Starting phenix.real_space_refine on Tue Feb 3 14:15:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zbv_74011/02_2026/9zbv_74011.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zbv_74011/02_2026/9zbv_74011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zbv_74011/02_2026/9zbv_74011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zbv_74011/02_2026/9zbv_74011.map" model { file = "/net/cci-nas-00/data/ceres_data/9zbv_74011/02_2026/9zbv_74011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zbv_74011/02_2026/9zbv_74011.cif" } resolution = 3.2 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= 0.033 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: 4 Type Number sf(0) Gaussians S 4 5.16 5 C 2287 2.51 5 N 587 2.21 5 O 695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3573 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "B" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "C" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 888 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Time building chain proxies: 0.66, per 1000 atoms: 0.18 Number of scatterers: 3573 At special positions: 0 Unit cell: (56.24, 67.34, 82.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 4 16.00 O 695 8.00 N 587 7.00 C 2287 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: 0.18 Conformation dependent library (CDL) restraints added in 92.7 milliseconds 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 870 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 8 sheets defined 7.8% alpha, 61.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 74 through 82 removed outlier: 3.633A pdb=" N TYR A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 82 removed outlier: 3.517A pdb=" N LEU B 82 " --> pdb=" O TYR B 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 82 removed outlier: 3.665A pdb=" N TYR C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 82 " --> pdb=" O TYR C 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 82 removed outlier: 3.508A pdb=" N TYR D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 82 " --> pdb=" O TYR D 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.513A pdb=" N MET A 13 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ALA A 109 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS A 15 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU A 111 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET B 13 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ALA B 109 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS B 15 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU B 111 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU B 17 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.513A pdb=" N MET A 13 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ALA A 109 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS A 15 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU A 111 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 17 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET B 13 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N ALA B 109 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS B 15 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LEU B 111 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU B 17 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 48 removed outlier: 6.681A pdb=" N VAL A 32 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER A 46 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A 30 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE A 68 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY A 67 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 97 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 41 through 48 removed outlier: 6.578A pdb=" N VAL B 32 " --> pdb=" O PHE B 44 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER B 46 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 30 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE B 68 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY B 67 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.507A pdb=" N MET C 13 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ALA C 109 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS C 15 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU C 111 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU C 17 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.709A pdb=" N VAL C 14 