Starting phenix.real_space_refine on Sat May 17 21:43:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwj_47252/05_2025/9dwj_47252.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwj_47252/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dwj_47252/05_2025/9dwj_47252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwj_47252/05_2025/9dwj_47252.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwj_47252/05_2025/9dwj_47252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwj_47252/05_2025/9dwj_47252.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.21, per 1000 atoms: 0.94 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: 3.11 Conformation dependent library (CDL) restraints added in 992.5 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: 6.27 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: 4.17 Time building geometry restraints manager: 3.63 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: 14.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 37.510 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.080 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (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 HIS 0.004 0.001 HIS F 75 PHE 0.040 0.002 PHE G 25 TYR 0.019 0.002 TYR H 42 ARG 0.011 0.001 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.10676 ( 765) hydrogen bonds : angle 4.42317 ( 1916) covalent geometry : bond 0.00505 (12691) covalent geometry : angle 0.69953 (18387) *********************** 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 : 0.987 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: 0.3329 time to fit residues: 57.3524 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 : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.129668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.085734 restraints weight = 23007.195| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.68 r_work: 0.2916 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.0592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12691 Z= 0.169 Angle : 0.573 8.631 18387 Z= 0.340 Chirality : 0.033 0.133 2096 Planarity : 0.004 0.040 1317 Dihedral : 30.581 143.432 4003 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.48 % Allowed : 7.89 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.30), residues: 732 helix: 1.80 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -0.67 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.013 0.001 PHE G 25 TYR 0.015 0.001 TYR C 39 ARG 0.005 0.001 ARG B 39 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 765) hydrogen bonds : angle 3.25720 ( 1916) covalent geometry : bond 0.00368 (12691) covalent geometry : angle 0.57290 (18387) *********************** 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 122 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.842 Fit side-chains REVERT: A 60 LEU cc_start: 0.7882 (mt) cc_final: 0.7407 (mt) REVERT: E 45 THR cc_start: 0.8620 (t) cc_final: 0.8377 (m) REVERT: E 79 LYS cc_start: 0.8419 (tptp) cc_final: 0.8024 (tptt) REVERT: E 118 THR cc_start: 0.9193 (m) cc_final: 0.8986 (p) REVERT: E 129 ARG cc_start: 0.8737 (tpt90) cc_final: 0.8094 (tpt90) outliers start: 3 outliers final: 2 residues processed: 121 average time/residue: 0.3227 time to fit residues: 51.3775 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 : 0.843 ------------------------------------------------------------------------------- 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 92 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 11 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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** ** H 84 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 = 0.3878 r_free = 0.3878 target = 0.130056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086257 restraints weight = 23388.580| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.69 r_work: 0.2929 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12691 Z= 0.148 Angle : 0.546 7.718 18387 Z= 0.328 Chirality : 0.032 0.132 2096 Planarity : 0.004 0.041 1317 Dihedral : 30.484 141.532 4003 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.81 % Allowed : 9.18 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.31), residues: 732 helix: 2.14 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.51 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 31 PHE 0.014 0.001 PHE G 25 TYR 0.027 0.001 TYR B 88 ARG 0.008 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 765) hydrogen bonds : angle 2.96882 ( 1916) covalent geometry : bond 0.00315 (12691) covalent geometry : angle 0.54551 (18387) *********************** 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 123 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.837 Fit side-chains REVERT: E 45 THR cc_start: 0.8574 (t) cc_final: 0.8268 (m) REVERT: E 48 LEU cc_start: 0.9372 (mp) cc_final: 0.9000 (mp) REVERT: E 51 ILE cc_start: 0.8876 (mt) cc_final: 0.8663 (mt) REVERT: E 79 LYS cc_start: 0.8410 (tptp) cc_final: 0.8016 (tptt) REVERT: E 129 ARG cc_start: 0.8704 (tpt90) cc_final: 0.8064 (tpt90) REVERT: H 42 TYR cc_start: 0.8329 (t80) cc_final: 0.8077 (t80) outliers start: 5 outliers final: 3 residues processed: 123 average time/residue: 0.3305 time to fit residues: 53.0727 Evaluate side-chains 112 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 0.5980 chunk 93 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 52 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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** D 47 GLN E 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.127862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083964 restraints weight = 23245.478| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.67 r_work: 0.2891 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1210 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= 0.207 Angle : 0.556 7.174 18387 Z= 0.332 Chirality : 0.034 0.133 2096 Planarity : 0.004 0.041 1317 Dihedral : 30.698 141.946 4003 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.29 % Allowed : 11.59 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.31), residues: 732 helix: 2.18 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.44 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.019 0.002 PHE G 25 TYR 