Starting phenix.real_space_refine on Wed Mar 4 01:13:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7psm_13614/03_2026/7psm_13614.cif Found real_map, /net/cci-nas-00/data/ceres_data/7psm_13614/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7psm_13614/03_2026/7psm_13614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7psm_13614/03_2026/7psm_13614.map" model { file = "/net/cci-nas-00/data/ceres_data/7psm_13614/03_2026/7psm_13614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7psm_13614/03_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-5986/lib/python3.9/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: 1.68, per 1000 atoms: 0.18 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: 0.72 Conformation dependent library (CDL) restraints added in 447.4 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: 0.26 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: 1.59 Time building geometry restraints manager: 0.97 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: 0.01 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: 2.860 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.960 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: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.660 ------------------------------------------------------------------------------- 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 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 covalent geometry : bond 0.00762 ( 9568) covalent geometry : angle 1.04402 (12942) hydrogen bonds : bond 0.11054 ( 612) hydrogen bonds : angle 5.33065 ( 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 : 0.334 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: 0.1158 time to fit residues: 28.0675 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 : 0.328 ------------------------------------------------------------------------------- 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... 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 = 0.3523 r_free = 0.3523 target = 0.120222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096348 restraints weight = 13368.826| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.68 r_work: 0.3101 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9568 Z= 0.177 Angle : 0.578 6.831 12942 Z= 0.301 Chirality : 0.041 0.149 1494 Planarity : 0.004 0.032 1616 Dihedral : 12.816 152.537 1408 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.10 % Allowed : 15.87 % Favored : 82.04 % 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: -0.91 (0.23), residues: 1166 helix: 0.48 (0.18), residues: 788 sheet: -2.61 (0.59), residues: 48 loop : -2.92 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 165 TYR 0.008 0.001 TYR B 321 PHE 0.010 0.001 PHE B 595 TRP 0.004 0.001 TRP A 463 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 9568) covalent geometry : angle 0.57771 (12942) hydrogen bonds : bond 0.05400 ( 612) hydrogen bonds : angle 4.05665 ( 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 174 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.337 Fit side-chains REVERT: A 199 MET cc_start: 0.8664 (tpp) cc_final: 0.8300 (mpp) REVERT: A 284 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7664 (ttp80) REVERT: A 350 PHE cc_start: 0.8077 (t80) cc_final: 0.7477 (t80) REVERT: A 383 PHE cc_start: 0.8544 (t80) cc_final: 0.8277 (t80) REVERT: A 396 TYR cc_start: 0.7540 (m-80) cc_final: 0.7261 (m-80) REVERT: A 572 MET cc_start: 0.8711 (mmm) cc_final: 0.8387 (mmm) REVERT: A 616 ARG cc_start: 0.8198 (ttp-110) cc_final: 0.7933 (ttp80) REVERT: A 628 TYR cc_start: 0.8814 (m-80) cc_final: 0.8500 (m-10) REVERT: B 199 MET cc_start: 0.8654 (tpp) cc_final: 0.8290 (mpp) REVERT: B 284 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7659 (ttp80) REVERT: B 350 PHE cc_start: 0.8069 (t80) cc_final: 0.7461 (t80) REVERT: B 359 TYR cc_start: 0.8576 (t80) cc_final: 0.8364 (t80) REVERT: B 383 PHE cc_start: 0.8534 (t80) cc_final: 0.8276 (t80) REVERT: B 396 TYR cc_start: 0.7588 (m-80) cc_final: 0.7301 (m-80) REVERT: B 572 MET cc_start: 0.8718 (mmm) cc_final: 0.8388 (mmm) REVERT: B 616 ARG cc_start: 0.8156 (ttp-110) cc_final: 0.7889 (ttp80) REVERT: B 628 TYR cc_start: 0.8831 (m-80) cc_final: 0.8514 (m-10) outliers start: 21 outliers final: 14 residues processed: 167 average time/residue: 0.0933 time to fit residues: 