Starting phenix.real_space_refine on Wed Jul 1 23:55:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ex9_28655/07_2026/8ex9_28655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ex9_28655/07_2026/8ex9_28655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ex9_28655/07_2026/8ex9_28655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ex9_28655/07_2026/8ex9_28655.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ex9_28655/07_2026/8ex9_28655.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ex9_28655/07_2026/8ex9_28655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ex9_28655/07_2026/8ex9_28655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ex9_28655/07_2026/8ex9_28655.map" } resolution = 2.96 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 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 139 5.49 5 S 1 5.16 5 C 2136 2.51 5 N 768 2.21 5 O 1155 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4199 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1277 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 162} Chain breaks: 1 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 7, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2179 Classifications: {'RNA': 102} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 50, 'rna3p_pyr': 44} Link IDs: {'rna2p': 8, 'rna3p': 93} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {' C%rna3p_pyr:plan': 1, ' C%rna3p_pyr:plan2': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 273 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {' DT:plan': 1, ' DC:plan': 1, ' DC:plan2': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Time building chain proxies: 1.10, per 1000 atoms: 0.26 Number of scatterers: 4199 At special positions: 0 Unit cell: (64.896, 83.2, 99.84, 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 1 16.00 P 139 15.00 O 1155 8.00 N 768 7.00 C 2136 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: 0.38 Conformation dependent library (CDL) restraints added in 56.5 milliseconds 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 308 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 45.2% alpha, 17.5% beta 50 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 14 through 46 removed outlier: 3.701A pdb=" N TYR A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 75 through 97 removed outlier: 3.542A pdb=" N LEU A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 121 removed outlier: 4.335A pdb=" N ASN A 156 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 158 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR A 167 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 171 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS A 143 " --> pdb=" O TYR A 12 " (cutoff:3.500A) 78 hydrogen bonds defined for protein. 222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 127 hydrogen bonds 222 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 0.69 Time building geometry restraints manager: 0.44 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: 710 1.33 - 1.45: 1878 1.45 - 1.57: 1705 1.57 - 1.69: 273 1.69 - 1.81: 1 Bond restraints: 4567 Sorted by residual: bond pdb=" C3' DT C 0 " pdb=" C2' DT C 0 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DA D 4 " pdb=" C2' DA D 4 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.62e+00 bond pdb=" C3' DG C -6 " pdb=" C2' DG C -6 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.09e+00 bond pdb=" C1' DC C 1 " pdb=" N1 DC C 1 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 6.97e+00 bond pdb=" C3' DT D -2 " pdb=" C2' DT D -2 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.80e+00 ... (remaining 4562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.79: 6097 0.79 - 1.59: 535 1.59 - 2.38: 156 2.38 - 3.17: 36 3.17 - 3.96: 6 Bond angle restraints: 6830 Sorted by residual: angle pdb=" N3 DT D -2 " pdb=" C4 DT D -2 " pdb=" O4 DT D -2 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT D 1 " pdb=" C4 DT D 1 " pdb=" O4 DT D 1 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT C -3 " pdb=" C4 DT C -3 " pdb=" O4 DT C -3 " ideal model delta sigma weight residual 119.90 122.31 -2.41 6.00e-01 2.78e+00 1.61e+01 angle pdb=" N3 DT D 8 " pdb=" C4 DT D 8 " pdb=" O4 DT D 8 " ideal model delta sigma weight residual 119.90 122.27 -2.37 6.00e-01 2.78e+00 1.56e+01 angle pdb=" N3 DT C 0 " pdb=" C4 DT C 0 " pdb=" O4 DT C 0 " ideal model delta sigma weight residual 119.90 122.25 -2.35 6.00e-01 2.78e+00 1.53e+01 ... (remaining 6825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.38: 2003 20.38 - 40.75: 243 40.75 - 61.13: 125 61.13 - 81.50: 4 81.50 - 101.88: 3 Dihedral angle restraints: 2378 sinusoidal: 1899 harmonic: 479 Sorted by residual: dihedral pdb=" O4' U B -89 " pdb=" C1' U B -89 " pdb=" N1 U B -89 " pdb=" C2 