Starting phenix.real_space_refine on Thu Aug 6 16:16:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwj_47252/08_2026/9dwj_47252.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwj_47252/08_2026/9dwj_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_47252/08_2026/9dwj_47252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwj_47252/08_2026/9dwj_47252.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwj_47252/08_2026/9dwj_47252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwj_47252/08_2026/9dwj_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-2.2rc3-6140/lib/python3.11/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: 2.11, per 1000 atoms: 0.18 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: 0.68 Conformation dependent library (CDL) restraints added in 318.1 milliseconds 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: 1.67 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: 2.13 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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: 17863 2.32 - 4.64: 495 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=" O4' DT I 77 " pdb=" C4' DT I 77 " pdb=" C3' DT I 77 " ideal model delta sigma weight residual 106.00 103.10 2.90 6.00e-01 2.78e+00 2.33e+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 ... (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: 1710 0.060 - 0.121: 347 0.121 - 0.181: 31 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: 21.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.530 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 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 : 0.007 0.056 12691 Z= 0.550 Angle : 0.853 11.605 18387 Z= 0.728 Chirality : 0.049 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 are 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/Z covalent geometry : bond 0.00664 / 0.55 (12691) covalent geometry : angle 0.85276 / 0.73 (18387) hydrogen bonds : bond 0.10676 / 7.23 ( 765) hydrogen bonds : angle 4.42317 / 3.19 ( 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 : 0.253 Fit side-chains REVERT: B 88 TYR cc_start: 0.8429 (m-80) cc_final: 0.8158 (m-80) REVERT: E 79 LYS cc_start: 0.8134 (tptp) cc_final: 0.7768 (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: 0.1482 time to fit residues: 25.9447 Evaluate side-chains 111 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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: 4.9990 chunk 97 optimal weight: 30.0000 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: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3876 r_free = 0.3876 target = 0.129752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.085925 restraints weight = 23188.165| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.68 r_work: 0.2922 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12691 Z= 0.158 Angle : 0.619 8.533 18387 Z= 0.375 Chirality : 0.042 0.202 2096 Planarity : 0.004 0.040 1317 Dihedral : 30.641 143.391 4003 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.32 % Allowed : 7.73 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (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 0.000 ARG B 39 TYR 0.014 0.001 TYR C 39 PHE 0.013 0.001 PHE G 25 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.16 (12691) covalent geometry : angle 0.61906 / 0.38 (18387) hydrogen bonds : bond 0.04821 / 3.27 ( 765) hydrogen bonds : angle 3.32015 / 2.41 ( 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 124 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.304 Fit side-chains REVERT: A 60 LEU cc_start: 0.7889 (mt) cc_final: 0.7398 (mt) REVERT: E 45 THR cc_start: 0.8613 (t) cc_final: 0.8377 (m) REVERT: E 79 LYS cc_start: 0.8428 (tptp) cc_final: 0.8026 (tptt) REVERT: E 118 THR cc_start: 0.9192 (m) cc_final: 0.8979 (p) REVERT: E 129 ARG cc_start: 0.8724 (tpt90) cc_final: 0.8089 (tpt90) outliers start: 2 outliers final: 2 residues processed: 122 average time/residue: 0.1419 time to fit residues: 23.2147 Evaluate side-chains 113 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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: 4.9990 chunk 91 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3860 r_free = 0.3860 target = 0.128656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.084854 restraints weight = 23477.519| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.67 r_work: 0.2898 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12691 Z= 0.185 Angle : 0.621 7.460 18387 Z= 0.370 Chirality : 0.042 0.207 2096 Planarity : 0.004 0.042 1317 Dihedral : 30.801 141.752 4003 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.71 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 are not related in a simple way. whole: 2.09 (0.31), residues: 732 helix: 2.04 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.55 (0.43), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 42 TYR 0.028 0.002 TYR B 88 PHE 0.019 0.002 