Starting phenix.real_space_refine on Thu Jul 2 00:43:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wb3_65832/07_2026/9wb3_65832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wb3_65832/07_2026/9wb3_65832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wb3_65832/07_2026/9wb3_65832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wb3_65832/07_2026/9wb3_65832.map" model { file = "/net/cci-nas-00/data/ceres_data/9wb3_65832/07_2026/9wb3_65832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wb3_65832/07_2026/9wb3_65832.cif" } resolution = 3.17 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= 0.001 sd= 0.018 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 75 5.49 5 S 15 5.16 5 C 2678 2.51 5 N 812 2.21 5 O 1142 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: 4722 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1382 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain: "B" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 973 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 2, 'TRANS': 124} Chain: "C" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 780 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "R" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1587 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 36} Link IDs: {'rna2p': 8, 'rna3p': 66} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.30, per 1000 atoms: 0.28 Number of scatterers: 4722 At special positions: 0 Unit cell: (88.32, 73.92, 132.48, 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 15 16.00 P 75 15.00 O 1142 8.00 N 812 7.00 C 2678 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: 0.40 Conformation dependent library (CDL) restraints added in 89.3 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.4% alpha, 47.7% beta 25 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 Processing helix chain 'A' and resid 38 through 42 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.685A pdb=" N ILE A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.775A pdb=" N GLN A 145 " --> pdb=" O LYS A 142 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS A 146 " --> pdb=" O THR A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.558A pdb=" N TYR A 177 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 178 " --> pdb=" O LYS A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'B' and resid 30 through 34 removed outlier: 3.622A pdb=" N SER B 33 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR B 34 " --> pdb=" O PHE B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 34' Processing helix chain 'C' and resid 26 through 30 removed outlier: 3.643A pdb=" N ASP C 29 " --> pdb=" O LYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.798A pdb=" N ASP C 81 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU C 82 " --> pdb=" O ALA C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 20 removed outlier: 3.519A pdb=" N LEU A 28 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 34 " --> pdb=" O ILE A 30 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU A 72 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 58 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP A 78 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 56 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 126 removed outlier: 6.980A pdb=" N MET A 120 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 135 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY A 122 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 133 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ARG A 133 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ALA A 171 " --> pdb=" O HIS A 160 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N HIS A 160 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU A 150 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA A 99 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 115 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER A 105 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 10 Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.098A pdb=" N ARG B 40 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TRP B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 14 removed outlier: 4.339A pdb=" N VAL B 117 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.596A pdb=" N THR C 104 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AA8, first strand: chain 'C' and resid 44 through 47 removed outlier: 6.848A pdb=" N TRP C 34 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 94 " --> pdb=" O ASP C 91 " (cutoff:3.500A) 126 hydrogen bonds defined for protein. 