U B -89 " ideal model delta sinusoidal sigma weight residual -160.00 -65.40 -94.60 1 1.50e+01 4.44e-03 4.61e+01 dihedral pdb=" O5' A B -95 " pdb=" C5' A B -95 " pdb=" C4' A B -95 " pdb=" C3' A B -95 " ideal model delta sinusoidal sigma weight residual -65.00 -123.14 58.14 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" O5' A B 2 " pdb=" C5' A B 2 " pdb=" C4' A B 2 " pdb=" C3' A B 2 " ideal model delta sinusoidal sigma weight residual 175.00 117.25 57.75 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 2375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 682 0.036 - 0.071: 118 0.071 - 0.107: 52 0.107 - 0.143: 6 0.143 - 0.178: 2 Chirality restraints: 860 Sorted by residual: chirality pdb=" C1' U B -34 " pdb=" O4' U B -34 " pdb=" C2' U B -34 " pdb=" N1 U B -34 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" C3' DA D -8 " pdb=" C4' DA D -8 " pdb=" O3' DA D -8 " pdb=" C2' DA D -8 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA PHE A 35 " pdb=" N PHE A 35 " pdb=" C PHE A 35 " pdb=" CB PHE A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.83e-01 ... (remaining 857 not shown) Planarity restraints: 359 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 3 " -0.027 2.00e-02 2.50e+03 1.11e-02 3.68e+00 pdb=" N9 G B 3 " 0.023 2.00e-02 2.50e+03 pdb=" C8 G B 3 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G B 3 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G B 3 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 3 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G B 3 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G B 3 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G B 3 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 3 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B 3 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 3 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B -34 " 0.023 2.00e-02 2.50e+03 1.25e-02 3.52e+00 pdb=" N1 U B -34 " -0.028 2.00e-02 2.50e+03 pdb=" C2 U B -34 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U B -34 " -0.001 2.00e-02 2.50e+03 pdb=" N3 U B -34 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U B -34 " -0.001 2.00e-02 2.50e+03 pdb=" O4 U B -34 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U B -34 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U B -34 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B-114 " -0.020 2.00e-02 2.50e+03 9.23e-03 2.56e+00 pdb=" N9 G B-114 " 0.021 2.00e-02 2.50e+03 pdb=" C8 G B-114 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B-114 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G B-114 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B-114 " -0.002 2.00e-02 2.50e+03 pdb=" O6 G B-114 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G B-114 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G B-114 " -0.005 2.00e-02 2.50e+03 pdb=" N2 G B-114 " 0.008 2.00e-02 2.50e+03 pdb=" N3 G B-114 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G B-114 " 0.001 2.00e-02 2.50e+03 ... (remaining 356 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 464 2.74 - 3.28: 3804 3.28 - 3.82: 8592 3.82 - 4.36: 10535 4.36 - 4.90: 13713 Nonbonded interactions: 37108 Sorted by model distance: nonbonded pdb=" N2 G B-106 " pdb=" O6 G B -5 " model vdw 2.200 3.120 nonbonded pdb=" OH TYR A 12 " pdb=" OP1 G B-106 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 170 " pdb=" O2' A B 2 " model vdw 2.246 3.040 nonbonded pdb=" OG SER A 117 " pdb=" OP1 U B 4 " model vdw 2.266 3.040 nonbonded pdb=" O2' C B -92 " pdb=" N1 A B -88 " model vdw 2.282 3.120 ... (remaining 37103 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.790 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 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 0.037 4567 Z= 0.323 Angle : 0.555 3.964 6830 Z= 0.402 Chirality : 0.034 0.178 860 Planarity : 0.004 0.038 359 Dihedral : 17.837 101.879 2070 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.79 % Allowed : 3.97 % Favored : 95.24 % 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: -1.52 (0.62), residues: 162 helix: 0.89 (0.60), residues: 73 sheet: -5.10 (0.72), residues: 19 loop : -1.83 (0.61), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.011 0.001 TYR A 118 PHE 0.015 0.001 PHE A 35 TRP 0.004 0.001 TRP A 70 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.32 ( 4567) covalent geometry : angle 0.55509 / 0.40 ( 6830) hydrogen bonds : bond 0.12893 / 8.04 ( 205) hydrogen bonds : angle 5.48072 / 4.53 ( 444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.082 Fit side-chains REVERT: A 52 TYR cc_start: 0.7894 (t80) cc_final: 0.7558 (t80) outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 0.6936 time to fit residues: 14.2949 Evaluate side-chains 17 