PHE G 25 HIS 0.007 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (12691) covalent geometry : angle 0.62101 / 0.37 (18387) hydrogen bonds : bond 0.04457 / 3.02 ( 765) hydrogen bonds : angle 3.08564 / 2.26 ( 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 126 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.301 Fit side-chains REVERT: A 60 LEU cc_start: 0.7967 (mt) cc_final: 0.7530 (mt) REVERT: E 45 THR cc_start: 0.8650 (t) cc_final: 0.8357 (m) REVERT: E 79 LYS cc_start: 0.8453 (tptp) cc_final: 0.8062 (tptt) REVERT: E 118 THR cc_start: 0.9211 (m) cc_final: 0.9005 (p) REVERT: E 129 ARG cc_start: 0.8724 (tpt90) cc_final: 0.8045 (tpt90) outliers start: 7 outliers final: 5 residues processed: 124 average time/residue: 0.1613 time to fit residues: 26.2063 Evaluate side-chains 116 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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: 20.0000 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 79 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3876 r_free = 0.3876 target = 0.129700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.085996 restraints weight = 23255.331| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.68 r_work: 0.2929 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12691 Z= 0.140 Angle : 0.573 6.815 18387 Z= 0.348 Chirality : 0.041 0.217 2096 Planarity : 0.004 0.041 1317 Dihedral : 30.878 141.157 4003 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.97 % Allowed : 11.27 % 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 are not related in a simple way. whole: 2.49 (0.31), residues: 732 helix: 2.31 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.38 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 42 TYR 0.042 0.002 TYR B 88 PHE 0.009 0.001 PHE A 67 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (12691) covalent geometry : angle 0.57320 / 0.35 (18387) hydrogen bonds : bond 0.03911 / 2.65 ( 765) hydrogen bonds : angle 2.88822 / 2.12 ( 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 128 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.337 Fit side-chains REVERT: A 65 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8601 (mp) REVERT: C 61 GLU cc_start: 0.8606 (tp30) cc_final: 0.8404 (tp30) REVERT: E 79 LYS cc_start: 0.8433 (tptp) cc_final: 0.8032 (tptt) REVERT: E 129 ARG cc_start: 0.8688 (tpt90) cc_final: 0.8014 (tpt90) REVERT: G 24 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7947 (mp10) outliers start: 6 outliers final: 4 residues processed: 126 average time/residue: 0.1636 time to fit residues: 26.8310 Evaluate side-chains 118 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 E residue 57 SER 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: 0.7980 chunk 89 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 30.0000 chunk 66 optimal weight: 5.9990 chunk 94 optimal weight: 30.0000 chunk 28 optimal weight: 2.9990 chunk 83 optimal weight: 30.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.126607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.082483 restraints weight = 23181.724| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.66 r_work: 0.2862 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1347 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= 0.236 Angle : 0.656 7.391 18387 Z= 0.377 Chirality : 0.044 0.209 2096 Planarity : 0.005 0.042 1317 Dihedral : 31.216 142.180 4003 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.61 % Allowed : 13.37 % Favored : 85.02 % 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: 2.13 (0.30), residues: 732 helix: 2.05 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.53 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 39 TYR 0.037 0.002 TYR B 88 PHE 0.027 0.002 PHE G 25 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.24 (12691) covalent geometry : angle 0.65553 / 0.38 (18387) hydrogen bonds : bond 0.04758 / 3.23 ( 765) hydrogen bonds : angle 3.06286 / 2.25 ( 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 123 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.341 Fit side-chains REVERT: A 60 LEU cc_start: 0.8035 (mt) cc_final: 0.7799 (mt) REVERT: B 88 TYR cc_start: 0.8750 (m-80) cc_final: 0.8430 (m-80) REVERT: C 61 GLU cc_start: 0.8700 (tp30) cc_final: 0.8486 (tp30) REVERT: E 129 ARG cc_start: 0.8807 (tpt90) cc_final: 0.8056 (tpt90) outliers start: 10 outliers final: 10 residues processed: 121 average time/residue: 0.1630 time to fit residues: 25.7136 Evaluate side-chains 117 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 C residue 110 ASN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 71 optimal weight: 40.0000 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 75 optimal weight: 30.0000 chunk 69 optimal weight: 1.9990 chunk 86 optimal weight: 30.