Starting phenix.real_space_refine on Thu Aug 6 16:18:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwf_47242/08_2026/9dwf_47242.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwf_47242/08_2026/9dwf_47242.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dwf_47242/08_2026/9dwf_47242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwf_47242/08_2026/9dwf_47242.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwf_47242/08_2026/9dwf_47242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwf_47242/08_2026/9dwf_47242.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5752 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 293 5.49 5 S 10 5.16 5 C 6598 2.51 5 N 2239 2.21 5 O 2809 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11949 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: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} 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: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} 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: 2383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2383 Classifications: {'DNA': 117} Link IDs: {'rna3p': 116} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 595 Classifications: {'DNA': 29} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 28} Time building chain proxies: 2.91, per 1000 atoms: 0.24 Number of scatterers: 11949 At special positions: 0 Unit cell: (73.927, 124.313, 118.531, 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 293 15.00 O 2809 8.00 N 2239 7.00 C 6598 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 372.8 milliseconds 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 72.8% alpha, 2.7% beta 145 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 50 through 55 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 131 removed outlier: 3.576A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.222A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.514A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.358A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.651A 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 removed outlier: 3.690A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.535A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 42 through 57 removed outlier: 4.132A pdb=" N VAL E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.611A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.676A 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: 3.638A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.589A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (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 45 through 73 removed outlier: 4.381A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.721A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.519A pdb=" N ILE H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 removed outlier: 3.767A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.313A 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 removed outlier: 6.546A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.439A 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 'E' and resid 83 through 84 removed outlier: 7.128A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.137A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 390 hydrogen bonds defined for protein. 1158 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 742 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2192 1.33 - 1.45: 4201 1.45 - 1.57: 5761 1.57 - 1.69: 585 1.69 - 1.81: 20 Bond restraints: 12759 Sorted by residual: bond pdb=" P DC K 119 " pdb=" OP3 DC K 119 " ideal model delta sigma weight residual 1.480 1.608 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" O3' DC J 27 " pdb=" P DT J 28 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.20e-02 6.94e+03 1.05e+01 bond pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 bond pdb=" C3' DG I 63 " pdb=" C2' DG I 63 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.98e+00 bond pdb=" C3' DG J 52 " pdb=" C2' DG J 52 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.69e+00 ... (remaining 12754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 18299 2.63 - 5.25: 171 5.25 - 7.88: 16 7.88 - 10.51: 1 10.51 - 13.13: 1 Bond angle restraints: 18488 Sorted by residual: angle pdb=" O3' DA K 120 " pdb=" C3' DA K 120 " pdb=" C2' DA K 120 " ideal model delta sigma weight residual 109.40 96.27 13.13 2.50e+00 1.60e-01 2.76e+01 angle pdb=" N3 DT J 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" C LYS C 74 " pdb=" N LYS C 75 " pdb=" CA LYS C 75 " ideal model delta sigma weight residual 122.94 116.30 6.64 1.50e+00 4.44e-01 1.96e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 ... (remaining 18483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.10: 5124 28.10 - 56.20: 1615 56.20 - 84.30: 171 84.30 - 112.40: 0 112.40 - 140.49: 3 Dihedral angle restraints: 6913 sinusoidal: 4744 harmonic: 2169 Sorted by residual: dihedral pdb=" CA GLU A 50 " pdb=" C GLU A 50 " pdb=" N ILE A 51 " pdb=" CA ILE A 51 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 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 79.51 140.49 1 3.50e+01 8.16e-04 1.39e+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 80.10 139.90 1 3.50e+01 8.16e-04 1.38e+01 ... (remaining 6910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 2094 0.133 - 0.266: 8 0.266 - 0.398: 0 0.398 - 0.531: 0 0.531 - 0.664: 3 Chirality restraints: 2105 Sorted by residual: chirality pdb=" P DC K 119 " pdb=" OP1 DC K 119 " pdb=" OP2 DC K 119 " pdb=" O5' DC K 119 " both_signs ideal model delta sigma weight residual True 2.34 3.00 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" P DA K 120 " pdb=" OP1 DA K 120 " pdb=" OP2 DA K 120 " pdb=" O5' DA K 120 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.58 2.00e-01 2.50e+01 8.32e+00 chirality pdb=" P DG J 29 " pdb=" OP1 DG J 29 " pdb=" OP2 DG J 29 " pdb=" O5' DG J 29 " both_signs ideal model delta sigma weight residual True 2.34 -2.91 -0.57 2.00e-01 2.50e+01 8.12e+00 ... (remaining 2102 not shown) Planarity restraints: 1322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 116 " -0.050 5.00e-02 4.00e+02 7.41e-02 8.80e+00 pdb=" N PRO C 117 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 117 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 117 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 50 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C GLU A 50 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU A 50 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 51 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 23 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" C ARG B 23 " 0.039 2.00e-02 2.50e+03 pdb=" O ARG B 23 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP B 24 " -0.013 2.00e-02 2.50e+03 ... (remaining 1319 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1685 2.76 - 3.30: 9962 3.30 - 3.83: 23782 3.83 - 4.37: 27984 4.37 - 4.90: 39584 Nonbonded interactions: 102997 Sorted by model distance: nonbonded pdb=" O ARG F 23 " pdb=" OD1 ASP F 24 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.335 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.369 3.040 nonbonded pdb=" N ALA A 47 " pdb=" OP2 DT J 83 " model vdw 2.387 3.120 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.408 3.040 ... (remaining 102992 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' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 19.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.870 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 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 : 0.006 0.128 12759 Z= 0.518 Angle : 0.789 13.135 18488 Z= 0.680 Chirality : 0.050 0.664 2105 Planarity : 0.005 0.074 1322 Dihedral : 27.534 140.495 5515 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.30), residues: 733 helix: 1.29 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -0.95 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 92 TYR 0.022 0.002 TYR H 40 PHE 0.012 0.002 PHE H 70 HIS 0.003 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.52 (12759) covalent geometry : angle 0.78882 / 0.68 (18488) hydrogen bonds : bond 0.13342 / 8.32 ( 761) hydrogen bonds : angle 4.26418 / 2.98 ( 1900) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.358 Fit side-chains REVERT: B 91 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8237 (ttpt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1633 time to fit residues: 33.9935 Evaluate side-chains 125 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS H 63 ASN H 95 GLN H 109 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.138456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094375 restraints weight = 18362.141| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.03 r_work: 0.2977 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 12759 Z= 0.290 Angle : 0.726 8.762 18488 Z= 0.413 Chirality : 0.049 0.234 2105 Planarity : 0.006 0.043 1322 Dihedral : 30.787 139.954 4034 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.09 % Allowed : 7.06 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.30), residues: 733 helix: 1.36 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -1.16 (0.38), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 35 TYR 0.022 0.003 TYR D 40 PHE 0.022 0.003 PHE C 25 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.29 (12759) covalent geometry : angle 0.72559 / 0.41 (18488) hydrogen bonds : bond 0.05974 / 3.80 ( 761) hydrogen bonds : angle 3.24665 / 2.24 ( 1900) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.321 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 130 average time/residue: 0.1463 time to fit residues: 25.2022 Evaluate side-chains 125 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 75 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** 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 = 0.3883 r_free = 0.3883 target = 0.140990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097493 restraints weight = 18655.684| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.04 r_work: 0.3039 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12759 Z= 0.139 Angle : 0.578 5.653 18488 Z= 0.351 Chirality : 0.042 0.246 2105 Planarity : 0.004 0.041 1322 Dihedral : 30.793 140.757 4034 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.93 % Allowed : 8.19 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.30), residues: 733 helix: 2.07 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.84 (0.38), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 92 TYR 0.015 0.001 TYR D 40 PHE 0.007 0.001 PHE E 84 HIS 0.003 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.14 (12759) covalent geometry : angle 0.57767 / 0.35 (18488) hydrogen bonds : bond 0.04404 / 2.83 ( 761) hydrogen bonds : angle 2.92598 / 1.99 ( 1900) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.348 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 137 average time/residue: 0.1399 time to fit residues: 25.8224 