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.233108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.182801 restraints weight = 4743.474| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 1.16 r_work: 0.4052 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3904 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4567 Z= 0.240 Angle : 0.609 8.892 6830 Z= 0.332 Chirality : 0.036 0.173 860 Planarity : 0.005 0.044 359 Dihedral : 18.646 101.309 1796 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.17 % Allowed : 13.49 % Favored : 83.33 % 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: -1.05 (0.65), residues: 162 helix: 0.84 (0.59), residues: 67 sheet: -3.02 (0.81), residues: 33 loop : -0.89 (0.78), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 133 TYR 0.010 0.002 TYR A 118 PHE 0.021 0.002 PHE A 35 TRP 0.003 0.001 TRP A 70 HIS 0.005 0.002 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.24 ( 4567) covalent geometry : angle 0.60865 / 0.33 ( 6830) hydrogen bonds : bond 0.06355 / 4.55 ( 205) hydrogen bonds : angle 4.12693 / 3.26 ( 444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.055 Fit side-chains REVERT: A 52 TYR cc_start: 0.8174 (t80) cc_final: 0.7925 (t80) outliers start: 4 outliers final: 2 residues processed: 15 average time/residue: 0.5347 time to fit residues: 8.3218 Evaluate side-chains 14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 = 0.4630 r_free = 0.4630 target = 0.226917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.175446 restraints weight = 4747.694| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 1.39 r_work: 0.3961 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 4567 Z= 0.388 Angle : 0.801 9.428 6830 Z= 0.418 Chirality : 0.046 0.251 860 Planarity : 0.006 0.047 359 Dihedral : 19.144 99.647 1796 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 6.35 % Allowed : 12.70 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.60), residues: 162 helix: -0.40 (0.55), residues: 69 sheet: -3.05 (0.81), residues: 33 loop : -1.68 (0.73), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 160 TYR 0.016 0.003 TYR A 118 PHE 0.022 0.003 PHE A 35 TRP 0.004 0.002 TRP A 70 HIS 0.008 0.003 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00792 / 0.39 ( 4567) covalent geometry : angle 0.80089 / 0.42 ( 6830) hydrogen bonds : bond 0.08188 / 5.93 ( 205) hydrogen bonds : angle 4.48462 / 3.45 ( 444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 11 time to evaluate : 0.107 Fit side-chains REVERT: A 23 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6926 (ttp-110) outliers start: 8 outliers final: 3 residues processed: 17 average time/residue: 0.5158 time to fit residues: 9.1577 Evaluate side-chains 14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.233757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.184095 restraints weight = 4691.047| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 1.15 r_work: 0.4066 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3918 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4567 Z= 0.161 Angle : 0.574 11.154 6830 Z= 0.311 Chirality : 0.033 0.154 860 Planarity : 0.004 0.049 359 Dihedral : 18.908 99.512 1796 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.17 % Allowed : 15.87 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.63), residues: 162 helix: 0.76 (0.59), residues: 67 sheet: -2.82 (0.82), residues: 33 loop : -1.01 (0.75), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 110 TYR 0.009 0.002 TYR A 118 PHE 0.017 0.002 PHE A 35 TRP 0.005 0.001 TRP A 70 HIS 0.003 0.002 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 ( 4567) covalent geometry : angle 0.57422 / 0.31 ( 6830) hydrogen bonds : bond 0.05976 / 4.35 ( 205) hydrogen bonds : angle 3.84305 / 2.97 ( 444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.058 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 16 average time/residue: 0.4894 time to fit residues: 8.1772 Evaluate side-chains 11 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.4684 r_free = 0.4684 target = 0.232610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.183021 restraints weight = 4699.715| |-----------------------------------------------------------------------------| r_work (start): 0.4231 rms_B_bonded: 1.17 r_work: 0.4056 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3916 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4567 Z= 0.202 Angle : 0.590 10.879 6830 Z= 0.319 Chirality : 0.034 0.163 860 Planarity : 0.005 0.049 359 Dihedral : 18.871 100.748 1796 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.76 % Allowed : 16.67 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.64), residues: 162 helix: 0.90 (0.59), residues: 67 sheet: -2.78 (0.83), residues: 33 loop : -0.99 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.022 