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N MET C 13 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ALA C 109 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS C 15 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU C 111 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU C 17 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL D 14 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 41 through 48 removed outlier: 5.636A pdb=" N ARG C 34 " --> pdb=" O PRO C 43 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ILE C 68 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 67 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 41 through 48 removed outlier: 6.537A pdb=" N ARG D 34 " --> pdb=" O PRO D 43 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE D 68 " --> pdb=" O LYS D 35 " (cutoff:3.500A) 198 hydrogen bonds defined for protein. 522 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: 0.33 Time building geometry restraints manager: 0.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1144 1.34 - 1.46: 847 1.46 - 1.57: 1669 1.57 - 1.69: 0 1.69 - 1.80: 8 Bond restraints: 3668 Sorted by residual: bond pdb=" CG LEU B 55 " pdb=" CD2 LEU B 55 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.55e-01 bond pdb=" CA ASP C 39 " pdb=" CB ASP C 39 " ideal model delta sigma weight residual 1.532 1.544 -0.012 1.53e-02 4.27e+03 5.83e-01 bond pdb=" CB ASP C 99 " pdb=" CG ASP C 99 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.06e-01 bond pdb=" CA PHE D 64 " pdb=" CB PHE D 64 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.30e-02 5.92e+03 4.34e-01 bond pdb=" CA ASP B 74 " pdb=" C ASP B 74 " ideal model delta sigma weight residual 1.530 1.522 0.007 1.11e-02 8.12e+03 4.06e-01 ... (remaining 3663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.73: 4435 0.73 - 1.46: 441 1.46 - 2.18: 89 2.18 - 2.91: 19 2.91 - 3.64: 24 Bond angle restraints: 5008 Sorted by residual: angle pdb=" N VAL D 20 " pdb=" CA VAL D 20 " pdb=" C VAL D 20 " ideal model delta sigma weight residual 111.81 109.30 2.51 8.60e-01 1.35e+00 8.49e+00 angle pdb=" N SER B 23 " pdb=" CA SER B 23 " pdb=" C SER B 23 " ideal model delta sigma weight residual 108.22 109.82 -1.60 9.00e-01 1.23e+00 3.15e+00 angle pdb=" N ASP C 39 " pdb=" CA ASP C 39 " pdb=" CB ASP C 39 " ideal model delta sigma weight residual 112.63 109.90 2.73 1.61e+00 3.86e-01 2.88e+00 angle pdb=" CA ASP B 74 " pdb=" C ASP B 74 " pdb=" N THR B 75 " ideal model delta sigma weight residual 114.60 116.78 -2.18 1.30e+00 5.92e-01 2.82e+00 angle pdb=" CA GLU C 62 " pdb=" CB GLU C 62 " pdb=" CG GLU C 62 " ideal model delta sigma weight residual 114.10 117.34 -3.24 2.00e+00 2.50e-01 2.62e+00 ... (remaining 5003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 1987 17.41 - 34.81: 123 34.81 - 52.22: 41 52.22 - 69.63: 2 69.63 - 87.03: 1 Dihedral angle restraints: 2154 sinusoidal: 805 harmonic: 1349 Sorted by residual: dihedral pdb=" CA ALA A 10 " pdb=" C ALA A 10 " pdb=" N PRO A 11 " pdb=" CA PRO A 11 " ideal model delta harmonic sigma weight residual -180.00 -161.08 -18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CB GLU D 92 " pdb=" CG GLU D 92 " pdb=" CD GLU D 92 " pdb=" OE1 GLU D 92 " ideal model delta sinusoidal sigma weight residual 0.00 -87.03 87.03 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CA LYS D 35 " pdb=" CB LYS D 35 " pdb=" CG LYS D 35 " pdb=" CD LYS D 35 " ideal model delta sinusoidal sigma weight residual 180.00 130.83 49.17 3 1.50e+01 4.44e-03 8.74e+00 ... (remaining 2151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 286 0.027 - 0.053: 171 0.053 - 0.080: 41 0.080 - 0.106: 31 0.106 - 0.133: 42 Chirality restraints: 571 Sorted by residual: chirality pdb=" CA ILE A 107 " pdb=" N ILE A 107 " pdb=" C ILE A 107 " pdb=" CB ILE A 107 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE C 107 " pdb=" N ILE C 107 " pdb=" C ILE C 107 " pdb=" CB ILE C 107 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 568 not shown) Planarity restraints: 638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 112 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO B 113 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 101 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.64e+00 pdb=" N PRO A 102 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 112 " 0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO D 113 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 113 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 