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.128753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.084664 restraints weight = 23233.330| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.67 r_work: 0.2906 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12691 Z= 0.140 Angle : 0.574 7.102 18387 Z= 0.345 Chirality : 0.041 0.218 2096 Planarity : 0.004 0.040 1317 Dihedral : 31.086 141.375 4003 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.61 % Allowed : 14.33 % Favored : 84.06 % 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: 2.58 (0.31), residues: 732 helix: 2.39 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.41 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 42 TYR 0.040 0.002 TYR B 88 PHE 0.008 0.001 PHE E 67 HIS 0.005 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (12691) covalent geometry : angle 0.57369 / 0.35 (18387) hydrogen bonds : bond 0.03827 / 2.62 ( 765) hydrogen bonds : angle 2.86798 / 2.11 ( 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 129 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.332 Fit side-chains REVERT: A 65 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8630 (mp) REVERT: E 79 LYS cc_start: 0.8451 (tptp) cc_final: 0.8059 (tptt) REVERT: E 94 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8297 (mm-30) REVERT: E 129 ARG cc_start: 0.8766 (tpt90) cc_final: 0.8068 (tpt90) outliers start: 10 outliers final: 8 residues processed: 126 average time/residue: 0.1475 time to fit residues: 24.3781 Evaluate side-chains 122 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 E residue 53 ARG Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 75 optimal weight: 30.0000 chunk 16 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.126169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.081859 restraints weight = 23281.739| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.66 r_work: 0.2846 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 12691 Z= 0.258 Angle : 0.670 7.244 18387 Z= 0.381 Chirality : 0.044 0.205 2096 Planarity : 0.005 0.041 1317 Dihedral : 31.341 142.639 4003 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.58 % Allowed : 14.81 % Favored : 82.61 % 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: 2.07 (0.30), residues: 732 helix: 2.03 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.64 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 42 TYR 0.032 0.002 TYR B 88 PHE 0.024 0.002 PHE G 25 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.26 (12691) covalent geometry : angle 0.66958 / 0.38 (18387) hydrogen bonds : bond 0.04881 / 3.32 ( 765) hydrogen bonds : angle 3.05554 / 2.24 ( 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 130 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.341 Fit side-chains REVERT: B 88 TYR cc_start: 0.8799 (m-80) cc_final: 0.8551 (m-80) REVERT: D 105 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7911 (mm-30) REVERT: E 65 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8927 (mp) REVERT: E 129 ARG cc_start: 0.8862 (tpt90) cc_final: 0.8116 (tpt90) outliers start: 16 outliers final: 14 residues processed: 124 average time/residue: 0.1627 time to fit residues: 26.5156 Evaluate side-chains 126 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 62 ILE 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 E residue 57 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 101 THR 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: 20.0000 chunk 11 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.128578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.084542 restraints weight = 22823.703| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.65 r_work: 0.2898 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12691 Z= 0.141 Angle : 0.582 7.024 18387 Z= 0.347 Chirality : 0.041 0.217 2096 Planarity : 0.004 0.040 1317 Dihedral : 31.188 141.706 4003 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.25 % Allowed : 14.65 % Favored : 83.09 % 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: 2.56 (0.31), residues: 732 helix: 2.41 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.52 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 42 TYR 0.028 0.001 TYR B 88 PHE 0.008 0.001 PHE G 25 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (12691) covalent geometry : angle 0.58244 / 0.35 (18387) hydrogen bonds : bond 0.03870 / 2.65 ( 765) hydrogen bonds : angle 2.87533 / 2.13 ( 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: 14 poor density : 116 time to evaluate : 0.327 Fit side-chains REVERT: A 65 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8639 (mp) REVERT: B 88 TYR cc_start: 0.8737 (m-80) cc_final: 0.8462 (m-80) REVERT: C 51 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8656 (tp) REVERT: E 129 ARG cc_start: 0.8795 (tpt90) cc_final: 0.8086 (tpt90) outliers start: 14 outliers final: 11 residues processed: 124 average time/residue: 0.1580 time to fit residues: 25.8059 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 : 0.353 ------------------------------------------------------------------------------- 