Starting phenix.real_space_refine on Thu Jul 2 00:43:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u5q_63879/07_2026/9u5q_63879.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u5q_63879/07_2026/9u5q_63879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u5q_63879/07_2026/9u5q_63879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u5q_63879/07_2026/9u5q_63879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u5q_63879/07_2026/9u5q_63879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u5q_63879/07_2026/9u5q_63879.map" } resolution = 3.35 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= 0.008 sd= 1.147 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: 1.07, per 1000 atoms: 0.23 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 134.8 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: 0.39 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: 0.53 Time building geometry restraints manager: 0.52 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: 2.050 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.440 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5318 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 52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.125 Fit side-chains REVERT: B 103 LYS cc_start: 0.8231 (mmpt) cc_final: 0.7925 (mmtt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0681 time to fit residues: 4.6872 Evaluate side-chains 44 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4727 r_free = 0.4727 target = 0.224305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.203247 restraints weight = 8548.585| |-----------------------------------------------------------------------------| r_work (start): 0.4514 rms_B_bonded: 2.25 r_work: 0.4423 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 4966 Z= 0.182 Angle : 0.579 5.788 7079 Z= 0.330 Chirality : 0.041 0.234 857 Planarity : 0.005 0.048 632 Dihedral : 20.716 120.282 1622 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.04 % Allowed : 18.37 % Favored : 79.59 % 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 (0.41), residues: 405 helix: 3.16 (1.63), residues: 11 sheet: 1.08 (0.39), residues: 169 loop : -1.17 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 74 TYR 0.014 0.002 TYR A 60 PHE 0.024 0.003 PHE B 31 TRP 0.013 0.002 TRP C 90 HIS 0.009 0.002 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 ( 4966) covalent geometry : angle 0.57860 / 0.33 ( 7079) hydrogen bonds : bond 0.05780 / 3.72 ( 185) hydrogen bonds : angle 4.48473 / 3.15 ( 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 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.147 Fit side-chains REVERT: B 103 LYS cc_start: 0.8267 (mmpt) cc_final: 0.7954 (mmtt) outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 0.0621 time to fit residues: 4.5584 Evaluate side-chains 50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE 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 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: 3.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN B 15 GLN B 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.202516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.180632 restraints weight = 7797.474| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 2.18 r_work: 0.4173 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 4966 Z= 0.271 Angle : 0.800 12.597 7079 Z= 0.429 Chirality : 0.048 0.265 857 Planarity : 0.006 0.046 632 Dihedral : 20.966 131.863 1622 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.66 % Allowed : 17.49 % Favored : 77.84 % 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: -0.55 (0.41), residues: 405 helix: 3.22 (1.55), residues: 11 sheet: 0.77 (0.42), residues: 151 loop : -1.37 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 133 TYR 0.027 0.004 TYR A 139 PHE 0.024 0.004 PHE B 31 TRP 0.029 0.004 TRP B 38 HIS 0.011 0.003 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.27 ( 4966) covalent geometry : angle 0.79965 / 0.43 ( 7079) hydrogen bonds : bond 0.08802 / 5.92 ( 185) hydrogen bonds : angle 5.14127 / 3.61 ( 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 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 CYS cc_start: 0.7378 (p) cc_final: 0.7133 (p) REVERT: C 9 SER cc_start: 0.7652 (p) cc_final: 0.7240 (m) outliers start: 16 outliers final: 8 residues processed: 60 average time/residue: 0.0575 time to fit residues: 4.6305 Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.079 ------------------------------------------------------------------------------- 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 52 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 46 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 30.0000 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 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 = 0.4507 r_free = 0.4507 target = 0.201232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.178934 restraints weight = 7787.962| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.29 r_work: 0.4148 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4966 Z= 0.167 Angle : 0.588 7.766 7079 Z= 0.331 Chirality : 0.041 0.225 857 Planarity : 0.005 0.037 632 Dihedral : 20.622 131.257 1622 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.79 % Allowed : 19.83 % Favored : 76.38 % 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: -0.37 (0.41), residues: 405 helix: 3.39 (1.58), residues: 11 sheet: 0.50 (0.39), residues: 169 