315 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 0.55 Time building geometry restraints manager: 0.53 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: 1206 1.33 - 1.45: 1328 1.45 - 1.57: 2262 1.57 - 1.69: 148 1.69 - 1.81: 22 Bond restraints: 4966 Sorted by residual: bond pdb=" CA ARG A 84 " pdb=" C ARG A 84 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.24e-02 6.50e+03 1.17e+01 bond pdb=" P A R 13 " pdb=" OP2 A R 13 " ideal model delta sigma weight residual 1.485 1.527 -0.042 2.00e-02 2.50e+03 4.45e+00 bond pdb=" P G R 12 " pdb=" OP2 G R 12 " ideal model delta sigma weight residual 1.485 1.526 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C ARG A 84 " pdb=" N ASP A 85 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.44e-02 4.82e+03 4.08e+00 bond pdb=" N VAL C 105 " pdb=" CA VAL C 105 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 4.04e+00 ... (remaining 4961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 6705 1.71 - 3.41: 322 3.41 - 5.12: 36 5.12 - 6.83: 14 6.83 - 8.54: 2 Bond angle restraints: 7079 Sorted by residual: angle pdb=" CA THR C 104 " pdb=" C THR C 104 " pdb=" O THR C 104 " ideal model delta sigma weight residual 120.36 124.63 -4.27 1.08e+00 8.57e-01 1.56e+01 angle pdb=" C1' C R 57 " pdb=" N1 C R 57 " pdb=" C2 C R 57 " ideal model delta sigma weight residual 118.80 122.61 -3.81 1.10e+00 8.26e-01 1.20e+01 angle pdb=" O3' A R 4 " pdb=" P A R 5 " pdb=" O5' A R 5 " ideal model delta sigma weight residual 104.00 98.81 5.19 1.50e+00 4.44e-01 1.20e+01 angle pdb=" O3' U R 14 " pdb=" C3' U R 14 " pdb=" C2' U R 14 " ideal model delta sigma weight residual 113.70 118.12 -4.42 1.50e+00 4.44e-01 8.69e+00 angle pdb=" C3' U R 14 " pdb=" O3' U R 14 " pdb=" P G R 15 " ideal model delta sigma weight residual 120.20 124.29 -4.09 1.50e+00 4.44e-01 7.43e+00 ... (remaining 7074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.95: 2660 22.95 - 45.90: 236 45.90 - 68.84: 139 68.84 - 91.79: 22 91.79 - 114.74: 1 Dihedral angle restraints: 3058 sinusoidal: 1901 harmonic: 1157 Sorted by residual: dihedral pdb=" O4' A R 59 " pdb=" C1' A R 59 " pdb=" N9 A R 59 " pdb=" C4 A R 59 " ideal model delta sinusoidal sigma weight residual 254.00 178.29 75.71 1 1.70e+01 3.46e-03 2.50e+01 dihedral pdb=" O4' U R 60 " pdb=" C1' U R 60 " pdb=" N1 U R 60 " pdb=" C2 U R 60 " ideal model delta sinusoidal sigma weight residual 232.00 178.74 53.26 1 1.70e+01 3.46e-03 1.33e+01 dihedral pdb=" O4' A R 4 " pdb=" C1' A R 4 " pdb=" N9 A R 4 " pdb=" C4 A R 4 " ideal model delta sinusoidal sigma weight residual -106.00 -154.62 48.62 1 1.70e+01 3.46e-03 1.13e+01 ... (remaining 3055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 689 0.101 - 0.203: 157 0.203 - 0.304: 2 0.304 - 0.406: 4 0.406 - 0.507: 5 Chirality restraints: 857 Sorted by residual: chirality pdb=" P C R 82 " pdb=" OP1 C R 82 " pdb=" OP2 C R 82 " pdb=" O5' C R 82 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" P A R 4 " pdb=" OP1 A R 4 " pdb=" OP2 A R 4 " pdb=" O5' A R 4 " both_signs ideal model delta sigma weight residual True 2.41 -2.90 -0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" P C R 25 " pdb=" OP1 C R 25 " pdb=" OP2 C R 25 " pdb=" O5' C R 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.79e+00 ... (remaining 854 not shown) Planarity restraints: 632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 83 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C PHE A 83 " -0.066 2.00e-02 2.50e+03 pdb=" O PHE A 83 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG A 84 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 7 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO C 8 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 8 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 8 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 71 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C GLU A 71 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU A 71 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 72 " 0.010 2.00e-02 2.50e+03 ... (remaining 629 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 740 2.76 - 3.30: 3870 3.30 - 3.83: 7900 3.83 - 4.37: 9545 4.37 - 4.90: 15180 Nonbonded interactions: 37235 Sorted by model distance: nonbonded pdb=" O2' U R 14 " pdb=" OP1 G R 15 " model vdw 2.227 3.040 nonbonded pdb=" OP2 C R 10 " pdb=" O2' U R 42 " model vdw 2.342 3.040 nonbonded pdb=" OH TYR C 2 " pdb=" O ASP C 25 " model vdw 2.344 3.040 nonbonded pdb=" N6 A R 36 " pdb=" O2 C R 51 " model vdw 2.366 3.120 nonbonded pdb=" NH1 ARG B 69 " pdb=" O SER B 87 " model vdw 2.371 3.120 ... (remaining 37230 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: 1.750 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.940 Find NCS groups from input model: 0.020 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5335 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 4966 Z= 0.366 Angle : 0.817 8.537 7079 Z= 0.506 Chirality : 0.082 0.507 857 Planarity : 0.005 0.064 632 Dihedral : 20.317 114.738 2328 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 14.87 % Favored : 85.13 % 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: 0.16 (0.43), residues: 405 helix: 1.97 (1.78), residues: 11 sheet: 1.08 (0.40), residues: 182 loop : -0.90 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 84 TYR 0.011 0.001 TYR B 97 PHE 0.011 0.001 PHE B 70 TRP 0.012 0.001 TRP C 90 HIS 0.002 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.37 ( 4966) covalent geometry : angle 0.81735 / 0.51 ( 7079) hydrogen bonds : bond 0.14654 / 9.14 ( 185) hydrogen bonds : angle 5.01367 / 3.52 ( 435) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.132 Fit side-chains REVERT: B 103 LYS cc_start: 0.8285 (mmpt) cc_final: 0.7993 (mmtt) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0728 time to fit residues: 5.4191 Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.0770 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 80 ASN B 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.240648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.205639 restraints weight = 7547.981| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 2.39 r_work: 0.4386 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4966 Z= 0.187 Angle : 0.597 6.286 7079 Z= 0.334 Chirality : 0.041 0.237 857 Planarity : 0.006 0.072 632 Dihedral : 20.621 115.106 1622 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.21 % Allowed : 18.08 % Favored : 78.72 % 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: -0.05 (0.41), residues: 405 helix: 3.14 (1.61), residues: 11 sheet: 1.04 (0.39), residues: 169 loop : -1.10 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 74 TYR 0.013 0.002 TYR A 60 PHE 0.016 0.003 PHE B 31 TRP 0.013 0.002 TRP C 90 HIS 0.010 0.003 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 ( 4966) covalent geometry : angle 0.59723 / 0.33 ( 7079) hydrogen bonds : bond 0.05224 / 3.36 ( 185) hydrogen bonds : angle 4.54324 / 3.19 ( 435) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: B 103 LYS cc_start: 0.8435 (mmpt) cc_final: 0.8187 (mmtt) outliers start: 11 outliers final: 9 residues processed: 63 average time/residue: 0.0799 time to fit residues: 6.4434 Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 64 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.222520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.184871 restraints weight = 6957.875| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 2.24 r_work: 0.4179 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4966 Z= 0.223 Angle : 0.699 10.062 7079 Z= 0.377 Chirality : 0.043 0.216 857 Planarity : 0.006 0.040 632 Dihedral : 20.642 118.625 1622 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.66 % Allowed : 19.24 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.41), residues: 405 helix: 3.28 (1.55), residues: 11 sheet: 0.73 (0.41), residues: 159 loop : -1.32 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 69 TYR 0.018 0.003 TYR B 96 PHE 0.021 0.004 PHE B 31 TRP 0.024 0.003 TRP B 38 HIS 0.013 0.003 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 ( 4966) covalent geometry : angle 0.69868 / 0.38 ( 7079) hydrogen bonds : bond 0.06249 / 4.04 ( 185) hydrogen bonds : angle 4.79350 / 3.37 ( 435) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.094 Fit side-chains REVERT: A 35 CYS cc_start: 0.7338 (p) cc_final: 0.7046 (p) REVERT: C 9 SER cc_start: 0.7705 (p) cc_final: 0.7410 (m) outliers start: 16 outliers final: 9 residues processed: 56 average time/residue: 0.0643 time to fit residues: 4.7972 Evaluate side-chains 53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 28 optimal weight: 0.7980 chunk 12 optimal weight: 20.0000 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 104 HIS B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.218872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.180981 restraints weight = 6916.092| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 2.15 r_work: 0.4135 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4966 Z= 0.177 Angle : 0.584 7.170 7079 Z= 0.324 Chirality : 0.040 0.220 857 Planarity : 0.004 0.038 632 Dihedral : 20.516 121.263 1622 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.08 % Allowed : 20.12 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.41), residues: 405 helix: 3.35 (1.54), residues: 11 sheet: 0.55 (0.38), residues: 176 loop : -1.05 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 21 TYR 0.016 0.002 TYR A 60 PHE 0.021 0.002 PHE A 25 TRP 0.015 0.002 TRP C 90 HIS 0.004 0.002 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 4966) covalent geometry : angle 0.58444 / 0.32 ( 7079) hydrogen bonds : bond 0.04802 / 3.18 ( 185) hydrogen bonds : angle 4.55421 / 3.16 ( 435) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.135 Fit side-chains REVERT: C 9 SER cc_start: 0.7619 (p) cc_final: 0.7311 (m) REVERT: C 42 SER cc_start: 0.7869 (OUTLIER) cc_final: 0.7399 (m) outliers start: 14 outliers final: 10 residues processed: 58 average time/residue: 0.0598 time to fit residues: 4.7649 Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 94 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN B 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.213944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.175756 restraints weight = 6823.737| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.15 r_work: 0.4077 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4966 Z= 0.197 Angle : 0.627 7.400 7079 Z= 0.348 Chirality : 0.043 0.273 857 Planarity : 0.005 0.038 632 Dihedral : 20.438 123.170 1622 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.54 % Allowed : 23.62 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.41), residues: 405 helix: 3.31 (1.57), residues: 11 sheet: 0.52 (0.39), residues: 168 loop : -0.90 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 69 TYR 0.022 0.003 TYR A 139 PHE 0.024 0.003 PHE A 25 TRP 0.012 0.002 TRP C 90 HIS 0.005 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 ( 4966) covalent geometry : angle 0.62716 / 0.35 ( 7079) hydrogen bonds : bond 0.05627 / 3.69 ( 185) hydrogen bonds : angle 4.78138 / 3.29 ( 435) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 172 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.6019 (tp40) REVERT: C 9 SER cc_start: 0.7472 (p) cc_final: 0.7225 (m) REVERT: C 42 SER cc_start: 0.8236 (p) cc_final: 0.7961 (m) outliers start: 19 outliers final: 13 residues processed: 58 average time/residue: 0.0596 time to fit residues: 4.6861 Evaluate side-chains 55 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 10.0000 chunk 30 optimal weight: 0.0270 chunk 14 optimal weight: 0.0870 chunk 40 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.215434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.177420 restraints weight = 6896.591| |-----------------------------------------------------------------------------| r_work (start): 0.4210 rms_B_bonded: 2.15 r_work: 0.4089 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4966 Z= 0.134 Angle : 0.550 6.843 7079 Z= 0.310 Chirality : 0.040 0.225 857 Planarity : 0.005 0.033 632 Dihedral : 20.352 124.434 1622 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.37 % Allowed : 26.24 % Favored : 69.39 % 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: -0.18 (0.42), residues: 405 helix: 3.59 (1.55), residues: 11 sheet: 0.59 (0.39), residues: 166 loop : -0.87 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 69 TYR 0.011 0.002 TYR B 97 PHE 0.014 0.002 