21.3659 Evaluate side-chains 157 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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: 0.9990 chunk 86 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.124768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101300 restraints weight = 13423.828| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.64 r_work: 0.3114 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1490 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= 0.139 Angle : 0.520 6.698 12942 Z= 0.272 Chirality : 0.040 0.147 1494 Planarity : 0.003 0.033 1616 Dihedral : 10.839 152.484 1408 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.60 % Allowed : 18.66 % 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: 0.04 (0.25), residues: 1166 helix: 1.32 (0.18), residues: 784 sheet: -2.46 (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 0.026 0.001 PHE A 234 TRP 0.004 0.001 TRP A 463 HIS 0.002 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9568) covalent geometry : angle 0.51995 (12942) hydrogen bonds : bond 0.04961 ( 612) hydrogen bonds : angle 3.86325 ( 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 165 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.375 Fit side-chains REVERT: A 199 MET cc_start: 0.8679 (tpp) cc_final: 0.8388 (mpp) REVERT: A 284 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7704 (ttp80) REVERT: A 350 PHE cc_start: 0.8085 (t80) cc_final: 0.7546 (t80) REVERT: A 383 PHE cc_start: 0.8537 (t80) cc_final: 0.8294 (t80) REVERT: A 572 MET cc_start: 0.8742 (mmm) cc_final: 0.8343 (mmm) REVERT: A 616 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.7985 (ttp80) REVERT: A 628 TYR cc_start: 0.8840 (m-80) cc_final: 0.8555 (m-10) REVERT: B 199 MET cc_start: 0.8647 (tpp) cc_final: 0.8376 (mpp) REVERT: B 232 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7459 (mmm) REVERT: B 284 ARG cc_start: 0.7968 (ttp80) cc_final: 0.7711 (ttp80) REVERT: B 350 PHE cc_start: 0.8136 (t80) cc_final: 0.7601 (t80) REVERT: B 359 TYR cc_start: 0.8551 (t80) cc_final: 0.8285 (t80) REVERT: B 383 PHE cc_start: 0.8540 (t80) cc_final: 0.8287 (t80) REVERT: B 572 MET cc_start: 0.8758 (mmm) cc_final: 0.8348 (mmm) REVERT: B 628 TYR cc_start: 0.8871 (m-80) cc_final: 0.8572 (m-10) outliers start: 16 outliers final: 14 residues processed: 160 average time/residue: 0.1047 time to fit residues: 22.8188 Evaluate side-chains 150 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 392 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 565 ILE 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: 0.5980 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 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 = 0.3585 r_free = 0.3585 target = 0.125750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102247 restraints weight = 13507.962| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.64 r_work: 0.3128 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9568 Z= 0.127 Angle : 0.505 6.593 12942 Z= 0.265 Chirality : 0.039 0.145 1494 Planarity : 0.003 0.032 1616 Dihedral : 10.315 152.201 1408 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.40 % Allowed : 19.66 % Favored : 77.94 % 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: 0.55 (0.25), residues: 1166 helix: 1.75 (0.19), residues: 784 sheet: -2.47 (0.61), residues: 48 loop : -2.71 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 616 TYR 0.012 0.001 TYR A 269 PHE 0.015 0.001 PHE B 234 TRP 0.003 0.001 TRP A 463 HIS 0.010 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9568) covalent geometry : angle 0.50543 (12942) hydrogen bonds : bond 0.04697 ( 612) hydrogen bonds : angle 3.73123 ( 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 177 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.333 Fit side-chains REVERT: A 199 MET cc_start: 0.8634 (tpp) cc_final: 0.8397 (mpp) REVERT: A 235 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6641 (m170) REVERT: A 284 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7709 (ttp80) REVERT: A 350 PHE cc_start: 0.8125 (t80) cc_final: 0.7610 (t80) REVERT: A 396 TYR cc_start: 0.7657 (m-80) cc_final: 0.6790 (m-80) REVERT: A 445 TYR cc_start: 0.8413 (m-80) cc_final: 0.8189 (m-80) REVERT: A 572 MET cc_start: 0.8691 (mmm) cc_final: 0.8332 (tpt) REVERT: A 616 ARG cc_start: 0.8208 (ttp-110) cc_final: 0.7966 (ttp80) REVERT: A 628 TYR cc_start: 0.8842 (m-80) cc_final: 0.8504 (m-10) REVERT: B 199 MET cc_start: 0.8611 (tpp) cc_final: 0.8376 (mpp) REVERT: B 232 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7502 (mmm) REVERT: B 235 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6692 (m170) REVERT: B 284 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7696 (ttp80) REVERT: B 350 PHE cc_start: 0.8127 (t80) cc_final: 0.7615 (t80) REVERT: B 359 TYR cc_start: 0.8542 (t80) cc_final: 0.8319 (t80) REVERT: B 396 TYR cc_start: 0.7688 (m-80) cc_final: 0.6765 (m-80) REVERT: B 445 TYR cc_start: 0.8426 (m-80) cc_final: 0.8162 (m-80) REVERT: B 572 MET cc_start: 0.8696 (mmm) cc_final: 0.8479 (mmm) REVERT: B 628 TYR cc_start: 0.8873 (m-80) cc_final: 0.8587 (m-10) outliers start: 24 outliers final: 15 residues processed: 170 average time/residue: 0.0925 time to fit residues: 21.7802 Evaluate side-chains 157 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.124970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.101488 restraints weight = 13533.243| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.62 r_work: 0.3117 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1782 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= 0.144 Angle : 0.522 6.572 12942 Z= 0.273 Chirality : 0.040 0.146 1494 Planarity : 0.003 0.031 1616 Dihedral : 9.989 148.514 1408 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.09 % Allowed : 19.96 % Favored : 76.95 % 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: 0.77 (0.25), residues: 1166 helix: 1.93 (0.19), residues: 784 sheet: -2.48 (0.61), residues: 48 loop : -2.62 (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 0.018 0.001 PHE B 234 TRP 0.004 0.001 TRP B 463 HIS 0.009 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9568) covalent geometry : angle 0.52199 (12942) hydrogen bonds : bond 0.04791 ( 612) hydrogen bonds : angle 3.76215 ( 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 178 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.329 Fit side-chains REVERT: A 235 HIS cc_start: 0.7185 (OUTLIER) cc_final: 0.6573 (m170) REVERT: A 284 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7723 (ttp80) REVERT: A 359 TYR cc_start: 0.8541 (t80) cc_final: 0.8294 (t80) REVERT: A 396 TYR cc_start: 0.7772 (m-80) cc_final: 0.6882 (m-80) REVERT: A 572 MET cc_start: 0.8656 (mmm) cc_final: 0.8412 (mmm) REVERT: A 616 ARG cc_start: 0.8208 (ttp-110) cc_final: 0.7964 (ttp80) REVERT: A 628 TYR cc_start: 0.8844 (m-80) cc_final: 0.8523 (m-10) REVERT: B 232 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7551 (mmm) REVERT: B 235 HIS cc_start: 0.7123 (OUTLIER) cc_final: 0.6583 (m170) REVERT: B 284 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7709 (ttp80) REVERT: B 392 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7690 (tp) REVERT: B 396 TYR cc_start: 0.7767 (m-80) cc_final: 0.6837 (m-80) REVERT: B 572 MET cc_start: 0.8672 (mmm) cc_final: 0.8430 (mmm) outliers start: 31 outliers final: 20 residues processed: 169 average time/residue: 0.0976 time to fit residues: 22.7764 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 : 0.336 ------------------------------------------------------------------------------- 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 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 392 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 4.9990 chunk 101 optimal weight: 0.0570 chunk 111 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.9504 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.122602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.098520 restraints weight = 13516.204| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.67 r_work: 0.3122 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9568 Z= 0.142 Angle : 0.525 6.550 12942 Z= 0.274 Chirality : 0.040 0.146 1494 Planarity : 0.003 0.030 1616 Dihedral : 9.709 146.428 1408 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.09 % Allowed : 20.76 % 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 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: 0.92 (0.25), residues: 1166 helix: 2.03 (0.19), residues: 784 sheet: -2.45 (0.61), residues: 48 loop : -2.54 (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 B 316 PHE 0.020 0.001 PHE B 234 TRP 0.008 0.001 TRP A 143 HIS 0.008 