Starting phenix.real_space_refine on Sat Jun 14 13:28:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwj_47252/06_2025/9dwj_47252.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwj_47252/06_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_47252/06_2025/9dwj_47252.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwj_47252/06_2025/9dwj_47252.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwj_47252/06_2025/9dwj_47252.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwj_47252/06_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-5710/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: 12.65, per 1000 atoms: 1.06 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: 2.86 Conformation dependent library (CDL) restraints added in 885.8 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: 9.58 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: 4.10 Time building geometry restraints manager: 3.50 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: 12.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 39.590 Find NCS groups from input model: 0.450 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.720 ------------------------------------------------------------------------------- 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 : 0.842 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: 0.3608 time to fit residues: 62.8189 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 : 1.646 ------------------------------------------------------------------------------- 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 : 0.981 Fit side-chains REVERT: A 60 LEU cc_start: 0.7882 (mt) cc_final: 0.7407 (mt) REVERT: E 45 THR cc_start: 0.8621 (t) cc_final: 0.8377 (m) REVERT: E 79 LYS cc_start: 0.8419 (tptp) cc_final: 0.8025 (tptt) REVERT: E 118 THR cc_start: 0.9193 (m) cc_final: 0.8987 (p) REVERT: E 129 ARG cc_start: 0.8733 (tpt90) cc_final: 0.8091 (tpt90) outliers start: 3 outliers final: 2 residues processed: 121 average time/residue: 0.3243 time to fit residues: 51.8363 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 : 0.838 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.5276 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.130455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.086642 restraints weight = 23390.661| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.69 r_work: 0.2937 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12691 Z= 0.143 Angle : 0.540 7.449 18387 Z= 0.325 Chirality : 0.032 0.133 2096 Planarity : 0.004 0.040 1317 Dihedral : 30.460 141.213 4003 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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: 2.29 (0.31), residues: 732 helix: 2.19 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.50 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 31 PHE 0.012 0.001 PHE G 25 TYR 0.028 0.001 TYR B 88 ARG 0.007 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 765) hydrogen bonds : angle 2.93394 ( 1916) covalent geometry : bond 0.00303 (12691) covalent geometry : angle 0.53961 (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 127 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.969 Fit side-chains REVERT: E 45 THR cc_start: 0.8575 (t) cc_final: 0.8271 (m) REVERT: E 48 LEU cc_start: 0.9364 (mp) cc_final: 0.9011 (mp) REVERT: E 79 LYS cc_start: 0.8408 (tptp) cc_final: 0.8015 (tptt) REVERT: E 129 ARG cc_start: 0.8698 (tpt90) cc_final: 0.8035 (tpt90) outliers start: 5 outliers final: 3 residues processed: 127 average time/residue: 0.3439 time to fit residues: 57.2900 Evaluate side-chains 113 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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: 0.8980 chunk 93 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 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: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.128067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.084119 restraints weight = 23242.263| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.66 r_work: 0.2885 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12691 Z= 0.209 Angle : 0.563 7.318 18387 Z= 0.335 Chirality : 0.034 0.132 2096 Planarity : 0.004 0.040 1317 Dihedral : 30.693 141.896 4003 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.61 % Allowed : 10.79 % Favored : 87.60 % 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: 2.39 (0.31), residues: 732 helix: 2.24 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.42 (0.43), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 31 PHE 0.020 0.002 PHE G 25 TYR 0.010 0.002 TYR G 57 ARG 0.007 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 765) hydrogen bonds : angle 2.91961 ( 1916) covalent geometry : bond 0.00477 (12691) covalent geometry : angle 0.56254 (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 131 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.847 Fit side-chains REVERT: E 79 LYS cc_start: 0.8442 (tptp) cc_final: 0.8052 (tptt) REVERT: E 129 ARG cc_start: 0.8761 (tpt90) cc_final: 0.8051 (tpt90) outliers start: 10 outliers final: 7 residues processed: 128 average time/residue: 0.3727 time to fit residues: 60.8975 Evaluate side-chains 115 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 76 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 = 0.3876 r_free = 0.3876 target = 0.129797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.086153 restraints weight = 23099.520| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.69 r_work: 0.2922 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12691 Z= 0.149 Angle : 0.523 6.832 18387 Z= 0.317 Chirality : 0.032 0.124 2096 Planarity : 0.004 0.041 