Starting phenix.real_space_refine on Sat May 17 21:50:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwf_47242/05_2025/9dwf_47242.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwf_47242/05_2025/9dwf_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_47242/05_2025/9dwf_47242.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwf_47242/05_2025/9dwf_47242.map" model { file = "/net/cci-nas-00/data/ceres_data/9dwf_47242/05_2025/9dwf_47242.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwf_47242/05_2025/9dwf_47242.cif" } resolution = 3.1 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 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.36, per 1000 atoms: 0.87 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: 2.90 Conformation dependent library (CDL) restraints added in 899.5 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: 5.75 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: 4.24 Time building geometry restraints manager: 3.45 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=" 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=" O3' DC J 27 " pdb=" P DT J 28 " ideal model delta sigma weight residual 1.607 1.646 -0.039 1.50e-02 4.44e+03 6.74e+00 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.54e-02 4.22e+03 5.14e+00 bond pdb=" P DA K 120 " pdb=" OP2 DA K 120 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.30e+00 ... (remaining 12754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 18424 3.05 - 6.09: 50 6.09 - 9.14: 13 9.14 - 12.19: 0 12.19 - 15.23: 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 111.50 96.27 15.23 1.50e+00 4.44e-01 1.03e+02 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=" C4' DA K 120 " pdb=" C3' DA K 120 " pdb=" O3' DA K 120 " ideal model delta sigma weight residual 110.00 103.81 6.19 1.50e+00 4.44e-01 1.70e+01 angle pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " pdb=" CG ASP F 24 " ideal model delta sigma weight residual 112.60 116.22 -3.62 1.00e+00 1.00e+00 1.31e+01 angle pdb=" N GLY G 37 " pdb=" CA GLY G 37 " pdb=" C GLY G 37 " ideal model delta sigma weight residual 113.27 117.93 -4.66 1.33e+00 5.65e-01 1.23e+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 - 0.131: 2094 0.131 - 0.262: 8 0.262 - 0.392: 0 0.392 - 0.523: 0 0.523 - 0.654: 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 2.35 3.00 -0.65 2.00e-01 2.50e+01 1.07e+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 2.35 -2.91 -0.57 2.00e-01 2.50e+01 8.02e+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 2.35 -2.91 -0.56 2.00e-01 2.50e+01 7.83e+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: 12.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 35.810 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 : 0.004 0.128 12759 Z= 0.183 Angle : 0.625 15.235 18488 Z= 0.369 Chirality : 0.042 0.654 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 (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: 1.00 (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 HIS 0.003 0.001 HIS H 109 PHE 0.012 0.002 PHE H 70 TYR 0.022 0.002 TYR H 40 ARG 0.007 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.13342 ( 761) hydrogen bonds : angle 4.26418 ( 1900) covalent geometry : bond 0.00386 (12759) covalent geometry : angle 0.62472 (18488) *********************** 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 : 0.875 Fit side-chains REVERT: B 91 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8237 (ttpt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3403 time to fit residues: 69.9921 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 : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN H 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.140047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096602 restraints weight = 18227.950| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.03 r_work: 0.3023 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12759 Z= 0.209 Angle : 0.570 5.247 18488 Z= 0.340 Chirality : 0.035 0.154 2105 Planarity : 0.004 0.033 1322 Dihedral : 30.464 140.370 4034 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.93 % Allowed : 6.10 % Favored : 91.97 % 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: 1.74 (0.31), residues: 733 helix: 1.80 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.80 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 82 PHE 0.012 0.002 PHE C 25 TYR 0.019 0.002 TYR D 40 ARG 0.005 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 761) hydrogen bonds : angle 3.01492 ( 1900) covalent geometry : bond 0.00475 (12759) covalent geometry : angle 0.56990 (18488) *********************** 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 143 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.977 Fit side-chains REVERT: C 73 ASN cc_start: 0.8165 (t0) cc_final: 0.7896 (t0) outliers start: 12 outliers final: 8 residues processed: 137 average time/residue: 0.3218 time to fit residues: 58.5064 Evaluate side-chains 135 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 F residue 84 MET Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.092298 restraints weight = 18492.575| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.10 r_work: 0.2948 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 12759 Z= 0.319 Angle : 0.653 6.183 18488 Z= 0.383 Chirality : 0.040 0.188 2105 Planarity : 0.005 0.050 1322 Dihedral : 31.079 141.979 4034 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.41 % Allowed : 8.83 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.30), residues: 733 helix: 1.68 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.01 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 109 PHE 0.012 0.003 PHE E 84 TYR 0.021 0.002 TYR D 40 ARG 0.006 0.001 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05421 ( 761) hydrogen bonds : angle 3.15600 ( 1900) covalent geometry : bond 0.00740 (12759) covalent geometry : angle 0.65325 (18488) *********************** 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 129 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.878 Fit side-chains REVERT: H 57 LYS cc_start: 0.8782 (mttt) cc_final: 0.8534 (mtpp) REVERT: H 116 LYS cc_start: 0.9126 (ttpt) cc_final: 0.8867 (ttpt) outliers start: 15 outliers final: 12 residues processed: 124 average time/residue: 0.3200 time to fit residues: 52.2459 Evaluate side-chains 124 