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9568) covalent geometry : angle 0.52475 (12942) hydrogen bonds : bond 0.04813 ( 612) hydrogen bonds : angle 3.79172 ( 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 174 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.376 Fit side-chains REVERT: A 235 HIS cc_start: 0.7079 (OUTLIER) cc_final: 0.6617 (m170) REVERT: A 284 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7680 (ttp80) REVERT: A 359 TYR cc_start: 0.8508 (t80) cc_final: 0.8295 (t80) REVERT: A 396 TYR cc_start: 0.7856 (m-80) cc_final: 0.7059 (m-80) REVERT: A 572 MET cc_start: 0.8563 (mmm) cc_final: 0.8292 (mmm) REVERT: A 616 ARG cc_start: 0.8197 (ttp-110) cc_final: 0.7947 (ttp80) REVERT: A 628 TYR cc_start: 0.8828 (m-80) cc_final: 0.8564 (m-10) REVERT: B 232 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7516 (mmm) REVERT: B 235 HIS cc_start: 0.7090 (OUTLIER) cc_final: 0.6590 (m170) REVERT: B 284 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7656 (ttp80) REVERT: B 392 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7619 (tp) REVERT: B 396 TYR cc_start: 0.7831 (m-80) cc_final: 0.6991 (m-80) REVERT: B 572 MET cc_start: 0.8586 (mmm) cc_final: 0.8325 (mmm) REVERT: B 628 TYR cc_start: 0.8859 (m-80) cc_final: 0.8587 (m-10) outliers start: 31 outliers final: 24 residues processed: 166 average time/residue: 0.1008 time to fit residues: 23.0854 Evaluate side-chains 161 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 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 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 335 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 85 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** A 618 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.126025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102540 restraints weight = 13461.515| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.63 r_work: 0.3133 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9568 Z= 0.133 Angle : 0.522 6.534 12942 Z= 0.273 Chirality : 0.040 0.145 1494 Planarity : 0.003 0.031 1616 Dihedral : 9.290 139.480 1408 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.39 % Allowed : 21.06 % 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: 1.09 (0.25), residues: 1166 helix: 2.15 (0.19), residues: 784 sheet: -2.38 (0.61), residues: 48 loop : -2.42 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 424 TYR 0.015 0.001 TYR B 316 PHE 0.020 0.001 PHE A 234 TRP 0.006 0.001 TRP A 143 HIS 0.008 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9568) covalent geometry : angle 0.52182 (12942) hydrogen bonds : bond 0.04718 ( 612) hydrogen bonds : angle 3.78107 ( 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: 34 poor density : 139 time to evaluate : 0.391 Fit side-chains REVERT: A 199 MET cc_start: 0.8629 (tpp) cc_final: 0.8162 (mpp) REVERT: A 235 HIS cc_start: 0.7100 (OUTLIER) cc_final: 0.6693 (m170) REVERT: A 284 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7680 (ttp80) REVERT: A 396 TYR cc_start: 0.7754 (m-80) cc_final: 0.7002 (m-80) REVERT: A 572 MET cc_start: 0.8505 (mmm) cc_final: 0.8301 (mmm) REVERT: A 616 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7962 (ttp80) REVERT: A 628 TYR cc_start: 0.8843 (m-80) cc_final: 0.8568 (m-10) REVERT: B 199 MET cc_start: 0.8616 (tpp) cc_final: 0.8145 (mpp) REVERT: B 232 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7537 (mmm) REVERT: B 235 HIS cc_start: 0.7117 (OUTLIER) cc_final: 0.6718 (m170) REVERT: B 284 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7675 (ttp80) REVERT: B 392 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7647 (tp) REVERT: B 572 MET cc_start: 0.8600 (mmm) cc_final: 0.8278 (mmm) REVERT: B 628 TYR cc_start: 0.8874 (m-80) cc_final: 0.8589 (m-10) outliers start: 34 outliers final: 26 residues processed: 165 average time/residue: 0.0936 time to fit residues: 21.5023 Evaluate side-chains 161 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 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 335 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 392 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=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: 0.6980 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 114 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3581 r_free = 0.3581 target = 