113 " 0.018 5.00e-02 4.00e+02 ... (remaining 635 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 837 2.79 - 3.32: 3073 3.32 - 3.85: 5411 3.85 - 4.37: 6180 4.37 - 4.90: 11804 Nonbonded interactions: 27305 Sorted by model distance: nonbonded pdb=" O ASP C 39 " pdb=" OD1 ASP C 39 " model vdw 2.269 3.040 nonbonded pdb=" O ILE C 26 " pdb=" OD1 ASN C 27 " model vdw 2.384 3.040 nonbonded pdb=" O ASP D 39 " pdb=" OD1 ASP D 39 " model vdw 2.428 3.040 nonbonded pdb=" OD1 ASP D 38 " pdb=" OG1 THR D 40 " model vdw 2.441 3.040 nonbonded pdb=" OD2 ASP B 74 " pdb=" OG SER B 77 " model vdw 2.464 3.040 ... (remaining 27300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 10 through 124) selection = (chain 'B' and resid 10 through 124) selection = (chain 'C' and resid 10 through 124) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 3.760 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 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 : 0.002 0.027 3668 Z= 0.121 Angle : 0.535 3.641 5008 Z= 0.302 Chirality : 0.049 0.133 571 Planarity : 0.004 0.037 638 Dihedral : 12.664 87.034 1284 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % 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: -0.37 (0.36), residues: 455 helix: -0.76 (0.80), residues: 34 sheet: 0.57 (0.33), residues: 207 loop : -0.94 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 103 TYR 0.010 0.001 TYR A 78 PHE 0.010 0.001 PHE A 64 TRP 0.006 0.001 TRP B 41 HIS 0.002 0.001 HIS C 56 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3668) covalent geometry : angle 0.53502 ( 5008) hydrogen bonds : bond 0.20375 ( 142) hydrogen bonds : angle 8.81687 ( 522) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 15 LYS cc_start: 0.7222 (tttt) cc_final: 0.7015 (tttt) REVERT: D 82 LEU cc_start: 0.7066 (mt) cc_final: 0.6807 (mp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0473 time to fit residues: 3.3417 Evaluate side-chains 49 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS B 98 ASN C 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.182005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151119 restraints weight = 4071.471| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.20 r_work: 0.3610 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3668 Z= 0.191 Angle : 0.614 6.809 5008 Z= 0.341 Chirality : 0.051 0.160 571 Planarity : 0.005 0.035 638 Dihedral : 4.857 17.648 495 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.87 % Allowed : 8.88 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.36), residues: 455 helix: -1.60 (0.68), residues: 36 sheet: 0.71 (0.33), residues: 216 loop : -1.35 (0.38), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 103 TYR 0.013 0.002 TYR D 116 PHE 0.011 0.002 PHE C 87 TRP 0.009 0.001 TRP C 79 HIS 0.005 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 3668) covalent geometry : angle 0.61418 ( 5008) hydrogen bonds : bond 0.04229 ( 142) hydrogen bonds : angle 5.66614 ( 522) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8416 (mtp85) cc_final: 0.8203 (mtp85) REVERT: A 38 ASP cc_start: 0.7382 (t0) cc_final: 0.6907 (p0) REVERT: B 92 GLU cc_start: 0.8336 (tt0) cc_final: 0.8110 (tt0) REVERT: C 103 ARG cc_start: 0.7226 (mmt-90) cc_final: 0.6450 (mmp80) REVERT: D 39 ASP cc_start: 0.8868 (t0) cc_final: 0.8627 (t0) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.0471 time to fit residues: 3.9782 Evaluate side-chains 55 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 0.0060 chunk 38 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS D 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.180536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.148257 restraints weight = 4057.102| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.37 r_work: 0.3657 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3668 Z= 0.107 Angle : 0.487 5.178 5008 Z= 0.266 Chirality : 0.049 0.166 571 Planarity : 0.004 0.034 638 Dihedral : 4.062 13.033 495 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.61 % Allowed : 9.40 % Favored : 87.99 % 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: -0.23 (0.37), residues: 455 helix: -0.83 (0.80), residues: 36 sheet: 0.92 (0.35), residues: 217 loop : -1.25 (0.37), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 103 TYR 0.011 0.001 TYR C 105 PHE 0.008 0.001 PHE C 33 TRP 0.003 0.001 TRP D 41 HIS 0.002 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 3668) covalent geometry : angle 0.48704 ( 5008) hydrogen bonds : bond 