Starting phenix.real_space_refine on Tue Aug 4 15:19:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ex9_28655/08_2026/8ex9_28655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ex9_28655/08_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8ex9_28655/08_2026/8ex9_28655.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ex9_28655/08_2026/8ex9_28655.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ex9_28655/08_2026/8ex9_28655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ex9_28655/08_2026/8ex9_28655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ex9_28655/08_2026/8ex9_28655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ex9_28655/08_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-2.2rc3-6140/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: {'RNAv2': 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: 1.21, per 1000 atoms: 0.29 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: 0.47 Conformation dependent library (CDL) restraints added in 76.5 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: 0.69 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: 0.79 Time building geometry restraints manager: 0.64 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 - 1.07: 6107 1.07 - 2.15: 408 2.15 - 3.22: 275 3.22 - 4.30: 23 4.30 - 5.37: 17 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 - 14.95: 1741 14.95 - 29.91: 296 29.91 - 44.86: 172 44.86 - 59.81: 150 59.81 - 74.76: 19 Dihedral angle restraints: 2378 sinusoidal: 1899 harmonic: 479 Sorted by residual: dihedral pdb=" C4' G B 1 " pdb=" C3' G B 1 " pdb=" C2' G B 1 " pdb=" C1' G B 1 " ideal model delta sinusoidal sigma weight residual 36.34 -38.42 74.76 1 3.10e+00 1.04e-01 7.36e+02 dihedral pdb=" C4' A B -76 " pdb=" C3' A B -76 " pdb=" C2' A B -76 " pdb=" C1' A B -76 " ideal model delta sinusoidal sigma weight residual 36.34 -37.96 74.31 1 3.10e+00 1.04e-01 7.29e+02 dihedral pdb=" C4' U B 8 " pdb=" C3' U B 8 " pdb=" C2' U B 8 " pdb=" C1' U B 8 " ideal model delta sinusoidal sigma weight residual 36.34 -37.96 74.30 1 3.10e+00 1.04e-01 7.29e+02 ... (remaining 2375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 665 0.061 - 0.123: 74 0.123 - 0.184: 3 0.184 - 0.246: 98 0.246 - 0.307: 20 Chirality restraints: 860 Sorted by residual: chirality pdb=" C3' A B -76 " pdb=" C4' A B -76 " pdb=" O3' A B -76 " pdb=" C2' A B -76 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C2' U B 8 " pdb=" C3' U B 8 " pdb=" O2' U B 8 " pdb=" C1' U B 8 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C2' G B 1 " pdb=" C3' G B 1 " pdb=" O2' G B 1 " pdb=" C1' G B 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (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: 1.340 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.160 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.750 ------------------------------------------------------------------------------- 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= 0.330 Angle : 0.802 5.374 6830 Z= 0.448 Chirality : 0.094 0.307 860 Planarity : 0.004 0.038 359 Dihedral : 21.182 74.762 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 0.00421 / 0.33 ( 4567) covalent geometry : angle 0.80246 / 0.45 ( 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 : 0.087 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: 0.7262 time to fit residues: 14.9746 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 : 0.085 ------------------------------------------------------------------------------- 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: 2.9990 chunk 28 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4773 r_free = 0.4773 target = 0.238951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.191587 restraints weight = 4772.316| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 1.13 r_work: 0.4157 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4567 Z= 0.265 Angle : 1.243 14.773 6830 Z= 0.526 Chirality : 0.111 1.339 860 Planarity : 0.005 0.041 359 Dihedral : 21.136 153.509 1796 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.38 % Allowed : 12.70 % Favored : 84.92 % 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: -0.73 (0.66), residues: 162 helix: 1.21 (0.61), residues: 67 sheet: -2.96 (0.81), residues: 33 loop : -0.77 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.009 0.002 TYR A 118 PHE 0.019 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 0.00531 / 0.27 ( 4567) covalent geometry : angle 1.24257 / 0.53 ( 6830) hydrogen bonds : bond 0.05585 / 3.94 ( 205) hydrogen bonds : angle 4.02104 / 3.19 ( 