0.124782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100663 restraints weight = 13407.129| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.69 r_work: 0.3142 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9568 Z= 0.124 Angle : 0.510 6.517 12942 Z= 0.268 Chirality : 0.039 0.145 1494 Planarity : 0.003 0.030 1616 Dihedral : 8.926 132.409 1408 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.29 % Allowed : 21.76 % Favored : 74.95 % 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: 1.28 (0.25), residues: 1166 helix: 2.29 (0.18), residues: 780 sheet: -2.33 (0.60), residues: 48 loop : -2.29 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 424 TYR 0.015 0.001 TYR A 316 PHE 0.019 0.001 PHE A 234 TRP 0.004 0.001 TRP B 463 HIS 0.008 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9568) covalent geometry : angle 0.50966 (12942) hydrogen bonds : bond 0.04595 ( 612) hydrogen bonds : angle 3.73611 ( 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 176 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.271 Fit side-chains REVERT: A 199 MET cc_start: 0.8611 (tpp) cc_final: 0.8165 (mpp) REVERT: A 235 HIS cc_start: 0.7072 (OUTLIER) cc_final: 0.6693 (m170) REVERT: A 284 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7641 (ttp80) REVERT: A 326 MET cc_start: 0.7948 (mmt) cc_final: 0.7671 (mmt) REVERT: A 572 MET cc_start: 0.8457 (mmm) cc_final: 0.8239 (mmm) REVERT: A 616 ARG cc_start: 0.8213 (ttp-110) cc_final: 0.7961 (ttp80) REVERT: A 628 TYR cc_start: 0.8825 (m-80) cc_final: 0.8552 (m-10) REVERT: B 199 MET cc_start: 0.8591 (tpp) cc_final: 0.8142 (mpp) REVERT: B 232 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7459 (mmm) REVERT: B 235 HIS cc_start: 0.6946 (OUTLIER) cc_final: 0.6690 (m170) REVERT: B 284 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7646 (ttp80) REVERT: B 326 MET cc_start: 0.7950 (mmt) cc_final: 0.7671 (mmt) REVERT: B 392 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7579 (tp) REVERT: B 572 MET cc_start: 0.8543 (mmm) cc_final: 0.8244 (mmm) REVERT: B 628 TYR cc_start: 0.8846 (m-80) cc_final: 0.8557 (m-10) outliers start: 33 outliers final: 26 residues processed: 167 average time/residue: 0.1037 time to fit residues: 23.6489 Evaluate side-chains 162 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 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 392 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 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: 0.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 11 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.125096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.101692 restraints weight = 13185.255| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.61 r_work: 0.3148 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2209 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= 0.128 Angle : 0.531 7.715 12942 Z= 0.280 Chirality : 0.040 0.145 1494 Planarity : 0.003 0.031 1616 Dihedral : 8.709 126.287 1408 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.39 % Allowed : 22.16 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.35 (0.25), residues: 1166 helix: 2.33 (0.19), residues: 780 sheet: -2.29 (0.61), residues: 48 loop : -2.25 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 424 TYR 0.017 0.001 TYR A 316 PHE 0.019 0.001 PHE A 234 TRP 0.011 0.001 TRP A 143 HIS 0.007 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9568) covalent geometry : angle 0.53064 (12942) hydrogen bonds : bond 0.04550 ( 612) hydrogen bonds : angle 3.72923 ( 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 172 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.362 Fit side-chains REVERT: A 199 MET cc_start: 0.8671 (tpp) cc_final: 0.8228 (mpp) REVERT: A 235 HIS cc_start: 0.6907 (OUTLIER) cc_final: 0.6666 (m170) REVERT: A 284 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7691 (ttp80) REVERT: A 572 MET cc_start: 0.8491 (mmm) cc_final: 0.8270 (mmm) REVERT: A 616 ARG cc_start: 0.8228 (ttp-110) cc_final: 0.7975 (ttp80) REVERT: A 628 TYR cc_start: 0.8836 (m-80) cc_final: 0.8544 (m-10) REVERT: B 199 MET cc_start: 0.8658 (tpp) cc_final: 0.8216 (mpp) REVERT: B 232 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7553 (mmm) REVERT: B 235 HIS cc_start: 0.6868 (OUTLIER) cc_final: 0.6640 (m170) REVERT: B 284 