0.010 0.001 TYR G 57 ARG 0.006 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 765) hydrogen bonds : angle 2.88931 ( 1916) covalent geometry : bond 0.00471 (12691) covalent geometry : angle 0.55615 (18387) *********************** 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 127 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.883 Fit side-chains REVERT: E 45 THR cc_start: 0.8673 (t) cc_final: 0.8394 (m) REVERT: E 79 LYS cc_start: 0.8434 (tptp) cc_final: 0.8049 (tptt) REVERT: E 129 ARG cc_start: 0.8777 (tpt90) cc_final: 0.8095 (tpt90) outliers start: 8 outliers final: 6 residues processed: 124 average time/residue: 0.3703 time to fit residues: 58.6494 Evaluate side-chains 116 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 E residue 53 ARG Chi-restraints excluded: chain E residue 71 VAL 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 89 optimal weight: 7.9990 chunk 38 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.0270 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 85 GLN H 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.130638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.087655 restraints weight = 23138.765| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.65 r_work: 0.2949 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1475 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= 0.138 Angle : 0.518 6.572 18387 Z= 0.315 Chirality : 0.032 0.127 2096 Planarity : 0.004 0.041 1317 Dihedral : 30.487 141.907 4003 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.13 % Allowed : 12.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.31), residues: 732 helix: 2.59 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.27 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE A 67 TYR 0.020 0.001 TYR B 88 ARG 0.007 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 765) hydrogen bonds : angle 2.68314 ( 1916) covalent geometry : bond 0.00295 (12691) covalent geometry : angle 0.51796 (18387) *********************** 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 136 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.976 Fit side-chains REVERT: B 88 TYR cc_start: 0.8672 (m-80) cc_final: 0.8422 (m-80) REVERT: C 61 GLU cc_start: 0.8570 (tp30) cc_final: 0.8352 (tp30) REVERT: E 45 THR cc_start: 0.8398 (t) cc_final: 0.8187 (m) REVERT: E 79 LYS cc_start: 0.8423 (tptp) cc_final: 0.8192 (tptp) REVERT: E 129 ARG cc_start: 0.8700 (tpt90) cc_final: 0.8031 (tpt90) outliers start: 7 outliers final: 6 residues processed: 133 average time/residue: 0.3637 time to fit residues: 61.9656 Evaluate side-chains 122 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 E residue 53 ARG Chi-restraints excluded: chain E residue 71 VAL 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 94 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN E 76 GLN E 85 GLN H 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.125430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.080994 restraints weight = 23336.131| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.67 r_work: 0.2840 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 12691 Z= 0.303 Angle : 0.631 7.734 18387 Z= 0.367 Chirality : 0.038 0.137 2096 Planarity : 0.005 0.063 1317 Dihedral : 31.182 144.886 4003 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.74 % Allowed : 13.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.30), residues: 732 helix: 2.04 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.46 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.018 0.002 PHE G 25 TYR 0.013 0.002 TYR G 39 ARG 0.006 0.001 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 765) hydrogen bonds : angle 3.07994 ( 1916) covalent geometry : bond 0.00698 (12691) covalent geometry : angle 0.63143 (18387) *********************** 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 134 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.865 Fit side-chains REVERT: B 88 TYR cc_start: 0.8791 (m-80) cc_final: 0.8547 (m-80) REVERT: C 61 GLU cc_start: 0.8736 (tp30) cc_final: 0.8532 (tp30) REVERT: D 105 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7913 (mm-30) REVERT: E 129 ARG cc_start: 0.8873 (tpt90) cc_final: 0.8116 (tpt90) outliers start: 17 outliers final: 15 residues processed: 129 average time/residue: 0.3298 time to fit residues: 55.5191 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 : 0.841 ------------------------------------------------------------------------------- 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 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 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 47 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.129543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.085694 restraints weight = 23065.638| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.66 r_work: 0.2919 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1939 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= 0.151 Angle : 0.537 6.543 18387 Z= 0.324 Chirality : 0.032 0.134 2096 Planarity : 0.004 0.042 1317 Dihedral : 30.577 143.793 4003 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.09 % Allowed : 14.65 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.31), residues: 732 helix: 2.47 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.35 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE G 25 TYR 0.011 0.001 TYR D 40 ARG 0.008 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 765) hydrogen bonds : angle 2.69701 ( 1916) covalent geometry : bond 0.00329 (12691) covalent geometry : angle 0.53669 (18387) *********************** 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 133 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.059 Fit side-chains REVERT: C 61 GLU cc_start: 0.8631 (tp30) cc_final: 0.8425 (tp30) REVERT: D 93 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8239 (mm-30) REVERT: E 129 ARG cc_start: 0.8783 (tpt90) cc_final: 0.8083 (tpt90) outliers start: 13 outliers final: 10 residues processed: 130 average time/residue: 0.3389 time to fit residues: 57.6351 Evaluate side-chains 127 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 E residue 53 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 47 SER 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 97 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 38 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.130265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.086246 restraints weight = 23157.810| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.67 r_work: 0.2930 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2039 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= 0.143 Angle : 0.531 6.843 18387 Z= 0.320 Chirality : 0.032 0.131 2096 Planarity : 0.004 0.042 1317 Dihedral : 30.565 142.946 4003 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.77 % Allowed : 15.