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 58 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 101 THR 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 97 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3875 r_free = 0.3875 target = 0.140226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097348 restraints weight = 18238.895| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.03 r_work: 0.3043 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12759 Z= 0.157 Angle : 0.527 5.202 18488 Z= 0.324 Chirality : 0.033 0.142 2105 Planarity : 0.004 0.042 1322 Dihedral : 30.611 140.177 4034 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.61 % Allowed : 10.11 % Favored : 88.28 % 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: 733 helix: 2.33 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.83 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE D 70 TYR 0.015 0.001 TYR D 40 ARG 0.003 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 761) hydrogen bonds : angle 2.77317 ( 1900) covalent geometry : bond 0.00341 (12759) covalent geometry : angle 0.52742 (18488) *********************** 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 138 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.946 Fit side-chains REVERT: C 73 ASN cc_start: 0.8167 (t0) cc_final: 0.7942 (t0) outliers start: 10 outliers final: 8 residues processed: 134 average time/residue: 0.3128 time to fit residues: 55.7884 Evaluate side-chains 132 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 F residue 49 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 101 THR 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 8 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.139515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096357 restraints weight = 18340.731| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.01 r_work: 0.3022 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12759 Z= 0.178 Angle : 0.539 5.241 18488 Z= 0.329 Chirality : 0.034 0.153 2105 Planarity : 0.004 0.045 1322 Dihedral : 30.659 139.639 4034 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.93 % Allowed : 11.08 % Favored : 87.00 % 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: 733 helix: 2.40 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.77 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.007 0.002 PHE H 70 TYR 0.015 0.001 TYR D 40 ARG 0.003 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 761) hydrogen bonds : angle 2.78107 ( 1900) covalent geometry : bond 0.00395 (12759) covalent geometry : angle 0.53900 (18488) *********************** 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 135 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.924 Fit side-chains REVERT: C 73 ASN cc_start: 0.8205 (t0) cc_final: 0.7896 (t0) outliers start: 12 outliers final: 10 residues processed: 131 average time/residue: 0.3165 time to fit residues: 54.9680 Evaluate side-chains 132 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 E residue 80 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.138200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.094419 restraints weight = 18508.166| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.04 r_work: 0.2986 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12759 Z= 0.208 Angle : 0.562 5.290 18488 Z= 0.340 Chirality : 0.035 0.155 2105 Planarity : 0.004 0.049 1322 Dihedral : 30.734 140.015 4034 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.93 % Allowed : 12.04 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.31), residues: 733 helix: 2.30 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.86 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 49 PHE 0.008 0.002 PHE H 70 TYR 0.014 0.002 TYR D 40 ARG 0.003 0.000 ARG A 53 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 761) hydrogen bonds : angle 2.86349 ( 1900) covalent geometry : bond 0.00471 (12759) covalent geometry : angle 0.56233 (18488) *********************** 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 132 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.918 Fit side-chains REVERT: C 73 ASN cc_start: 0.8278 (t0) cc_final: 0.7968 (t0) REVERT: H 113 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7891 (mm-30) outliers start: 12 outliers final: 12 residues processed: 128 average time/residue: 0.3151 time to fit residues: 53.6358 Evaluate side-chains 130 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 E residue 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 101 THR 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 10 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.139170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095989 restraints weight = 18245.769| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.02 r_work: 0.3015 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2462 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= 0.152 Angle : 0.541 5.227 18488 Z= 0.331 Chirality : 0.034 0.154 2105 Planarity : 0.004 0.048 1322 Dihedral : 30.738 140.475 4034 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.09 % Allowed : 12.20 % Favored : 85.71 % 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: 2.43 (0.31), residues: 733 helix: 2.44 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.80 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.006 0.001 PHE D 70 TYR 0.015 0.001 TYR D 40 ARG 0.002 0.000 ARG B 40 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 761) hydrogen bonds : angle 2.82038 ( 1900) covalent geometry : bond 0.00323 (12759) covalent geometry : angle 0.54089 (18488) *********************** 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 134 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.911 Fit side-chains REVERT: C 73 ASN cc_start: 0.8245 (t0) cc_final: 0.7922 (t0) REVERT: D 106 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8793 (mp) outliers start: 13 outliers final: 10 residues processed: 131 average time/residue: 0.3110 time to fit residues: 54.3633 Evaluate side-chains 131 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 F residue 49 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 114 VAL 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 90 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 94 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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** ** 