0.03709 ( 142) hydrogen bonds : angle 5.24116 ( 522) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.137 Fit side-chains REVERT: A 38 ASP cc_start: 0.7522 (t0) cc_final: 0.7066 (p0) REVERT: A 92 GLU cc_start: 0.8167 (pt0) cc_final: 0.7878 (pt0) REVERT: B 54 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6585 (tt0) REVERT: B 92 GLU cc_start: 0.8498 (tt0) cc_final: 0.8270 (tt0) REVERT: C 103 ARG cc_start: 0.7448 (mmt-90) cc_final: 0.6931 (mpt180) outliers start: 10 outliers final: 9 residues processed: 61 average time/residue: 0.0519 time to fit residues: 3.9436 Evaluate side-chains 58 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 124 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 34 optimal weight: 0.0570 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.161201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.129277 restraints weight = 4075.426| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.34 r_work: 0.3453 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.7145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3668 Z= 0.168 Angle : 0.568 7.648 5008 Z= 0.309 Chirality : 0.051 0.178 571 Planarity : 0.004 0.035 638 Dihedral : 4.675 17.059 495 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.39 % Allowed : 9.66 % Favored : 86.95 % 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: -0.37 (0.37), residues: 455 helix: -0.77 (0.82), residues: 34 sheet: 0.85 (0.34), residues: 216 loop : -1.40 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 21 TYR 0.014 0.002 TYR B 78 PHE 0.012 0.002 PHE B 44 TRP 0.010 0.002 TRP D 41 HIS 0.006 0.002 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 3668) covalent geometry : angle 0.56843 ( 5008) hydrogen bonds : bond 0.03887 ( 142) hydrogen bonds : angle 5.33498 ( 522) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 ARG cc_start: 0.7963 (mmt90) cc_final: 0.7510 (mmm-85) REVERT: C 54 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6780 (mp0) REVERT: C 74 ASP cc_start: 0.8327 (t0) cc_final: 0.7771 (t70) REVERT: D 123 THR cc_start: 0.6258 (OUTLIER) cc_final: 0.5939 (p) outliers start: 13 outliers final: 11 residues processed: 61 average time/residue: 0.0474 time to fit residues: 3.5315 Evaluate side-chains 60 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 85 SER Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 40 optimal weight: 0.0270 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.171257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.140738 restraints weight = 3950.931| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.92 r_work: 0.3461 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.7845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3668 Z= 0.174 Angle : 0.533 6.437 5008 Z= 0.289 Chirality : 0.050 0.165 571 Planarity : 0.004 0.033 638 Dihedral : 4.325 13.073 495 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.35 % Allowed : 11.23 % Favored : 86.42 % 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: -0.34 (0.37), residues: 455 helix: -0.59 (0.89), residues: 34 sheet: 0.80 (0.34), residues: 216 loop : -1.31 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 103 TYR 0.011 0.001 TYR B 78 PHE 0.012 0.002 PHE B 64 TRP 0.006 0.001 TRP D 41 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 3668) covalent geometry : angle 0.53316 ( 5008) hydrogen bonds : bond 0.03671 ( 142) hydrogen bonds : angle 5.23393 ( 522) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 ARG cc_start: 0.7971 (mmt90) cc_final: 0.7533 (mmm-85) REVERT: C 54 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6960 (mp0) REVERT: C 55 LEU cc_start: 0.8010 (mt) cc_final: 0.7770 (mp) REVERT: D 123 THR cc_start: 0.6188 (OUTLIER) cc_final: 0.5903 (p) outliers start: 9 outliers final: 7 residues processed: 58 average time/residue: 0.0542 time to fit residues: 3.8719 Evaluate side-chains 56 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 16 optimal weight: 0.0570 chunk 2 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.167945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137093 restraints weight = 4013.443| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 3.10 r_work: 0.3446 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.7981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3668 Z= 0.127 Angle : 0.500 5.556 5008 Z= 0.273 Chirality : 0.048 0.162 571 Planarity : 0.003 0.029 638 Dihedral : 4.253 16.970 495 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.61 % Allowed : 13.05 % Favored : 84.33 % 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: -0.25 (0.37), residues: 455 helix: -0.66 (0.88), residues: 34 sheet: 0.83 (0.34), residues: 216 loop : -1.19 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 103 TYR 0.011 0.001 TYR B 78 PHE 0.009 0.002 PHE D 33 TRP 0.006 0.001 TRP D 41 HIS 0.002 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3668) covalent geometry : angle 0.50006 ( 5008) hydrogen bonds : bond 0.03286 ( 142) hydrogen bonds : angle 5.04143 ( 522) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 ARG cc_start: 0.8041 (mmt90) cc_final: 0.7603 (mmm-85) REVERT: C 54 GLU cc_start: 0.7253 (mt-10) cc_final: 0.7009 (mp0) REVERT: C 103 ARG cc_start: 0.8011 (mmt-90) cc_final: 0.7179 (mmt180) REVERT: D 123 THR cc_start: 0.6443 (OUTLIER) cc_final: 0.6159 (p) outliers start: 10 outliers final: 8 residues processed: 58 average time/residue: 0.0634 time to fit residues: 4.4536 Evaluate side-chains 59 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.165333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.134789 restraints weight = 4082.611| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.93 r_work: 0.3437 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.8494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 3668 Z= 0.284 Angle : 0.619 6.888 5008 Z= 0.337 Chirality : 0.053 0.171 571 Planarity : 0.004 0.032 638 Dihedral : 4.855 23.013 495 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.44 % Allowed : 13.32 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.37), residues: 455 helix: -0.75 (0.91), residues: 34 sheet: 0.76 (0.35), residues: 207 loop : -1.35 (0.37), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 103 TYR 0.016 0.002 TYR B 78 PHE 0.019 0.003 PHE B 64 TRP 0.011 0.001 TRP D 41 HIS 0.014 0.002 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00677 ( 3668) covalent geometry : angle 0.61949 ( 5008) hydrogen bonds : bond 0.04347 ( 142) hydrogen bonds : angle 5.48392 ( 522) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: A 46 SER cc_start: 0.8827 (OUTLIER) cc_final: 0.8366 (m) REVERT: A 92 GLU cc_start: 0.8595 (pt0) cc_final: 0.8157 (pt0) REVERT: B 103 ARG cc_start: 0.8249 (mmt90) cc_final: 0.7852 (mmm-85) REVERT: C 74 ASP cc_start: 0.8301 (t0) cc_final: 0.7780 (t70) REVERT: C 103 ARG cc_start: 0.8098 (mmt-90) cc_final: 0.7692 (mmt180) REVERT: D 123 THR cc_start: 0.6350 (OUTLIER) cc_final: 0.6021 (p) outliers start: 17 outliers final: 12 residues processed: 61 average time/residue: 0.0646 time to fit residues: 4.7842 Evaluate side-chains 62 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 0.0470 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS B 27 ASN B 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.171896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140600 restraints weight = 3988.098| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.03 r_work: 0.3501 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.8621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3668 Z= 0.114 Angle : 0.516 5.981 5008 Z= 0.280 Chirality : 0.049 0.160 571 Planarity : 0.003 0.028 638 Dihedral : 4.452 18.552 495 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.39 % Allowed : 14.10 % Favored : 82.51 % 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: -0.34 (0.38), residues: 455 helix: -0.77 (0.89), residues: 34 sheet: 0.83 (0.35), residues: 216 loop : -1.30 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 103 TYR 0.011 0.001 TYR C 116 PHE 0.008 0.001 PHE D 95 TRP 0.004 0.001 TRP C 79 HIS 0.005 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 3668) covalent geometry : angle 0.51555 ( 5008) hydrogen bonds : bond 0.03150 ( 142) hydrogen bonds : angle 5.09978 ( 522) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: B 103 ARG cc_start: 0.8214 (mmt90) cc_final: 0.7656 (mmm-85) REVERT: C 103 ARG cc_start: 0.8070 (mmt-90) cc_final: 0.7218 (mmt180) REVERT: D 39 ASP cc_start: 0.8713 (t0) cc_final: 0.8464 (t0) REVERT: D 123 THR cc_start: 0.6455 (OUTLIER) cc_final: 0.6196 (p) outliers start: 13 outliers final: 11 residues processed: 61 average time/residue: 0.0649 time to fit residues: 4.7613 Evaluate side-chains 62 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 0.0370 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.173188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141758 restraints weight = 3898.037| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.92 r_work: 