PHE A 25 TRP 0.013 0.001 TRP C 90 HIS 0.005 0.002 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 4966) covalent geometry : angle 0.54962 / 0.31 ( 7079) hydrogen bonds : bond 0.04713 / 3.09 ( 185) hydrogen bonds : angle 4.57024 / 3.18 ( 435) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.137 Fit side-chains REVERT: C 9 SER cc_start: 0.7406 (p) cc_final: 0.7131 (m) REVERT: C 42 SER cc_start: 0.8204 (p) cc_final: 0.7890 (m) outliers start: 15 outliers final: 12 residues processed: 52 average time/residue: 0.0561 time to fit residues: 4.0762 Evaluate side-chains 51 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.0670 chunk 40 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.213183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.175345 restraints weight = 6834.188| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 2.07 r_work: 0.4066 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4966 Z= 0.155 Angle : 0.562 7.165 7079 Z= 0.317 Chirality : 0.040 0.228 857 Planarity : 0.005 0.034 632 Dihedral : 20.307 126.282 1622 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.37 % Allowed : 26.24 % Favored : 69.39 % 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: -0.16 (0.42), residues: 405 helix: 3.60 (1.52), residues: 11 sheet: 0.54 (0.39), residues: 166 loop : -0.79 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 69 TYR 0.015 0.002 TYR A 139 PHE 0.015 0.002 PHE A 25 TRP 0.013 0.002 TRP C 90 HIS 0.008 0.002 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 4966) covalent geometry : angle 0.56198 / 0.32 ( 7079) hydrogen bonds : bond 0.04866 / 3.22 ( 185) hydrogen bonds : angle 4.48984 / 3.17 ( 435) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.128 Fit side-chains REVERT: A 172 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.5983 (tp40) REVERT: B 47 LEU cc_start: 0.8007 (mt) cc_final: 0.7730 (mt) REVERT: C 9 SER cc_start: 0.7388 (p) cc_final: 0.7168 (m) REVERT: C 42 SER cc_start: 0.8215 (p) cc_final: 0.7925 (m) outliers start: 15 outliers final: 13 residues processed: 51 average time/residue: 0.0529 time to fit residues: 3.7543 Evaluate side-chains 55 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 3 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 0.0980 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.213415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.175514 restraints weight = 6890.584| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 2.08 r_work: 0.4065 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.6282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4966 Z= 0.129 Angle : 0.526 6.630 7079 Z= 0.298 Chirality : 0.039 0.228 857 Planarity : 0.004 0.033 632 Dihedral : 20.247 127.440 1622 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.08 % Allowed : 27.41 % Favored : 68.51 % 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: -0.06 (0.42), residues: 405 helix: 3.80 (1.51), residues: 11 sheet: 0.62 (0.40), residues: 166 loop : -0.73 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 18 TYR 0.011 0.002 TYR B 97 PHE 0.013 0.001 PHE A 25 TRP 0.012 0.001 TRP C 90 HIS 0.005 0.002 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 4966) covalent geometry : angle 0.52576 / 0.30 ( 7079) hydrogen bonds : bond 0.04573 / 3.02 ( 185) hydrogen bonds : angle 4.39943 / 3.10 ( 435) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.135 Fit side-chains REVERT: B 47 LEU cc_start: 0.7989 (mt) cc_final: 0.7695 (mt) REVERT: C 9 SER cc_start: 0.7376 (p) cc_final: 0.7171 (m) REVERT: C 42 SER cc_start: 0.8207 (p) cc_final: 0.7910 (m) outliers start: 14 outliers final: 12 residues processed: 49 average time/residue: 0.0458 time to fit residues: 3.1539 Evaluate side-chains 52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 14 optimal weight: 0.0670 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.4612 r_free = 0.4612 target = 0.211628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.174711 restraints weight = 6739.423| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 1.91 r_work: 0.4068 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4966 Z= 0.140 Angle : 0.541 7.053 7079 Z= 0.303 Chirality : 0.039 0.229 857 Planarity : 0.005 0.035 632 Dihedral : 20.124 129.851 1622 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.08 % Allowed : 26.82 % Favored : 69.10 % 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: 0.02 (0.43), residues: 405 helix: 3.90 (1.52), residues: 11 sheet: 0.57 (0.40), residues: 168 loop : -0.61 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 21 TYR 0.016 0.002 TYR A 139 PHE 0.014 0.002 PHE A 25 TRP 0.012 0.002 TRP C 90 HIS 0.006 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 4966) covalent geometry : angle 0.54063 / 0.30 ( 7079) hydrogen bonds : bond 0.04589 / 3.07 ( 185) hydrogen bonds : angle 4.38023 / 3.09 ( 435) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.130 Fit side-chains REVERT: B 47 LEU cc_start: 0.8064 (mt) cc_final: 0.7747 (mt) REVERT: C 9 SER cc_start: 0.7470 (p) cc_final: 0.7256 (m) REVERT: C 42 SER cc_start: 0.8226 (p) cc_final: 0.7914 (m) outliers start: 14 outliers final: 13 residues processed: 58 average time/residue: 0.0644 time to fit residues: 4.9775 Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 0.0170 chunk 25 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 28 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.0470 overall best weight: 0.2714 ------------------------------------------------------------------------------- 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 = 0.4623 r_free = 0.4623 target = 0.213369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.174439 restraints weight = 6879.184| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 2.30 r_work: 0.4059 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.6757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4966 Z= 0.105 Angle : 0.507 6.820 7079 Z= 0.288 Chirality : 0.038 0.229 857 Planarity : 0.004 0.036 632 Dihedral : 20.099 130.559 1622 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.79 % Allowed : 26.53 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.43), residues: 405 helix: 4.14 (1.52), residues: 11 sheet: 0.65 (0.41), residues: 168 loop : -0.47 (0.44), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 18 TYR 0.012 0.001 TYR B 97 PHE 0.008 0.001 PHE C 61 TRP 0.011 0.001 TRP C 90 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 ( 4966) covalent geometry : angle 0.50739 / 0.29 ( 7079) hydrogen bonds : bond 0.04190 / 2.76 ( 185) hydrogen bonds : angle 4.32629 / 3.06 ( 435) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.135 Fit side-chains REVERT: A 172 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.5953 (tp40) REVERT: B 47 LEU cc_start: 0.8005 (mt) cc_final: 0.7700 (mt) REVERT: C 9 SER cc_start: 0.7263 (p) cc_final: 0.6993 (m) REVERT: C 42 SER cc_start: 0.8248 (p) cc_final: 0.7916 (m) outliers start: 13 outliers final: 12 residues processed: 55 average time/residue: 0.0664 time to fit residues: 4.7673 Evaluate side-chains 59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.0070 chunk 40 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.0470 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 chunk 29 optimal weight: 0.4980 overall best weight: 0.2594 ------------------------------------------------------------------------------- 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 = 0.4626 r_free = 0.4626 target = 0.213785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.175083 restraints weight = 6905.088| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 2.29 r_work: 0.4069 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4966 Z= 0.105 Angle : 0.492 6.783 7079 Z= 0.278 Chirality : 0.038 0.229 857 Planarity : 0.004 0.037 632 Dihedral : 20.075 131.914 1622 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.37 % Allowed : 26.53 % Favored : 69.10 % 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: 0.29 (0.44), residues: 405 helix: 3.99 (1.45), residues: 11 sheet: 0.69 (0.41), residues: 168 loop : -0.35 (0.44), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 18 TYR 0.012 0.001 TYR B 97 PHE 0.009 0.001 PHE A 25 TRP 0.011 0.001 TRP C 90 HIS 0.006 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 4966) covalent geometry : angle 0.49174 / 0.28 ( 7079) hydrogen bonds : bond 0.04063 / 2.67 ( 185) hydrogen bonds : angle 4.22333 / 2.99 ( 435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1353.36 seconds wall clock time: 23 minutes 50.40 seconds (1430.40 seconds total)