0.002 TYR A 52 PHE 0.019 0.002 PHE A 35 TRP 0.004 0.001 TRP A 70 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 ( 4567) covalent geometry : angle 0.59022 / 0.32 ( 6830) hydrogen bonds : bond 0.06150 / 4.43 ( 205) hydrogen bonds : angle 3.82997 / 2.95 ( 444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.096 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 16 average time/residue: 0.4427 time to fit residues: 7.4807 Evaluate side-chains 13 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 9 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 0.5980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.4661 r_free = 0.4661 target = 0.230055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.179289 restraints weight = 4820.752| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.24 r_work: 0.4004 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3857 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4567 Z= 0.274 Angle : 0.660 10.582 6830 Z= 0.350 Chirality : 0.038 0.178 860 Planarity : 0.005 0.050 359 Dihedral : 18.976 99.044 1796 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 5.56 % Allowed : 17.46 % Favored : 76.98 % 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: -1.38 (0.63), residues: 162 helix: 0.44 (0.58), residues: 67 sheet: -2.85 (0.82), residues: 33 loop : -1.12 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 160 TYR 0.017 0.003 TYR A 52 PHE 0.022 0.002 PHE A 35 TRP 0.003 0.001 TRP A 70 HIS 0.004 0.002 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.27 ( 4567) covalent geometry : angle 0.66009 / 0.35 ( 6830) hydrogen bonds : bond 0.06830 / 4.93 ( 205) hydrogen bonds : angle 4.04334 / 3.10 ( 444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 10 time to evaluate : 0.083 Fit side-chains REVERT: A 23 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6858 (ttp-110) outliers start: 7 outliers final: 5 residues processed: 15 average time/residue: 0.4307 time to fit residues: 6.7837 Evaluate side-chains 14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 8 time to evaluate : 0.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.0770 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.4711 r_free = 0.4711 target = 0.235627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.186761 restraints weight = 4772.971| |-----------------------------------------------------------------------------| r_work (start): 0.4267 rms_B_bonded: 1.16 r_work: 0.4103 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3957 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4567 Z= 0.148 Angle : 0.548 11.382 6830 Z= 0.298 Chirality : 0.032 0.153 860 Planarity : 0.004 0.050 359 Dihedral : 18.826 99.815 1796 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.97 % Allowed : 19.05 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.66), residues: 162 helix: 1.30 (0.61), residues: 67 sheet: -2.68 (0.83), residues: 33 loop : -0.84 (0.78), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.013 0.002 TYR A 52 PHE 0.017 0.002 PHE A 35 TRP 0.005 0.001 TRP A 70 HIS 0.003 0.002 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.15 ( 4567) covalent geometry : angle 0.54795 / 0.30 ( 6830) hydrogen bonds : bond 0.05685 / 4.13 ( 205) hydrogen bonds : angle 3.65099 / 2.81 ( 444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 9 time to evaluate : 0.060 Fit side-chains REVERT: A 52 TYR cc_start: 0.8121 (t80) cc_final: 0.7495 (t80) outliers start: 5 outliers final: 4 residues processed: 13 average time/residue: 0.2979 time to fit residues: 4.1055 Evaluate side-chains 13 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 9 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.4692 r_free = 0.4692 target = 0.233466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.183693 restraints weight = 4764.328| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 1.16 r_work: 0.4056 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3909 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4567 Z= 0.196 Angle : 0.579 10.928 6830 Z= 0.312 Chirality : 0.034 0.161 860 Planarity : 0.004 0.048 359 Dihedral : 18.827 101.279 1796 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.76 % Allowed : 18.25 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.64), residues: 162 helix: 1.12 (0.60), residues: 67 sheet: -2.68 (0.82), residues: 33 loop : -0.92 (0.77), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.013 0.002 TYR A 52 PHE 0.020 0.002 PHE A 35 TRP 0.004 0.001 TRP A 70 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.20 ( 4567) covalent geometry : angle 0.57912 / 0.31 ( 6830) hydrogen bonds : bond 0.06025 / 4.36 ( 205) hydrogen bonds : angle 3.74615 / 2.88 ( 444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.084 Fit