Starting phenix.real_space_refine on Thu Sep 18 10:45:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwj_47252/09_2025/9dwj_47252.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwj_47252/09_2025/9dwj_47252.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 { model { file = "/net/cci-nas-00/data/ceres_data/9dwj_47252/09_2025/9dwj_47252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwj_47252/09_2025/9dwj_47252.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwj_47252/09_2025/9dwj_47252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwj_47252/09_2025/9dwj_47252.map" } 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5790 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 291 5.49 5 S 10 5.16 5 C 6567 2.51 5 N 2223 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11887 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 805 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 802 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 2165 Classifications: {'DNA': 106} Link IDs: {'rna3p': 105} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 790 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Time building chain proxies: 3.30, per 1000 atoms: 0.28 Number of scatterers: 11887 At special positions: 0 Unit cell: (76.83, 120.564, 117.018, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 291 15.00 O 2796 8.00 N 2223 7.00 C 6567 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: 1.24 Conformation dependent library (CDL) restraints added in 411.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 72.3% alpha, 2.9% beta 143 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.644A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.117A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.544A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.531A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.416A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.721A pdb=" N THR D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.552A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.875A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.690A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.507A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.049A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.421A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.991A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.236A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.399A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 398 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1438 1.32 - 1.44: 4761 1.44 - 1.57: 5893 1.57 - 1.69: 579 1.69 - 1.81: 20 Bond restraints: 12691 Sorted by residual: bond pdb=" N LEU A 65 " pdb=" CA LEU A 65 " ideal model delta sigma weight residual 1.462 1.498 -0.036 7.70e-03 1.69e+04 2.20e+01 bond pdb=" N GLU E 50 " pdb=" CA GLU E 50 " ideal model delta sigma weight residual 1.457 1.505 -0.047 1.29e-02 6.01e+03 1.34e+01 bond pdb=" N LEU E 48 " pdb=" CA LEU E 48 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.16e-02 7.43e+03 1.33e+01 bond pdb=" N LEU A 61 " pdb=" CA LEU A 61 " ideal model delta sigma weight residual 1.457 1.502 -0.044 1.29e-02 6.01e+03 1.18e+01 bond pdb=" N LEU A 60 " pdb=" CA LEU A 60 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.32e-02 5.74e+03 1.14e+01 ... (remaining 12686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 18116 2.32 - 4.64: 242 4.64 - 6.96: 23 6.96 - 9.28: 5 9.28 - 11.60: 1 Bond angle restraints: 18387 Sorted by residual: angle pdb=" N ILE E 51 " pdb=" CA ILE E 51 " pdb=" C ILE E 51 " ideal model delta sigma weight residual 111.58 99.98 11.60 1.06e+00 8.90e-01 1.20e+02 angle pdb=" N VAL E 46 " pdb=" CA VAL E 46 " pdb=" C VAL E 46 " ideal model delta sigma weight residual 112.98 105.99 6.99 1.25e+00 6.40e-01 3.13e+01 angle pdb=" N LEU E 48 " pdb=" CA LEU E 48 " pdb=" C LEU E 48 " ideal model delta sigma weight residual 111.02 105.08 5.94 1.22e+00 6.72e-01 2.37e+01 angle pdb=" N GLU E 50 " pdb=" CA GLU E 50 " pdb=" CB GLU E 50 " ideal model delta sigma weight residual 110.49 118.57 -8.08 1.69e+00 3.50e-01 2.29e+01 angle pdb=" CA ARG E 49 " pdb=" C ARG E 49 " pdb=" N GLU E 50 " ideal model delta sigma weight residual 115.85 121.75 -5.90 1.29e+00 6.01e-01 2.09e+01 ... (remaining 18382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.78: 5098 28.78 - 57.56: 1630 57.56 - 86.35: 138 86.35 - 115.13: 2 115.13 - 143.91: 3 Dihedral angle restraints: 6871 sinusoidal: 4705 harmonic: 2166 Sorted by residual: dihedral pdb=" C4' DG J 82 " pdb=" C3' DG J 82 " pdb=" O3' DG J 82 " pdb=" P DT J 83 " ideal model delta sinusoidal sigma weight residual 220.00 76.09 143.91 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" N GLU E 50 " pdb=" C GLU E 50 " pdb=" CA GLU E 50 " pdb=" CB