds : angle 3.69067 ( 1824) covalent geometry : bond 0.00288 ( 9568) covalent geometry : angle 0.50822 (12942) *********************** 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 166 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.998 Fit side-chains REVERT: A 199 MET cc_start: 0.8570 (tpp) cc_final: 0.8152 (mpp) REVERT: A 235 HIS cc_start: 0.7102 (OUTLIER) cc_final: 0.6736 (m170) REVERT: A 284 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7668 (ttp80) REVERT: A 572 MET cc_start: 0.8542 (mmm) cc_final: 0.8209 (mmm) REVERT: A 616 ARG cc_start: 0.8204 (ttp-110) cc_final: 0.7959 (ttp80) REVERT: A 628 TYR cc_start: 0.8797 (m-80) cc_final: 0.8487 (m-10) REVERT: B 199 MET cc_start: 0.8573 (tpp) cc_final: 0.8155 (mpp) REVERT: B 232 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7535 (mmm) REVERT: B 235 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.6658 (m170) REVERT: B 284 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7653 (ttp80) REVERT: B 572 MET cc_start: 0.8739 (mmt) cc_final: 0.8409 (mmt) REVERT: B 628 TYR cc_start: 0.8816 (m-80) cc_final: 0.8560 (m-10) outliers start: 28 outliers final: 23 residues processed: 158 average time/residue: 0.2303 time to fit residues: 49.8432 Evaluate side-chains 160 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 0.0980 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 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 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 = 0.3565 r_free = 0.3565 target = 0.123481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.099373 restraints weight = 13388.975| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.68 r_work: 0.3132 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9568 Z= 0.142 Angle : 0.533 7.825 12942 Z= 0.282 Chirality : 0.040 0.147 1494 Planarity : 0.003 0.031 1616 Dihedral : 9.333 156.189 1408 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.59 % Allowed : 22.06 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1166 helix: 2.29 (0.18), residues: 780 sheet: -1.87 (0.63), residues: 48 loop : -2.21 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 463 HIS 0.008 0.001 HIS A 235 PHE 0.017 0.001 PHE B 234 TYR 0.010 0.001 TYR B 269 ARG 0.007 0.000 ARG B 424 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 612) hydrogen bonds : angle 3.76909 ( 1824) covalent geometry : bond 0.00326 ( 9568) covalent geometry : angle 0.53350 (12942) *********************** 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 166 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 1.096 Fit side-chains REVERT: A 199 MET cc_start: 0.8628 (tpp) cc_final: 0.8207 (mpp) REVERT: A 235 HIS cc_start: 0.7093 (OUTLIER) cc_final: 0.6725 (m170) REVERT: A 284 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7659 (ttp80) REVERT: A 359 TYR cc_start: 0.8489 (t80) cc_final: 0.8234 (t80) REVERT: A 572 MET cc_start: 0.8506 (mmm) cc_final: 0.8204 (mmm) REVERT: A 616 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7956 (ttp80) REVERT: A 628 TYR cc_start: 0.8788 (m-80) cc_final: 0.8487 (m-10) REVERT: B 199 MET cc_start: 0.8620 (tpp) cc_final: 0.8199 (mpp) REVERT: B 232 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7491 (mmm) REVERT: B 235 HIS cc_start: 0.7188 (OUTLIER) cc_final: 0.6653 (m170) REVERT: B 284 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7646 (ttp80) REVERT: B 396 TYR cc_start: 0.7607 (m-80) cc_final: 0.6950 (m-80) REVERT: B 572 MET cc_start: 0.8702 (mmt) cc_final: 0.8350 (mmt) REVERT: B 628 TYR cc_start: 0.8817 (m-80) cc_final: 0.8506 (m-10) outliers start: 26 outliers final: 23 residues processed: 158 average time/residue: 0.2464 time to fit residues: 54.0217 Evaluate side-chains 160 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 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 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 79 optimal weight: 0.3980 chunk 108 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 25 optimal weight: 0.0030 chunk 14 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3605 r_free = 0.3605 target = 0.126886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102639 restraints weight = 13421.456| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.72 r_work: 0.3178 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2283 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= 0.113 Angle : 0.518 8.561 12942 Z= 0.274 Chirality : 0.039 0.141 1494 Planarity : 0.003 0.030 1616 Dihedral : 9.061 154.450 1408 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.50 % Allowed : 22.16 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.25), residues: 1166 helix: 2.36 (0.19), residues: 786 sheet: -1.74 (0.63), residues: 48 loop : -2.42 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 463 HIS 0.008 0.001 HIS A 235 PHE 0.015 0.001 PHE A 234 TYR 0.010 0.001 TYR A 269 ARG 0.007 0.000 ARG B 424 Details of bonding type rmsd hydrogen bonds : bond 0.04301 ( 612) hydrogen bonds : angle 3.65246 ( 1824) covalent geometry : bond 0.00243 ( 9568) covalent geometry : angle 0.51765 (12942) ********************** 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 166 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.045 Fit side-chains REVERT: A 199 MET cc_start: 0.8612 (tpp) cc_final: 0.8221 (mpp) REVERT: A 235 HIS cc_start: 0.6891 (OUTLIER) cc_final: 0.6644 (m170) REVERT: A 284 ARG cc_start: 0.7876 (ttp80) cc_final: 0.7638 (ttp80) REVERT: A 396 TYR cc_start: 0.7719 (m-80) cc_final: 0.6963 (m-80) REVERT: A 572 MET cc_start: 0.8503 (mmm) cc_final: 0.8186 (mmm) REVERT: A 616 ARG cc_start: 0.8193 (ttp-110) cc_final: 0.7955 (ttp80) REVERT: A 628 TYR cc_start: 0.8791 (m-80) cc_final: 0.8531 (m-10) REVERT: B 199 MET cc_start: 0.8596 (tpp) cc_final: 0.8237 (mpp) REVERT: B 232 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7476 (mmm) REVERT: B 235 HIS cc_start: 0.7008 (OUTLIER) cc_final: 0.6608 (m170) REVERT: B 284 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7643 (ttp80) REVERT: B 572 MET cc_start: 0.8739 (mmt) cc_final: 0.8226 (mmt) REVERT: B 628 TYR cc_start: 0.8803 (m-80) cc_final: 0.8523 (m-10) outliers start: 25 outliers final: 19 residues processed: 158 average time/residue: 0.2326 time to fit residues: 51.2915 Evaluate side-chains 156 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 235 HIS Chi-restraints excluded: chain A residue 239 ILE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3587 r_free = 0.3587 target = 0.125378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101286 restraints weight = 13409.480| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.70 r_work: 0.3158 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2295 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= 0.124 Angle : 0.528 9.302 12942 Z= 0.277 Chirality : 0.040 0.144 1494 Planarity : 0.003 0.030 1616 Dihedral : 9.023 153.218 1408 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.59 % Allowed : 22.26 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.54 (0.25), residues: 1166 helix: 2.41 (0.19), residues: 780 sheet: -1.52 (0.63), residues: 48 loop : -2.09 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 463 HIS 0.008 0.001 HIS A 235 PHE 0.014 0.001 PHE B 234 TYR 0.010 0.001 TYR A 269 ARG 0.007 0.000 ARG B 424 Details of bonding type rmsd hydrogen bonds : bond 0.04427 ( 612) hydrogen bonds : angle 3.70666 ( 1824) covalent geometry : bond 0.00277 ( 9568) covalent geometry : angle 0.52824 (12942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4374.24 seconds wall clock time: 78 minutes 46.24 seconds (4726.24 seconds total)