side-chains REVERT: A 52 TYR cc_start: 0.8152 (t80) cc_final: 0.7457 (t80) outliers start: 6 outliers final: 4 residues processed: 15 average time/residue: 0.4106 time to fit residues: 6.5416 Evaluate side-chains 14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.4672 r_free = 0.4672 target = 0.231160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.180823 restraints weight = 4774.913| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 1.18 r_work: 0.4025 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3875 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4567 Z= 0.249 Angle : 0.633 10.699 6830 Z= 0.337 Chirality : 0.037 0.173 860 Planarity : 0.005 0.047 359 Dihedral : 18.924 98.746 1796 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.97 % Allowed : 19.05 % Favored : 76.98 % 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: -1.13 (0.63), residues: 162 helix: 0.69 (0.58), residues: 67 sheet: -2.75 (0.82), residues: 33 loop : -1.01 (0.76), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 160 TYR 0.015 0.002 TYR A 52 PHE 0.022 0.002 PHE A 35 TRP 0.003 0.001 TRP A 70 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.25 ( 4567) covalent geometry : angle 0.63337 / 0.34 ( 6830) hydrogen bonds : bond 0.06603 / 4.78 ( 205) hydrogen bonds : angle 3.93058 / 3.01 ( 444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 12 time to evaluate : 0.105 Fit side-chains REVERT: A 52 TYR cc_start: 0.8192 (t80) cc_final: 0.7673 (t80) REVERT: A 148 GLN cc_start: 0.7110 (tt0) cc_final: 0.6530 (mt0) outliers start: 5 outliers final: 4 residues processed: 16 average time/residue: 0.4707 time to fit residues: 7.8713 Evaluate side-chains 14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 0.0770 chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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 = 0.4718 r_free = 0.4718 target = 0.236272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.187344 restraints weight = 4695.955| |-----------------------------------------------------------------------------| r_work (start): 0.4272 rms_B_bonded: 1.14 r_work: 0.4102 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3955 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4567 Z= 0.151 Angle : 0.547 11.481 6830 Z= 0.296 Chirality : 0.032 0.149 860 Planarity : 0.004 0.050 359 Dihedral : 18.789 100.003 1796 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.97 % Allowed : 19.05 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.66), residues: 162 helix: 1.43 (0.62), residues: 67 sheet: -2.54 (0.82), residues: 33 loop : -0.79 (0.78), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 29 TYR 0.012 0.002 TYR A 52 PHE 0.016 0.002 PHE A 35 TRP 0.005 0.001 TRP A 70 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 ( 4567) covalent geometry : angle 0.54703 / 0.30 ( 6830) hydrogen bonds : bond 0.05601 / 4.08 ( 205) hydrogen bonds : angle 3.60736 / 2.77 ( 444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 324 Ramachandran restraints generated. 162 Oldfield, 0 Emsley, 162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 11 time to evaluate : 0.080 Fit side-chains REVERT: A 52 TYR cc_start: 0.8039 (t80) cc_final: 0.7367 (t80) outliers start: 5 outliers final: 4 residues processed: 15 average time/residue: 0.5005 time to fit residues: 7.8648 Evaluate side-chains 16 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 12 optimal weight: 0.0370 chunk 28 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 7 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.0462 ------------------------------------------------------------------------------- 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 = 0.4701 r_free = 0.4701 target = 0.235822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.186028 restraints weight = 4839.361| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 1.31 r_work: 0.4065 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4567 Z= 0.180 Angle : 0.563 11.095 6830 Z= 0.304 Chirality : 0.033 0.159 860 Planarity : 0.004 0.048 359 Dihedral : 18.771 101.253 1796 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.97 % Allowed : 19.84 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.65), residues: 162 helix: 1.29 (0.61), residues: 67 sheet: -2.59 (0.81), residues: 33 loop : -0.83 (0.77), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.012 0.002 TYR A 52 PHE 0.021 0.002 PHE A 35 TRP 0.004 0.001 TRP A 70 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 ( 4567) covalent geometry : angle 0.56320 / 0.30 ( 6830) hydrogen bonds : bond 0.05880 / 4.27 ( 205) hydrogen bonds : angle 3.66833 / 2.82 ( 444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1292.47 seconds wall clock time: 22 minutes 47.21 seconds (1367.21 seconds total)