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 = 0.3846 r_free = 0.3846 target = 0.138331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094174 restraints weight = 18422.261| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.07 r_work: 0.2980 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12759 Z= 0.197 Angle : 0.553 5.275 18488 Z= 0.336 Chirality : 0.034 0.149 2105 Planarity : 0.004 0.048 1322 Dihedral : 30.687 139.533 4034 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.09 % Allowed : 13.00 % Favored : 84.91 % 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: 2.32 (0.31), residues: 733 helix: 2.35 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.83 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 109 PHE 0.008 0.002 PHE D 70 TYR 0.013 0.002 TYR D 42 ARG 0.002 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 761) hydrogen bonds : angle 2.82505 ( 1900) covalent geometry : bond 0.00445 (12759) covalent geometry : angle 0.55259 (18488) *********************** 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 130 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.934 Fit side-chains REVERT: A 39 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7509 (p-80) REVERT: C 73 ASN cc_start: 0.8285 (t0) cc_final: 0.7967 (t0) REVERT: D 106 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8796 (mp) REVERT: H 113 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8015 (mm-30) REVERT: H 116 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.9012 (pttm) outliers start: 13 outliers final: 10 residues processed: 127 average time/residue: 0.3082 time to fit residues: 52.0980 Evaluate side-chains 130 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS 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 80 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 116 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.138853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.094908 restraints weight = 18286.164| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.07 r_work: 0.2995 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12759 Z= 0.162 Angle : 0.543 5.256 18488 Z= 0.332 Chirality : 0.033 0.156 2105 Planarity : 0.004 0.047 1322 Dihedral : 30.697 140.021 4034 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.93 % Allowed : 13.64 % Favored : 84.43 % 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: 2.43 (0.31), residues: 733 helix: 2.43 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.79 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.006 0.001 PHE A 67 TYR 0.014 0.001 TYR D 40 ARG 0.001 0.000 ARG G 88 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 761) hydrogen bonds : angle 2.80943 ( 1900) covalent geometry : bond 0.00353 (12759) covalent geometry : angle 0.54296 (18488) *********************** 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 132 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.844 Fit side-chains REVERT: C 73 ASN cc_start: 0.8293 (t0) cc_final: 0.7970 (t0) REVERT: D 106 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8797 (mp) outliers start: 12 outliers final: 8 residues processed: 130 average time/residue: 0.3021 time to fit residues: 52.2122 Evaluate side-chains 126 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 F residue 84 MET 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 2 optimal weight: 0.6980 chunk 63 optimal weight: 0.0050 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.139523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096130 restraints weight = 18185.055| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.03 r_work: 0.3017 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2520 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= 0.150 Angle : 0.539 5.884 18488 Z= 0.329 Chirality : 0.033 0.156 2105 Planarity : 0.004 0.047 1322 Dihedral : 30.681 139.824 4034 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.93 % Allowed : 13.64 % Favored : 84.43 % 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: 2.52 (0.31), residues: 733 helix: 2.50 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.75 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS H 109 PHE 0.006 0.001 PHE A 67 TYR 0.016 0.001 TYR D 42 ARG 0.002 0.000 ARG G 42 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 761) hydrogen bonds : angle 2.79639 ( 1900) covalent geometry : bond 0.00320 (12759) covalent geometry : angle 0.53924 (18488) ********************** 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 131 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.886 Fit side-chains REVERT: A 39 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7507 (p-80) REVERT: C 73 ASN cc_start: 0.8240 (t0) cc_final: 0.7909 (t0) REVERT: C 95 LYS cc_start: 0.9008 (tptt) cc_final: 0.8705 (tppt) REVERT: D 106 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8810 (mp) outliers start: 12 outliers final: 8 residues processed: 129 average time/residue: 0.3009 time to fit residues: 51.9844 Evaluate side-chains 129 residues out of total 623 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS 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 F residue 84 MET 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 59 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.139213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.095373 restraints weight = 18195.491| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.06 r_work: 0.3005 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12759 Z= 0.167 Angle : 0.540 7.288 18488 Z= 0.330 Chirality : 0.034 0.167 2105 Planarity : 0.004 0.048 1322 Dihedral : 30.623 139.728 4034 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.77 % Allowed : 14.13 % Favored : 84.11 % 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: 2.51 (0.31), residues: 733 helix: 2.49 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.72 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 109 PHE 0.007 0.001 PHE D 70 TYR 0.014 0.001 TYR D 42 ARG 0.002 0.000 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 761) hydrogen bonds : angle 2.77836 ( 1900) covalent geometry : bond 0.00368 (12759) covalent geometry : angle 0.54041 (18488) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7840.72 seconds wall clock time: 136 minutes 13.26 seconds (8173.26 seconds total)