GLU E 50 " ideal model delta harmonic sigma weight residual 122.80 132.17 -9.37 0 2.50e+00 1.60e-01 1.40e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 78.77 141.23 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 6868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1888 0.060 - 0.121: 176 0.121 - 0.181: 24 0.181 - 0.241: 6 0.241 - 0.302: 2 Chirality restraints: 2096 Sorted by residual: chirality pdb=" CA ILE E 51 " pdb=" N ILE E 51 " pdb=" C ILE E 51 " pdb=" CB ILE E 51 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA LEU E 48 " pdb=" N LEU E 48 " pdb=" C LEU E 48 " pdb=" CB LEU E 48 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ILE C 102 " pdb=" N ILE C 102 " pdb=" C ILE C 102 " pdb=" CB ILE C 102 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2093 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.018 2.00e-02 2.50e+03 1.75e-02 5.38e+00 pdb=" CG PHE G 25 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 63 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.18e+00 pdb=" C GLU B 63 " -0.039 2.00e-02 2.50e+03 pdb=" O GLU B 63 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN B 64 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 117 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C VAL A 117 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL A 117 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A 118 " -0.013 2.00e-02 2.50e+03 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2590 2.81 - 3.33: 10554 3.33 - 3.85: 24300 3.85 - 4.38: 27641 4.38 - 4.90: 38978 Nonbonded interactions: 104063 Sorted by model distance: nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.289 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH1 ARG E 131 " model vdw 2.291 3.120 nonbonded pdb=" O ARG E 49 " pdb=" CG GLU E 50 " model vdw 2.298 3.440 nonbonded pdb=" O GLU E 59 " pdb=" NH2 ARG F 40 " model vdw 2.330 3.120 ... (remaining 104058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = (chain 'G' and resid 15 through 117) } ncs_group { reference = (chain 'D' and resid 34 through 124) selection = chain 'H' } 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: 19.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.240 Find NCS groups from input model: 0.130 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.005 0.056 12691 Z= 0.262 Angle : 0.700 11.605 18387 Z= 0.438 Chirality : 0.041 0.302 2096 Planarity : 0.006 0.053 1317 Dihedral : 28.025 143.909 5475 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.64 % Allowed : 1.45 % Favored : 97.91 % 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 aren not related in a simple way. whole: 0.84 (0.30), residues: 732 helix: 1.12 (0.22), residues: 539 sheet: None (None), residues: 0 loop : -0.94 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 42 TYR 0.019 0.002 TYR H 42 PHE 0.040 0.002 PHE G 25 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00505 (12691) covalent geometry : angle 0.69953 (18387) hydrogen bonds : bond 0.10676 ( 765) hydrogen bonds : angle 4.42317 ( 1916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.352 Fit side-chains REVERT: B 88 TYR cc_start: 0.8429 (m-80) cc_final: 0.8157 (m-80) REVERT: E 79 LYS cc_start: 0.8134 (tptp) cc_final: 0.7764 (tptt) REVERT: E 118 THR cc_start: 0.8980 (m) cc_final: 0.8648 (p) REVERT: E 129 ARG cc_start: 0.8174 (tpt90) cc_final: 0.7703 (tpt90) outliers start: 4 outliers final: 0 residues processed: 132 average time/residue: 0.1737 time to fit residues: 29.9830 Evaluate side-chains 110 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN D 84 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.129932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.086029 restraints weight = 23136.443| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.68 r_work: 0.2922 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12691 Z= 0.160 Angle : 0.568 8.780 18387 Z= 0.338 Chirality : 0.033 0.134 2096 Planarity : 0.004 0.040 1317 Dihedral : 30.571 143.402 4003 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.48 % Allowed : 8.05 % Favored : 91.47 % 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 aren not related in a simple way. whole: 1.80 (0.30), residues: 732 helix: 1.82 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.65 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 39 TYR 0.015 0.001 TYR C 39 PHE 0.012 0.001 PHE G 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00343 (12691) covalent geometry : angle 0.56803 (18387) hydrogen bonds : bond 0.04102 ( 765) hydrogen bonds : angle 3.24208 ( 1916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 0.359 Fit side-chains REVERT: A 60 LEU cc_start: 0.7881 (mt) cc_final: 0.7411 (mt) REVERT: E 45 THR cc_start: 0.8599 (t) cc_final: 0.8358 (m) REVERT: E 79 LYS cc_start: 0.8414 (tptp) cc_final: 0.8021 (tptt) REVERT: E 118 THR cc_start: 0.9192 (m) cc_final: 0.8989 (p) REVERT: E 129 ARG cc_start: 0.8726 (tpt90) cc_final: 0.8090 (tpt90) outliers start: 3 outliers final: 2 residues processed: 122 average time/residue: 0.1640 time to fit residues: 26.3400 Evaluate side-chains 112 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 38 optimal weight: 0.0980 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 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 = 0.3865 r_free = 0.3865 target = 0.128957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.085078 restraints weight = 23507.294| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.68 r_work: 0.2901 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 12691 Z= 0.193 Angle : 0.562 7.564 18387 Z= 0.336 Chirality : 0.033 0.130 2096 Planarity : 0.004 0.042 1317 Dihedral : 30.525 141.454 4003 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.13 % Allowed : 9.18 % Favored : 89.69 % 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 aren not related in a simple way. whole: 2.14 (0.31), residues: 732 helix: 2.07 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.54 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 42 TYR 0.027 0.002 TYR B 88 PHE 0.017 0.002 PHE G 25 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00436 (12691) covalent geometry : angle 0.56245 (18387) hydrogen bonds : bond 0.03858 ( 765) hydrogen bonds : angle 3.00060 ( 1916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.343 Fit side-chains REVERT: A 60 LEU cc_start: 0.7972 (mt) cc_final: 0.7537 (mt) REVERT: E 45 THR cc_start: 0.8643 (t) cc_final: 0.8333 (m) REVERT: E 48 LEU cc_start: 0.9399 (mp) cc_final: 0.9183 (mp) REVERT: E 51 ILE cc_start: 0.8924 (mt) cc_final: 0.8700 (mt) REVERT: E 79 LYS cc_start: 0.8437 (tptp) cc_final: 0.8042 (tptt) REVERT: E 118 THR cc_start: 0.9212 (m) cc_final: 0.9010 (p) REVERT: E 129 ARG cc_start: 0.8740 (tpt90) cc_final: 0.8053 (tpt90) outliers start: 7 outliers final: 5 residues processed: 123 average time/residue: 0.1661 time to fit residues: 26.3765 Evaluate side-chains 113 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain F residue 47 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 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 = 0.3869 r_free = 0.3869 target = 0.129324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.085716 restraints weight = 23219.019| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.68 r_work: 0.2917 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12691 Z= 0.156 Angle : 0.533 6.879 18387 Z= 0.322 Chirality : 0.032 0.129 2096 Planarity : 0.004 0.041 1317 Dihedral : 30.531 140.900 4003 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.64 % Allowed : 11.59 % Favored : 87.76 % 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 aren not related in a simple way. whole: 2.41 (0.31), residues: 732 helix: 2.25 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.40 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 42 TYR 0.046 0.002 TYR B 88 PHE 0.012 0.001 PHE G 25 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00341 (12691) covalent geometry : angle 0.53276 (18387) hydrogen bonds : bond 0.03420 ( 765) hydrogen bonds : angle 2.85222 ( 1916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8597 (tp30) cc_final: 0.8397 (tp30) REVERT: D 93 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8171 (mm-30) REVERT: E 45 THR cc_start: 0.8592 (t) cc_final: 0.8293 (m) REVERT: E 79 LYS cc_start: 0.8418 (tptp) cc_final: 0.8027 (tptt) REVERT: E 129 ARG cc_start: 0.8706 (tpt90) cc_final: 0.8038 (tpt90) REVERT: G 24 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7955 (mp10) outliers start: 4 outliers final: 4 residues processed: 125 average time/residue: 0.1480 time to fit residues: 23.8963 Evaluate side-chains 118 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain F residue 47 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.127039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082968 restraints weight = 23254.168| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.69 r_work: 0.2869 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12691 Z= 0.227 Angle : 0.573 7.465 18387 Z= 0.340 Chirality : 0.035 0.132 2096 Planarity : 0.004 0.041 1317 Dihedral : 30.818 142.469 4003 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.29 % Allowed : 12.72 % Favored : 85.99 % 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 aren not related in a simple way. whole: 2.34 (0.30), residues: 732 helix: 2.21 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.46 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 42 TYR 0.037 0.002 TYR B 88 PHE 0.020 0.002 PHE G 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00522 (12691) covalent geometry : angle 0.57333 (18387) hydrogen bonds : bond 0.03901 ( 765) hydrogen bonds : angle 2.94396 ( 1916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.416 Fit side-chains REVERT: A 60 LEU cc_start: 0.8031 (mt) cc_final: 0.7701 (mt) REVERT: B 88 TYR cc_start: 0.8740 (m-80) cc_final: 0.8435 (m-80) REVERT: C 61 GLU cc_start: 0.8692 (tp30) cc_final: 0.8488 (tp30) REVERT: E 129 ARG cc_start: 0.8810 (tpt90) cc_final: 0.8076 (tpt90) outliers start: 8 outliers final: 7 residues processed: 124 average time/residue: 0.1570 time to fit residues: 25.1616 Evaluate side-chains 115 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain F residue 47 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.128990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.085126 restraints weight = 23317.339| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.67 r_work: 0.2904 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12691 Z= 0.158 Angle : 0.533 7.011 18387 Z= 0.322 Chirality : 0.032 0.126 2096 Planarity : 0.004 0.042 1317 Dihedral : 30.654 141.773 4003 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.45 % Allowed : 13.37 % Favored : 85.19 % 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 aren not related in a simple way. whole: 2.60 (0.31), residues: 732 helix: 2.41 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.38 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 42 TYR 0.029 0.001 TYR B 88 PHE 0.011 0.001 PHE G 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00349 (12691) covalent geometry : angle 0.53254 (18387) hydrogen bonds : bond 0.03316 ( 765) hydrogen bonds : angle 2.78336 ( 1916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.332 Fit side-chains REVERT: C 51 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8650 (tp) REVERT: E 94 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8284 (mm-30) REVERT: E 129 ARG cc_start: 0.8781 (tpt90) cc_final: 0.8083 (tpt90) outliers start: 9 outliers final: 7 residues processed: 123 average time/residue: 0.1583 time to fit residues: 25.0945 Evaluate side-chains 117 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 44 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.127413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.083174 restraints weight = 23190.483| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.68 r_work: 0.2876 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12691 Z= 0.212 Angle : 0.563 7.182 18387 Z= 0.335 Chirality : 0.034 0.136 2096 Planarity : 0.005 0.063 1317 Dihedral : 30.783 142.447 4003 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.77 % Allowed : 14.65 % Favored : 83.57 % 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 aren not related in a simple way. whole: 2.43 (0.31), residues: 732 helix: 2.29 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.49 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 42 TYR 0.026 0.002 TYR B 88 PHE 0.014 0.002 PHE G 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00483 (12691) covalent geometry : angle 0.56321 (18387) hydrogen bonds : bond 0.03750 ( 765) hydrogen bonds : angle 2.87148 ( 1916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.340 Fit side-chains REVERT: B 88 TYR cc_start: 0.8761 (m-80) cc_final: 0.8492 (m-80) REVERT: D 93 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8256 (mm-30) REVERT: E 129 ARG cc_start: 0.8815 (tpt90) cc_final: 0.8097 (tpt90) outliers start: 11 outliers final: 10 residues processed: 127 average time/residue: 0.1497 time to fit residues: 24.7557 Evaluate side-chains 124 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.129131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.085213 restraints weight = 22939.728| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.67 r_work: 0.2913 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12691 Z= 0.157 Angle : 0.539 6.958 18387 Z= 0.325 Chirality : 0.032 0.125 2096 Planarity : 0.004 0.042 1317 Dihedral : 30.651 141.988 4003 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.09 % Allowed : 14.49 % Favored : 83.41 % 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 aren not related in a simple way. whole: 2.62 (0.31), residues: 732 helix: 2.43 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.43 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 42 TYR 0.024 0.001 TYR B 88 PHE 0.009 0.001 PHE G 25 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00348 (12691) covalent geometry : angle 0.53941 (18387) hydrogen bonds : bond 0.03340 ( 765) hydrogen bonds : angle 2.75422 ( 1916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.337 Fit side-chains REVERT: B 88 TYR cc_start: 0.8733 (m-80) cc_final: 0.8484 (m-80) REVERT: C 51 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8653 (tp) REVERT: D 93 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8209 (mm-30) REVERT: E 65 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8867 (mp) REVERT: E 129 ARG cc_start: 0.8776 (tpt90) cc_final: 0.8070 (tpt90) outliers start: 13 outliers final: 11 residues processed: 126 average time/residue: 0.1589 time to fit residues: 26.1318 Evaluate side-chains 125 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.129367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.085359 restraints weight = 22856.706| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.68 r_work: 0.2913 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12691 Z= 0.153 Angle : 0.538 6.973 18387 Z= 0.324 Chirality : 0.032 0.125 2096 Planarity : 0.004 0.044 1317 Dihedral : 30.621 142.288 4003 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.09 % Allowed : 14.98 % Favored : 82.93 % 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 aren not related in a simple way. whole: 2.72 (0.31), residues: 732 helix: 2.50 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.38 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 42 TYR 0.023 0.001 TYR B 88 PHE 0.015 0.001 PHE G 25 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00336 (12691) covalent geometry : angle 0.53804 (18387) hydrogen bonds : bond 0.03372 ( 765) hydrogen bonds : angle 2.72886 ( 1916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.341 Fit side-chains REVERT: B 88 TYR cc_start: 0.8732 (m-80) cc_final: 0.8486 (m-80) REVERT: C 51 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8670 (tp) REVERT: D 93 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8194 (mm-30) REVERT: E 65 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8865 (mp) REVERT: E 129 ARG cc_start: 0.8746 (tpt90) cc_final: 0.8057 (tpt90) outliers start: 13 outliers final: 10 residues processed: 122 average time/residue: 0.1395 time to fit residues: 22.3893 Evaluate side-chains 124 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 76 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 23 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** G 24 GLN ** 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 = 0.3885 r_free = 0.3885 target = 0.130478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.086696 restraints weight = 23232.081| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.69 r_work: 0.2939 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12691 Z= 0.140 Angle : 0.531 6.907 18387 Z= 0.320 Chirality : 0.032 0.126 2096 Planarity : 0.004 0.043 1317 Dihedral : 30.545 142.102 4003 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.61 % Allowed : 15.46 % Favored : 82.93 % 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 aren not related in a simple way. whole: 2.86 (0.31), residues: 732 helix: 2.58 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.25 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 42 TYR 0.028 0.001 TYR D 40 PHE 0.006 0.001 PHE D 65 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00300 (12691) covalent geometry : angle 0.53135 (18387) hydrogen bonds : bond 0.03232 ( 765) hydrogen bonds : angle 2.65941 ( 1916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.261 Fit side-chains REVERT: B 88 TYR cc_start: 0.8711 (m-80) cc_final: 0.8465 (m-80) REVERT: C 51 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8619 (tp) REVERT: E 59 GLU cc_start: 0.7837 (pm20) cc_final: 0.7630 (pm20) REVERT: E 65 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8844 (mp) REVERT: E 129 ARG cc_start: 0.8693 (tpt90) cc_final: 0.8027 (tpt90) outliers start: 10 outliers final: 8 residues processed: 129 average time/residue: 0.1543 time to fit residues: 25.9393 Evaluate side-chains 125 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.128963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.084628 restraints weight = 23065.093| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.67 r_work: 0.2908 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12691 Z= 0.185 Angle : 0.554 7.126 18387 Z= 0.330 Chirality : 0.033 0.127 2096 Planarity : 0.004 0.045 1317 Dihedral : 30.633 142.364 4003 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.09 % Allowed : 15.62 % Favored : 82.29 % 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 aren not related in a simple way. whole: 2.72 (0.31), residues: 732 helix: 2.47 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.26 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 42 TYR 0.033 0.002 TYR D 40 PHE 0.012 0.001 PHE G 25 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00418 (12691) covalent geometry : angle 0.55439 (18387) hydrogen bonds : bond 0.03605 ( 765) hydrogen bonds : angle 2.75930 ( 1916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2878.02 seconds wall clock time: 49 minutes 53.38 seconds (2993.38 seconds total)