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7698 (ttp80) REVERT: B 392 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7706 (tp) REVERT: B 396 TYR cc_start: 0.7674 (m-80) cc_final: 0.6929 (m-80) REVERT: B 572 MET cc_start: 0.8535 (mmm) cc_final: 0.8288 (mmm) REVERT: B 628 TYR cc_start: 0.8857 (m-80) cc_final: 0.8548 (m-10) outliers start: 34 outliers final: 29 residues processed: 163 average time/residue: 0.0931 time to fit residues: 21.1826 Evaluate side-chains 169 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 261 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 458 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 545 VAL 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 392 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 51 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.124290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101182 restraints weight = 13417.086| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.62 r_work: 0.3124 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9568 Z= 0.154 Angle : 0.550 6.756 12942 Z= 0.290 Chirality : 0.041 0.146 1494 Planarity : 0.003 0.031 1616 Dihedral : 8.657 123.740 1408 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.49 % Allowed : 22.16 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.26 (0.25), residues: 1166 helix: 2.24 (0.18), residues: 780 sheet: -2.32 (0.60), residues: 48 loop : -2.20 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 424 TYR 0.018 0.001 TYR A 316 PHE 0.018 0.001 PHE A 234 TRP 0.010 0.001 TRP A 143 HIS 0.008 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9568) covalent geometry : angle 0.54985 (12942) hydrogen bonds : bond 0.04811 ( 612) hydrogen bonds : angle 3.81484 ( 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 172 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.332 Fit side-chains REVERT: A 199 MET cc_start: 0.8662 (tpp) cc_final: 0.8222 (mpp) REVERT: A 235 HIS cc_start: 0.7052 (OUTLIER) cc_final: 0.6682 (m170) REVERT: A 284 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7380 (tpp-160) REVERT: A 572 MET cc_start: 0.8454 (mmm) cc_final: 0.8232 (mmm) REVERT: A 628 TYR cc_start: 0.8843 (m-80) cc_final: 0.8575 (m-10) REVERT: B 199 MET cc_start: 0.8652 (tpp) cc_final: 0.8199 (mpp) REVERT: B 232 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7557 (mmm) REVERT: B 235 HIS cc_start: 0.6962 (OUTLIER) cc_final: 0.6651 (m170) REVERT: B 284 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7681 (ttp80) REVERT: B 392 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7666 (tp) REVERT: B 572 MET cc_start: 0.8509 (mmm) cc_final: 0.8235 (mmm) REVERT: B 628 TYR cc_start: 0.8828 (m-80) cc_final: 0.8542 (m-10) outliers start: 35 outliers final: 30 residues processed: 165 average time/residue: 0.0963 time to fit residues: 22.1015 Evaluate side-chains 166 residues out of total 1002 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 261 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 458 THR 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 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 392 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 78 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.127720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103937 restraints weight = 13150.449| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.53 r_work: 0.3144 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2275 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= 0.134 Angle : 0.535 6.865 12942 Z= 0.283 Chirality : 0.040 0.143 1494 Planarity : 0.003 0.030 1616 Dihedral : 8.505 120.483 1408 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.49 % Allowed : 21.96 % Favored : 74.55 % 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: 1.37 (0.25), residues: 1166 helix: 2.31 (0.19), residues: 780 sheet: -2.24 (0.60), residues: 48 loop : -2.14 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 424 TYR 0.018 0.001 TYR A 316 PHE 0.018 0.001 PHE A 234 TRP 0.007 0.001 TRP A 143 HIS 0.007 0.001 HIS B 235 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9568) covalent geometry : angle 0.53469 (12942) hydrogen bonds : bond 0.04656 ( 612) hydrogen bonds : angle 3.75618 ( 1824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1700.51 seconds wall clock time: 29 minutes 58.26 seconds (1798.26 seconds total)