1317 Dihedral : 30.557 141.702 4003 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.13 % Allowed : 13.04 % Favored : 85.83 % 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: 2.76 (0.31), residues: 732 helix: 2.52 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.32 (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 0.021 0.001 TYR B 88 ARG 0.007 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03257 ( 765) hydrogen bonds : angle 2.74450 ( 1916) covalent geometry : bond 0.00325 (12691) covalent geometry : angle 0.52335 (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 129 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.963 Fit side-chains REVERT: A 60 LEU cc_start: 0.7926 (mt) cc_final: 0.7718 (mt) REVERT: B 88 TYR cc_start: 0.8691 (m-80) cc_final: 0.8437 (m-80) REVERT: C 61 GLU cc_start: 0.8598 (tp30) cc_final: 0.8382 (tp30) REVERT: E 79 LYS cc_start: 0.8424 (tptp) cc_final: 0.8034 (tptt) REVERT: E 129 ARG cc_start: 0.8698 (tpt90) cc_final: 0.7996 (tpt90) outliers start: 7 outliers final: 7 residues processed: 127 average time/residue: 0.3675 time to fit residues: 59.8159 Evaluate side-chains 120 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 97 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.126645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.082363 restraints weight = 23282.297| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.68 r_work: 0.2863 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12691 Z= 0.255 Angle : 0.589 7.650 18387 Z= 0.347 Chirality : 0.036 0.144 2096 Planarity : 0.005 0.061 1317 Dihedral : 30.916 143.283 4003 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.42 % Allowed : 13.53 % 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: 2.31 (0.30), residues: 732 helix: 2.18 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.46 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.018 0.002 PHE G 25 TYR 0.012 0.002 TYR B 88 ARG 0.007 0.001 ARG F 45 Details of bonding type rmsd hydrogen bonds : bond 0.04068 ( 765) hydrogen bonds : angle 2.95568 ( 1916) covalent geometry : bond 0.00585 (12691) covalent geometry : angle 0.58910 (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 135 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.895 Fit side-chains REVERT: B 88 TYR cc_start: 0.8786 (m-80) cc_final: 0.8563 (m-80) REVERT: C 51 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8743 (tp) REVERT: C 61 GLU cc_start: 0.8712 (tp30) cc_final: 0.8501 (tp30) REVERT: D 93 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8253 (mm-30) REVERT: D 105 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7872 (mm-30) REVERT: E 94 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8241 (mm-30) REVERT: E 129 ARG cc_start: 0.8808 (tpt90) cc_final: 0.8074 (tpt90) outliers start: 15 outliers final: 13 residues processed: 131 average time/residue: 0.3529 time to fit residues: 59.5484 Evaluate side-chains 128 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain 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 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: 1.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.130759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.086972 restraints weight = 23024.889| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.67 r_work: 0.2938 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12691 Z= 0.140 Angle : 0.529 6.573 18387 Z= 0.319 Chirality : 0.032 0.132 2096 Planarity : 0.004 0.041 1317 Dihedral : 30.481 143.132 4003 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.25 % Allowed : 13.85 % Favored : 83.90 % 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: 2.61 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.29 (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 G 25 TYR 0.012 0.001 TYR D 40 ARG 0.008 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 765) hydrogen bonds : angle 2.64779 ( 1916) covalent geometry : bond 0.00302 (12691) covalent geometry : angle 0.52869 (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 137 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.820 Fit side-chains REVERT: C 51 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8594 (tp) REVERT: D 93 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8145 (mm-30) REVERT: E 59 GLU cc_start: 0.7575 (pm20) cc_final: 0.7343 (pm20) REVERT: E 129 ARG cc_start: 0.8720 (tpt90) cc_final: 0.8047 (tpt90) outliers start: 14 outliers final: 11 residues processed: 135 average time/residue: 0.3396 time to fit residues: 59.7702 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 : 0.845 ------------------------------------------------------------------------------- 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 C residue 51 LEU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain 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: 6.9990 chunk 72 optimal weight: 10.0000 chunk 38 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.130732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.086960 restraints weight = 23135.503| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.69 r_work: 0.2939 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1962 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= 0.142 Angle : 0.529 6.759 18387 Z= 0.318 Chirality : 0.032 0.132 2096 Planarity : 0.004 0.041 1317 Dihedral : 30.510 142.417 4003 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.93 % Allowed : 15.46 % 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: 2.99 (0.31), residues: 732 helix: 2.67 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.18 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE G 