Evaluate side-chains 135 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 5 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.141203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.097832 restraints weight = 18578.151| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.04 r_work: 0.3051 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12759 Z= 0.140 Angle : 0.567 5.843 18488 Z= 0.343 Chirality : 0.041 0.254 2105 Planarity : 0.004 0.035 1322 Dihedral : 30.818 139.608 4034 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.77 % Allowed : 9.15 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.31), residues: 733 helix: 2.22 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.69 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 72 TYR 0.015 0.001 TYR D 40 PHE 0.006 0.001 PHE E 84 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.14 (12759) covalent geometry : angle 0.56684 / 0.34 (18488) hydrogen bonds : bond 0.04092 / 2.62 ( 761) hydrogen bonds : angle 2.83019 / 1.92 ( 1900) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.317 Fit side-chains REVERT: G 91 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.7848 (tt0) outliers start: 11 outliers final: 9 residues processed: 136 average time/residue: 0.1448 time to fit residues: 26.5474 Evaluate side-chains 134 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 84 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS B 25 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.138561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.094727 restraints weight = 18383.244| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.03 r_work: 0.2987 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12759 Z= 0.207 Angle : 0.631 6.897 18488 Z= 0.367 Chirality : 0.045 0.272 2105 Planarity : 0.005 0.044 1322 Dihedral : 31.053 139.860 4034 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.41 % Allowed : 8.99 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.30), residues: 733 helix: 2.13 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.84 (0.38), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.014 0.002 TYR D 40 PHE 0.011 0.002 PHE E 84 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 (12759) covalent geometry : angle 0.63119 / 0.37 (18488) hydrogen bonds : bond 0.05005 / 3.17 ( 761) hydrogen bonds : angle 2.97634 / 2.05 ( 1900) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.336 Fit side-chains REVERT: D 106 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8831 (mp) REVERT: G 91 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: H 57 LYS cc_start: 0.8773 (mttt) cc_final: 0.8548 (mtpp) outliers start: 15 outliers final: 10 residues processed: 128 average time/residue: 0.1385 time to fit residues: 24.1236 Evaluate side-chains 128 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 0.0020 chunk 92 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.140611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097280 restraints weight = 18433.285| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.03 r_work: 0.3040 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12759 Z= 0.129 Angle : 0.568 7.031 18488 Z= 0.342 Chirality : 0.042 0.273 2105 Planarity : 0.004 0.038 1322 Dihedral : 30.977 140.161 4034 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.93 % Allowed : 9.95 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.31), residues: 733 helix: 2.45 (0.22), residues: 537 sheet: None (None), residues: 0 loop : -0.63 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.013 0.001 TYR D 40 PHE 0.006 0.001 PHE E 84 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.13 (12759) covalent geometry : angle 0.56780 / 0.34 (18488) hydrogen bonds : bond 0.04062 / 2.63 ( 761) hydrogen bonds : angle 2.80348 / 1.90 ( 1900) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.371 Fit side-chains REVERT: G 91 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: H 57 LYS cc_start: 0.8679 (mttt) cc_final: 0.8473 (mtpp) outliers start: 12 outliers final: 10 residues processed: 130 average time/residue: 0.1388 time to fit residues: 24.5884 Evaluate side-chains 132 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.140685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097358 restraints weight = 18568.091| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.04 r_work: 0.3037 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12759 Z= 0.137 Angle : 0.561 6.983 18488 Z= 0.340 Chirality : 0.041 0.273 2105 Planarity : 0.004 0.039 1322 Dihedral : 30.904 140.069 4034 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.77 % Allowed : 10.43 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.31), residues: 733 helix: 2.42 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.57 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.013 0.001 TYR D 40 PHE 0.006 0.001 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.14 (12759) covalent geometry : angle 0.56103 / 0.34 (18488) hydrogen bonds : bond 0.04005 / 2.57 ( 761) hydrogen bonds : angle 2.76604 / 1.88 ( 1900) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.324 Fit side-chains REVERT: C 73 ASN cc_start: 0.7994 (t0) cc_final: 0.7730 (t0) REVERT: G 91 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7981 (tt0) outliers start: 11 outliers final: 9 residues processed: 131 average time/residue: 0.1342 time to fit residues: 23.7826 Evaluate side-chains 133 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 86 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 