0.3500 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.8731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3668 Z= 0.119 Angle : 0.500 7.341 5008 Z= 0.270 Chirality : 0.048 0.157 571 Planarity : 0.003 0.028 638 Dihedral : 4.216 16.337 495 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.39 % Allowed : 14.10 % Favored : 82.51 % 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: -0.26 (0.38), residues: 455 helix: -0.80 (0.87), residues: 34 sheet: 0.90 (0.35), residues: 216 loop : -1.28 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 103 TYR 0.012 0.001 TYR B 78 PHE 0.009 0.001 PHE B 64 TRP 0.003 0.001 TRP B 41 HIS 0.002 0.001 HIS D 56 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3668) covalent geometry : angle 0.50038 ( 5008) hydrogen bonds : bond 0.03166 ( 142) hydrogen bonds : angle 4.92381 ( 522) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 85 SER cc_start: 0.7758 (t) cc_final: 0.7452 (p) REVERT: B 103 ARG cc_start: 0.8214 (mmt90) cc_final: 0.7656 (mmm-85) REVERT: C 103 ARG cc_start: 0.8053 (mmt-90) cc_final: 0.7114 (mmt180) REVERT: D 123 THR cc_start: 0.6359 (OUTLIER) cc_final: 0.6103 (p) outliers start: 13 outliers final: 11 residues processed: 61 average time/residue: 0.0831 time to fit residues: 6.0691 Evaluate side-chains 62 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.0770 chunk 36 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 90 HIS B 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.174894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.143081 restraints weight = 3931.320| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.96 r_work: 0.3500 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.8854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3668 Z= 0.103 Angle : 0.489 6.455 5008 Z= 0.265 Chirality : 0.048 0.155 571 Planarity : 0.003 0.027 638 Dihedral : 4.088 15.885 495 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.66 % Allowed : 13.84 % Favored : 82.51 % 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: -0.12 (0.38), residues: 455 helix: -0.69 (0.87), residues: 34 sheet: 1.00 (0.35), residues: 216 loop : -1.18 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 103 TYR 0.016 0.001 TYR B 78 PHE 0.008 0.001 PHE B 64 TRP 0.004 0.001 TRP C 41 HIS 0.001 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 3668) covalent geometry : angle 0.48865 ( 5008) hydrogen bonds : bond 0.02997 ( 142) hydrogen bonds : angle 4.83738 ( 522) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 910 Ramachandran restraints generated. 455 Oldfield, 0 Emsley, 455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.080 Fit side-chains REVERT: B 103 ARG cc_start: 0.8185 (mmt90) cc_final: 0.7589 (mmm-85) REVERT: C 103 ARG cc_start: 0.8062 (mmt-90) cc_final: 0.7602 (mmt180) REVERT: D 54 GLU cc_start: 0.7380 (pt0) cc_final: 0.6706 (pt0) REVERT: D 123 THR cc_start: 0.6367 (OUTLIER) cc_final: 0.6143 (p) outliers start: 14 outliers final: 10 residues processed: 58 average time/residue: 0.0515 time to fit residues: 3.6368 Evaluate side-chains 58 residues out of total 383 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 13 MET Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.0070 chunk 23 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 34 optimal weight: 0.0570 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.179022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.147564 restraints weight = 3880.536| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.89 r_work: 0.3558 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.8961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3668 Z= 0.091 Angle : 0.471 5.651 5008 Z= 0.257 Chirality : 0.047 0.153 571 Planarity : 0.003 0.026 638 Dihedral : 3.909 15.411 495 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.61 % Allowed : 14.88 % Favored : 82.51 % 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: 0.05 (0.39), residues: 455 helix: -0.62 (0.88), residues: 34 sheet: 1.12 (0.35), residues: 216 loop : -1.08 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 103 TYR 0.014 0.001 TYR B 78 PHE 0.006 0.001 PHE A 64 TRP 0.004 0.001 TRP C 41 HIS 0.001 0.000 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 3668) covalent geometry : angle 0.47104 ( 5008) hydrogen bonds : bond 0.02774 ( 142) hydrogen bonds : angle 4.66005 ( 522) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 769.80 seconds wall clock time: 13 minutes 53.57 seconds (833.57 seconds total)