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 15 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.082 Fit side-chains REVERT: A 52 TYR cc_start: 0.7990 (t80) cc_final: 0.7733 (t80) outliers start: 3 outliers final: 1 residues processed: 14 average time/residue: 0.7767 time to fit residues: 11.2278 Evaluate side-chains 13 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 VAL 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: 3.9990 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4723 r_free = 0.4723 target = 0.233405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.185164 restraints weight = 4751.071| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 1.19 r_work: 0.4083 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 4567 Z= 0.332 Angle : 1.099 16.511 6830 Z= 0.480 Chirality : 0.092 1.391 860 Planarity : 0.006 0.046 359 Dihedral : 21.111 165.699 1796 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.76 % Allowed : 13.49 % Favored : 81.75 % 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: -1.56 (0.61), residues: 162 helix: 0.32 (0.58), residues: 67 sheet: -2.89 (0.82), residues: 33 loop : -1.28 (0.72), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 160 TYR 0.012 0.002 TYR A 118 PHE 0.021 0.003 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 0.00683 / 0.33 ( 4567) covalent geometry : angle 1.09883 / 0.48 ( 6830) hydrogen bonds : bond 0.07021 / 5.07 ( 205) hydrogen bonds : angle 4.19332 / 3.25 ( 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 16 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.083 Fit side-chains REVERT: A 23 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6756 (ttp-110) outliers start: 6 outliers final: 3 residues processed: 14 average time/residue: 0.4807 time to fit residues: 7.0589 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 : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4756 r_free = 0.4756 target = 0.237211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.190723 restraints weight = 4738.110| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 1.13 r_work: 0.4145 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4567 Z= 0.214 Angle : 0.967 14.392 6830 Z= 0.420 Chirality : 0.079 1.004 860 Planarity : 0.005 0.046 359 Dihedral : 21.088 176.482 1796 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.97 % Allowed : 15.08 % 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: -0.97 (0.64), residues: 162 helix: 0.93 (0.59), residues: 67 sheet: -2.77 (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 0.016 0.002 TYR A 52 PHE 0.017 0.002 PHE A 35 TRP 0.005 0.001 TRP A 70 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.21 ( 4567) covalent geometry : angle 0.96706 / 0.42 ( 6830) hydrogen bonds : bond 0.05807 / 4.20 ( 205) hydrogen bonds : angle 3.80021 / 2.94 ( 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 16 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 11 time to evaluate : 0.083 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 15 average time/residue: 0.4945 time to fit residues: 7.7860 Evaluate side-chains 11 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 8 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 158 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.0570 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 overall best weight: 1.0100 ------------------------------------------------------------------------------- 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 = 0.4765 r_free = 0.4765 target = 0.238107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.191764 restraints weight = 4761.245| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 1.14 r_work: 0.4141 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4567 Z= 0.194 Angle : 0.935 12.416 6830 Z= 0.404 Chirality : 0.071 0.727 860 Planarity : 0.005 0.047 359 Dihedral : 20.949 159.783 1796 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.97 % Allowed : 16.67 % Favored : 79.37 % 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: -0.76 (0.64), residues: 162 helix: 1.09 (0.60), residues: 67 sheet: -2.66 (0.83), residues: 33 loop : -0.89 (0.77), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.015 0.002 TYR A 52 PHE 0.018 0.002 PHE A 35 TRP 0.003 0.001 TRP A 70 HIS 0.002 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 ( 4567) covalent geometry : angle 0.93538 / 0.40 ( 6830) hydrogen bonds : bond 0.06049 / 4.44 ( 205) hydrogen bonds : angle 3.69000 / 2.85 ( 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 15 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 10 time to evaluate : 0.083 Fit side-chains REVERT: A 52 TYR cc_start: 0.8021 (t80) cc_final: 0.7336 (t80) outliers start: 5 outliers final: 4 residues processed: 14 average time/residue: 0.5696 time to fit residues: 8.3432 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 : 0.083 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 4 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.4741 r_free = 0.4741 target = 0.235454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.188539 restraints weight = 4873.631| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 1.14 r_work: 0.4113 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 4567 Z= 0.250 Angle : 0.969 10.801 6830 Z= 0.419 Chirality : 0.073 0.719 860 Planarity : 0.005 0.047 359 Dihedral : 20.897 148.882 1796 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.76 % Allowed : 17.46 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.64), residues: 162 helix: 0.73 (0.58), residues: 67 sheet: -2.84 (0.82), residues: 33 loop : -0.94 (0.77), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 133 TYR 0.013 0.002 TYR A 52 PHE 0.021 0.002 PHE A 35 TRP 0.002 0.001 TRP A 70 HIS 0.004 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.25 ( 4567) covalent geometry : angle 0.96934 / 0.42 ( 6830) hydrogen bonds : bond 0.06381 / 4.64 ( 205) hydrogen bonds : angle 3.86143 / 2.97 ( 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: 6 poor density : 11 time to evaluate : 0.113 Fit side-chains REVERT: A 23 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6702 (ttp-110) REVERT: A 52 TYR cc_start: 0.8105 (t80) cc_final: 0.7647 (t80) REVERT: A 148 GLN cc_start: 0.7219 (tt0) cc_final: 0.6770 (mt0) outliers start: 6 outliers final: 4 residues processed: 15 average time/residue: 0.5993 time to fit residues: 9.3534 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 : 0.083 ------------------------------------------------------------------------------- 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 158 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.4785 r_free = 0.4785 target = 0.240212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.194676 restraints weight = 4863.222| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 1.16 r_work: 0.4186 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4567 Z= 0.168 Angle : 0.898 11.240 6830 Z= 0.387 Chirality : 0.069 0.680 860 Planarity : 0.004 0.049 359 Dihedral : 20.832 148.861 1796 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.97 % Allowed : 17.46 % 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: -0.49 (0.66), residues: 162 helix: 1.39 (0.61), residues: 67 sheet: -2.66 (0.83), residues: 33 loop : -0.73 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.009 0.001 TYR A 52 PHE 0.016 0.002 PHE A 35 TRP 0.004 0.001 TRP A 70 HIS 0.003 0.002 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 ( 4567) covalent geometry : angle 0.89804 / 0.39 ( 6830) hydrogen bonds : bond 0.05738 / 4.19 ( 205) hydrogen bonds : angle 3.54396 / 2.73 ( 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 : 0.083 Fit side-chains REVERT: A 52 TYR cc_start: 0.7935 (t80) cc_final: 0.7227 (t80) outliers start: 5 outliers final: 4 residues processed: 13 average time/residue: 0.3274 time to fit residues: 4.5473 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 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: 0.0670 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.1522 ------------------------------------------------------------------------------- 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 = 0.4760 r_free = 0.4760 target = 0.237484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.191233 restraints weight = 4832.946| |-----------------------------------------------------------------------------| r_work (start): 0.4333 rms_B_bonded: 1.15 r_work: 0.4134 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4567 Z= 0.212 Angle : 0.922 10.513 6830 Z= 0.398 Chirality : 0.069 0.655 860 Planarity : 0.005 0.046 359 Dihedral : 20.798 149.188 1796 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.17 % Allowed : 18.25 % 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: -0.67 (0.65), residues: 162 helix: 1.19 (0.60), residues: 67 sheet: -2.70 (0.82), residues: 33 loop : -0.81 (0.77), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 110 TYR 0.010 0.002 TYR A 52 PHE 0.020 0.002 PHE A 35 TRP 0.003 0.001 TRP A 70 HIS 0.003 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.21 ( 4567) covalent geometry : angle 0.92182 / 0.40 ( 6830) hydrogen bonds : bond 0.06138 / 4.46 ( 205) hydrogen bonds : angle 3.67433 / 2.83 ( 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 14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.098 Fit side-chains REVERT: A 52 TYR cc_start: 0.7984 (t80) cc_final: 0.7313 (t80) outliers start: 4 outliers final: 4 residues processed: 13 average time/residue: 0.5159 time to fit residues: 7.0338 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 : 0.071 ------------------------------------------------------------------------------- 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: 20.0000 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.4744 r_free = 0.4744 target = 0.235127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.187937 restraints weight = 4794.034| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 1.11 r_work: 0.4107 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4567 Z= 0.280 Angle : 0.989 10.144 6830 Z= 0.428 Chirality : 0.072 0.645 860 Planarity : 0.005 0.046 359 Dihedral : 20.866 149.412 1796 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.17 % Allowed : 19.84 % 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: -1.21 (0.63), residues: 162 helix: 0.56 (0.58), 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 0.003 0.001 ARG A 160 TYR 0.013 0.002 TYR A 52 PHE 0.023 0.002 PHE A 35 TRP 0.002 0.001 TRP A 70 HIS 0.005 0.002 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.28 ( 4567) covalent geometry : angle 0.98853 / 0.43 ( 6830) hydrogen bonds : bond 0.06822 / 4.96 ( 205) hydrogen bonds : angle 3.94214 / 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 14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.088 Fit side-chains REVERT: A 52 TYR cc_start: 0.8116 (t80) cc_final: 0.7736 (t80) outliers start: 4 outliers final: 4 residues processed: 13 average time/residue: 0.5153 time to fit residues: 7.0096 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 : 0.049 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4770 r_free = 0.4770 target = 0.238491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.192851 restraints weight = 4785.761| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 1.13 r_work: 0.4158 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4567 Z= 0.187 Angle : 0.903 10.941 6830 Z= 0.390 Chirality : 0.068 0.669 860 Planarity : 0.004 0.049 359 Dihedral : 20.845 149.328 1796 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.17 % Allowed : 19.84 % 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: -0.68 (0.65), residues: 162 helix: 1.18 (0.60), residues: 67 sheet: -2.71 (0.83), residues: 33 loop : -0.80 (0.78), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 133 TYR 0.011 0.002 TYR A 52 PHE 0.016 0.002 PHE A 35 TRP 0.004 0.001 TRP A 70 HIS 0.002 0.001 HIS A 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 ( 4567) covalent geometry : angle 0.90294 / 0.39 ( 6830) hydrogen bonds : bond 0.06069 / 4.44 ( 205) hydrogen bonds : angle 3.65358 / 2.81 ( 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 14 residues out of total 143 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 10 time to evaluate : 0.110 Fit side-chains REVERT: A 52 TYR cc_start: 0.8003 (t80) cc_final: 0.7379 (t80) outliers start: 4 outliers final: 4 residues processed: 13 average time/residue: 0.4821 time to fit residues: 6.6514 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 : 0.083 ------------------------------------------------------------------------------- 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: 0.0970 chunk 28 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4780 r_free = 0.4780 target = 0.239341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.193601 restraints weight = 4820.986| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 1.15 r_work: 0.4185 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4567 Z= 0.189 Angle : 0.888 10.728 6830 Z= 0.384 Chirality : 0.066 0.656 860 Planarity : 0.004 0.048 359 Dihedral : 20.789 149.705 1796 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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: -0.41 (0.66), residues: 162 helix: 1.48 (0.61), residues: 67 sheet: -2.64 (0.80), residues: 33 loop : -0.71 (0.79), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 110 TYR 0.011 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 0.00376 / 0.19 ( 4567) covalent geometry : angle 0.88752 / 0.38 ( 6830) hydrogen bonds : bond 0.06093 / 4.45 ( 205) hydrogen bonds : angle 3.55951 / 2.74 ( 444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1204.17 seconds wall clock time: 21 minutes 17.96 seconds (1277.96 seconds total)