25 TYR 0.028 0.001 TYR H 83 ARG 0.009 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 765) hydrogen bonds : angle 2.62630 ( 1916) covalent geometry : bond 0.00308 (12691) covalent geometry : angle 0.52948 (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 129 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.882 Fit side-chains REVERT: C 51 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8590 (tp) REVERT: E 129 ARG cc_start: 0.8747 (tpt90) cc_final: 0.8031 (tpt90) outliers start: 12 outliers final: 11 residues processed: 127 average time/residue: 0.3626 time to fit residues: 59.3884 Evaluate side-chains 124 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 80 THR 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 E residue 80 THR 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: 6.9990 chunk 31 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.3848 r_free = 0.3848 target = 0.127777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.083656 restraints weight = 22955.430| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.65 r_work: 0.2889 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12691 Z= 0.219 Angle : 0.578 7.400 18387 Z= 0.340 Chirality : 0.035 0.139 2096 Planarity : 0.005 0.043 1317 Dihedral : 30.807 142.827 4003 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.06 % Allowed : 15.30 % 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: 2.60 (0.31), residues: 732 helix: 2.37 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.29 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.014 0.002 PHE G 25 TYR 0.022 0.002 TYR H 83 ARG 0.010 0.001 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 765) hydrogen bonds : angle 2.86639 ( 1916) covalent geometry : bond 0.00501 (12691) covalent geometry : angle 0.57788 (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 132 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.943 Fit side-chains REVERT: B 88 TYR cc_start: 0.8737 (m-80) cc_final: 0.8512 (m-80) REVERT: C 51 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8692 (tp) REVERT: E 65 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8910 (mp) REVERT: E 94 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8308 (mm-30) REVERT: E 129 ARG cc_start: 0.8723 (tpt90) cc_final: 0.8025 (tpt90) outliers start: 19 outliers final: 15 residues processed: 128 average time/residue: 0.3380 time to fit residues: 56.9475 Evaluate side-chains 129 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 80 THR 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 C residue 51 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 61 LEU 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 81 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 78 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 = 0.130337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.086436 restraints weight = 23026.302| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.67 r_work: 0.2936 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2174 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= 0.146 Angle : 0.544 6.715 18387 Z= 0.324 Chirality : 0.032 0.132 2096 Planarity : 0.004 0.041 1317 Dihedral : 30.574 142.954 4003 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.42 % Allowed : 16.10 % Favored : 81.48 % 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: 2.56 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.14 (0.44), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.023 0.001 TYR H 83 ARG 0.009 0.001 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 765) hydrogen bonds : angle 2.69931 ( 1916) covalent geometry : bond 0.00317 (12691) covalent geometry : angle 0.54425 (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: 15 poor density : 118 time to evaluate : 0.806 Fit side-chains REVERT: C 51 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8585 (tp) REVERT: E 65 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8827 (mp) REVERT: E 94 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8282 (mm-30) REVERT: E 129 ARG cc_start: 0.8623 (tpt90) cc_final: 0.7977 (tpt90) outliers start: 15 outliers final: 12 residues processed: 129 average time/residue: 0.3642 time to fit residues: 60.6349 Evaluate side-chains 129 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 61 LEU 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: 4.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 25 optimal weight: 0.0270 chunk 2 optimal weight: 0.0010 chunk 55 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 overall best weight: 0.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.131860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.088025 restraints weight = 22982.907| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.66 r_work: 0.2967 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12691 Z= 0.136 Angle : 0.537 6.752 18387 Z= 0.320 Chirality : 0.032 0.125 2096 Planarity : 0.004 0.046 1317 Dihedral : 30.515 142.601 4003 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.25 % Allowed : 16.26 % Favored : 81.48 % 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: 3.02 (0.31), residues: 732 helix: 2.65 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.01 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 75 PHE 0.007 0.001 PHE A 67 TYR 0.023 0.002 TYR B 88 ARG 0.010 0.001 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 765) hydrogen bonds : angle 2.66869 ( 1916) covalent geometry : bond 0.00289 (12691) covalent geometry : angle 0.53705 (18387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6518.63 seconds wall clock time: 113 minutes 24.47 seconds (6804.47 seconds total)