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 38 ASN 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 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain G residue 101 THR 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: 30.0000 chunk 90 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 84 optimal weight: 30.0000 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.128549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.084195 restraints weight = 22749.643| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.66 r_work: 0.2899 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12691 Z= 0.148 Angle : 0.589 7.025 18387 Z= 0.348 Chirality : 0.041 0.214 2096 Planarity : 0.004 0.044 1317 Dihedral : 31.183 142.140 4003 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.09 % Allowed : 15.46 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.31), residues: 732 helix: 2.45 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.48 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 42 TYR 0.027 0.001 TYR B 88 PHE 0.011 0.001 PHE G 25 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (12691) covalent geometry : angle 0.58865 / 0.35 (18387) hydrogen bonds : bond 0.03960 / 2.71 ( 765) hydrogen bonds : angle 2.86302 / 2.11 ( 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 128 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.335 Fit side-chains REVERT: A 65 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8639 (mp) REVERT: B 88 TYR cc_start: 0.8742 (m-80) cc_final: 0.8482 (m-80) REVERT: C 51 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8687 (tp) REVERT: E 129 ARG cc_start: 0.8767 (tpt90) cc_final: 0.8080 (tpt90) outliers start: 13 outliers final: 10 residues processed: 125 average time/residue: 0.1584 time to fit residues: 26.0792 Evaluate side-chains 127 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 E residue 50 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain G residue 101 THR 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: 30.0000 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 81 optimal weight: 50.0000 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.128949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.084818 restraints weight = 23171.879| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.66 r_work: 0.2903 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12691 Z= 0.143 Angle : 0.580 6.843 18387 Z= 0.345 Chirality : 0.040 0.218 2096 Planarity : 0.004 0.043 1317 Dihedral : 31.148 142.253 4003 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.77 % Allowed : 15.78 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.31), residues: 732 helix: 2.47 (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 0.010 0.000 ARG G 42 TYR 0.026 0.001 TYR B 88 PHE 0.009 0.001 PHE G 25 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (12691) covalent geometry : angle 0.58048 / 0.35 (18387) hydrogen bonds : bond 0.03877 / 2.66 ( 765) hydrogen bonds : angle 2.83295 / 2.09 ( 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 127 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 60 LEU cc_start: 0.7880 (mt) cc_final: 0.7610 (mt) REVERT: A 65 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8641 (mp) REVERT: B 88 TYR cc_start: 0.8730 (m-80) cc_final: 0.8467 (m-80) REVERT: C 51 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8649 (tp) REVERT: E 129 ARG cc_start: 0.8737 (tpt90) cc_final: 0.8059 (tpt90) outliers start: 11 outliers final: 7 residues processed: 125 average time/residue: 0.1605 time to fit residues: 26.2707 Evaluate side-chains 122 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 50 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 93 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 chunk 97 optimal weight: 30.0000 chunk 78 optimal weight: 20.0000 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 71 optimal weight: 40.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.128223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083839 restraints weight = 23034.778| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.66 r_work: 0.2891 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12691 Z= 0.168 Angle : 0.593 6.938 18387 Z= 0.349 Chirality : 0.041 0.215 2096 Planarity : 0.004 0.043 1317 Dihedral : 31.175 142.375 4003 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.93 % Allowed : 15.78 % 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 are 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 0.010 0.000 ARG G 42 TYR 0.025 0.001 TYR B 88 PHE 0.012 0.001 PHE G 25 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (12691) covalent geometry : angle 0.59310 / 0.35 (18387) hydrogen bonds : bond 0.04024 / 2.76 ( 765) hydrogen bonds : angle 2.85352 / 2.10 ( 1916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2909.08 seconds wall clock time: 50 minutes 35.44 seconds (3035.44 seconds total)