85 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** 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 = 0.3881 r_free = 0.3881 target = 0.140801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097485 restraints weight = 18369.655| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.02 r_work: 0.3046 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12759 Z= 0.134 Angle : 0.562 8.721 18488 Z= 0.340 Chirality : 0.041 0.273 2105 Planarity : 0.004 0.039 1322 Dihedral : 30.907 140.111 4034 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.61 % Allowed : 11.72 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.31), residues: 733 helix: 2.45 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.52 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.016 0.001 TYR D 42 PHE 0.006 0.001 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.13 (12759) covalent geometry : angle 0.56208 / 0.34 (18488) hydrogen bonds : bond 0.03932 / 2.53 ( 761) hydrogen bonds : angle 2.76235 / 1.87 ( 1900) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.324 Fit side-chains REVERT: C 73 ASN cc_start: 0.8019 (t0) cc_final: 0.7732 (t0) REVERT: G 91 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7969 (tt0) outliers start: 10 outliers final: 8 residues processed: 131 average time/residue: 0.1290 time to fit residues: 22.9472 Evaluate side-chains 132 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 79 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** 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 = 0.3845 r_free = 0.3845 target = 0.138106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094132 restraints weight = 18295.330| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.02 r_work: 0.2983 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12759 Z= 0.220 Angle : 0.637 8.304 18488 Z= 0.369 Chirality : 0.045 0.286 2105 Planarity : 0.005 0.048 1322 Dihedral : 31.108 139.720 4034 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.77 % Allowed : 11.88 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.30), residues: 733 helix: 2.24 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.75 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 53 TYR 0.014 0.002 TYR A 54 PHE 0.010 0.002 PHE E 84 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.22 (12759) covalent geometry : angle 0.63745 / 0.37 (18488) hydrogen bonds : bond 0.05009 / 3.18 ( 761) hydrogen bonds : angle 2.95510 / 2.03 ( 1900) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.309 Fit side-chains REVERT: G 91 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8012 (tt0) outliers start: 11 outliers final: 9 residues processed: 124 average time/residue: 0.1224 time to fit residues: 20.6338 Evaluate side-chains 124 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.139133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.095411 restraints weight = 18395.728| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 1.03 r_work: 0.3004 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12759 Z= 0.150 Angle : 0.600 8.927 18488 Z= 0.355 Chirality : 0.044 0.282 2105 Planarity : 0.004 0.048 1322 Dihedral : 31.110 140.370 4034 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.25 % Allowed : 11.56 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.30), residues: 733 helix: 2.36 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.72 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.019 0.001 TYR D 42 PHE 0.006 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (12759) covalent geometry : angle 0.60021 / 0.35 (18488) hydrogen bonds : bond 0.04429 / 2.82 ( 761) hydrogen bonds : angle 2.88671 / 1.97 ( 1900) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1466 Ramachandran restraints generated. 733 Oldfield, 0 Emsley, 733 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.224 Fit side-chains REVERT: C 73 ASN cc_start: 0.8019 (t0) cc_final: 0.7816 (t0) REVERT: D 106 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8824 (mp) REVERT: G 91 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7967 (tt0) outliers start: 14 outliers final: 11 residues processed: 130 average time/residue: 0.1152 time to fit residues: 20.2694 Evaluate side-chains 133 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 38 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 63 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** 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 = 0.3855 r_free = 0.3855 target = 0.138865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095108 restraints weight = 18274.278| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.02 r_work: 0.3004 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12759 Z= 0.170 Angle : 0.604 8.594 18488 Z= 0.355 Chirality : 0.043 0.289 2105 Planarity : 0.004 0.048 1322 Dihedral : 31.093 140.190 4034 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.77 % Allowed : 12.04 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.30), residues: 733 helix: 2.38 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.72 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 42 TYR 0.013 0.001 TYR D 42 PHE 0.007 0.002 PHE D 70 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (12759) covalent geometry : angle 0.60384 / 0.36 (18488) hydrogen bonds : bond 0.04450 / 2.84 ( 761) hydrogen bonds : angle 2.87485 / 1.96 ( 1900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3819.71 seconds wall clock time: 65 minutes 42.07 seconds (3942.07 seconds total)