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.31), residues: 732 helix: 2.60 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.26 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.006 0.001 PHE G 25 TYR 0.020 0.001 TYR D 40 ARG 0.009 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 765) hydrogen bonds : angle 2.68475 ( 1916) covalent geometry : bond 0.00308 (12691) covalent geometry : angle 0.53110 (18387) *********************** 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 132 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.850 Fit side-chains REVERT: E 65 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8862 (mp) REVERT: E 129 ARG cc_start: 0.8704 (tpt90) cc_final: 0.8034 (tpt90) outliers start: 11 outliers final: 10 residues processed: 129 average time/residue: 0.3317 time to fit residues: 55.7214 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 : 0.925 ------------------------------------------------------------------------------- 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 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 G residue 101 THR 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 90 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.127066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.082568 restraints weight = 23022.884| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.65 r_work: 0.2870 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12691 Z= 0.239 Angle : 0.595 7.489 18387 Z= 0.349 Chirality : 0.036 0.138 2096 Planarity : 0.005 0.042 1317 Dihedral : 30.926 143.537 4003 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.25 % Allowed : 15.78 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.30), residues: 732 helix: 2.25 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.35 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.016 0.002 PHE G 25 TYR 0.029 0.002 TYR H 83 ARG 0.009 0.001 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 765) hydrogen bonds : angle 2.95171 ( 1916) covalent geometry : bond 0.00549 (12691) covalent geometry : angle 0.59505 (18387) *********************** 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 127 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 1.021 Fit side-chains REVERT: B 88 TYR cc_start: 0.8746 (m-80) cc_final: 0.8515 (m-80) REVERT: E 65 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8918 (mp) REVERT: E 129 ARG cc_start: 0.8778 (tpt90) cc_final: 0.8071 (tpt90) outliers start: 14 outliers final: 13 residues processed: 124 average time/residue: 0.3258 time to fit residues: 53.3998 Evaluate side-chains 125 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 E residue 50 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 65 LEU 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 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 81 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.129758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.085658 restraints weight = 23013.841| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.69 r_work: 0.2920 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2216 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= 0.149 Angle : 0.545 6.822 18387 Z= 0.325 Chirality : 0.032 0.130 2096 Planarity : 0.004 0.044 1317 Dihedral : 30.626 143.488 4003 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.09 % Allowed : 15.78 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.31), residues: 732 helix: 2.50 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.23 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.009 0.001 PHE G 25 TYR 0.028 0.002 TYR H 83 ARG 0.009 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03422 ( 765) hydrogen bonds : angle 2.72724 ( 1916) covalent geometry : bond 0.00324 (12691) covalent geometry : angle 0.54458 (18387) ********************** 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 133 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.891 Fit side-chains REVERT: B 88 TYR cc_start: 0.8697 (m-80) cc_final: 0.8468 (m-80) REVERT: E 65 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8858 (mp) REVERT: E 129 ARG cc_start: 0.8681 (tpt90) cc_final: 0.8035 (tpt90) outliers start: 13 outliers final: 11 residues processed: 129 average time/residue: 0.3093 time to fit residues: 52.4758 Evaluate side-chains 128 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 A residue 124 ILE 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 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 54 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 0.0050 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.130568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.086446 restraints weight = 22982.299| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.66 r_work: 0.2935 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2278 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= 0.143 Angle : 0.542 6.804 18387 Z= 0.324 Chirality : 0.032 0.133 2096 Planarity : 0.004 0.042 1317 Dihedral : 30.609 143.042 4003 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.77 % Allowed : 16.59 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.31), residues: 732 helix: 2.58 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.19 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE A 67 TYR 0.022 0.001 TYR D 40 ARG 0.010 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 765) hydrogen bonds : angle 2.69311 ( 1916) covalent geometry : bond 0.00311 (12691) covalent geometry : angle 0.54176 (18387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5872.34 seconds wall clock time: 104 minutes 2.59 seconds (6242.59 seconds total)