loop : -1.04 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 21 TYR 0.016 0.002 TYR B 82 PHE 0.019 0.002 PHE A 25 TRP 0.015 0.002 TRP C 90 HIS 0.005 0.002 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 4966) covalent geometry : angle 0.58812 / 0.33 ( 7079) hydrogen bonds : bond 0.06288 / 4.13 ( 185) hydrogen bonds : angle 4.66622 / 3.33 ( 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 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.080 Fit side-chains REVERT: A 35 CYS cc_start: 0.7468 (p) cc_final: 0.7194 (p) REVERT: B 115 MET cc_start: 0.6169 (mpp) cc_final: 0.5957 (mtt) REVERT: C 9 SER cc_start: 0.7583 (p) cc_final: 0.7141 (m) REVERT: C 42 SER cc_start: 0.7971 (p) cc_final: 0.7421 (m) outliers start: 13 outliers final: 10 residues processed: 55 average time/residue: 0.0464 time to fit residues: 3.6919 Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 46 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 92 SER 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: 4.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4411 r_free = 0.4411 target = 0.191321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.171419 restraints weight = 7688.103| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.03 r_work: 0.4075 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 4966 Z= 0.262 Angle : 0.773 8.504 7079 Z= 0.429 Chirality : 0.048 0.271 857 Planarity : 0.006 0.039 632 Dihedral : 20.979 137.648 1622 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 4.96 % Allowed : 21.57 % Favored : 73.47 % 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: -0.63 (0.41), residues: 405 helix: 3.01 (1.57), residues: 11 sheet: 0.44 (0.40), residues: 154 loop : -1.22 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 40 TYR 0.021 0.003 TYR A 139 PHE 0.022 0.004 PHE A 25 TRP 0.014 0.003 TRP C 90 HIS 0.007 0.003 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.26 ( 4966) covalent geometry : angle 0.77308 / 0.43 ( 7079) hydrogen bonds : bond 0.08862 / 5.96 ( 185) hydrogen bonds : angle 4.96083 / 3.53 ( 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 60 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 43 time to evaluate : 0.133 Fit side-chains REVERT: A 172 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.5901 (tp-100) REVERT: C 9 SER cc_start: 0.7464 (p) cc_final: 0.7181 (m) REVERT: C 42 SER cc_start: 0.8222 (p) cc_final: 0.7973 (m) outliers start: 17 outliers final: 13 residues processed: 55 average time/residue: 0.0403 time to fit residues: 3.1357 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 : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 34 VAL 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 C residue 10 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4439 r_free = 0.4439 target = 0.193624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.173664 restraints weight = 7796.750| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 2.03 r_work: 0.4104 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.6824 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= 0.151 Angle : 0.582 6.603 7079 Z= 0.334 Chirality : 0.042 0.227 857 Planarity : 0.005 0.035 632 Dihedral : 20.601 135.058 1622 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.79 % Allowed : 25.07 % Favored : 71.14 % 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: -0.36 (0.42), residues: 405 helix: 3.30 (1.62), residues: 11 sheet: 0.45 (0.39), residues: 168 loop : -0.97 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 69 TYR 0.014 0.002 TYR B 82 PHE 0.019 0.002 PHE A 25 TRP 0.013 0.001 TRP C 90 HIS 0.007 0.002 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 4966) covalent geometry : angle 0.58193 / 0.33 ( 7079) hydrogen bonds : bond 0.06390 / 4.22 ( 185) hydrogen bonds : angle 4.68233 / 3.35 ( 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 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.100 Fit side-chains REVERT: A 134 MET cc_start: 0.5613 (mmt) cc_final: 0.5411 (mmp) REVERT: B 65 SER cc_start: 0.7189 (OUTLIER) cc_final: 0.6755 (t) REVERT: C 9 SER cc_start: 0.7323 (p) cc_final: 0.7023 (m) REVERT: C 42 SER cc_start: 0.8221 (p) cc_final: 0.7893 (m) outliers start: 13 outliers final: 10 residues processed: 51 average time/residue: 0.0442 time to fit residues: 3.1683 Evaluate side-chains 50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 65 SER Chi-restraints excluded: chain C residue 19 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: 3.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.0020 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.0992 ------------------------------------------------------------------------------- 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 = 0.4372 r_free = 0.4372 target = 0.187131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.168287 restraints weight = 7572.662| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 1.96 r_work: 0.4048 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4966 Z= 0.251 Angle : 0.719 7.571 7079 Z= 0.405 Chirality : 0.047 0.230 857 Planarity : 0.006 0.041 632 Dihedral : 20.726 136.231 1622 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 5.83 % Allowed : 23.03 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.41), residues: 405 helix: 2.97 (1.66), residues: 11 sheet: 0.61 (0.41), residues: 151 loop : -1.29 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 18 TYR 0.027 0.003 TYR A 139 PHE 0.027 0.004 PHE A 25 TRP 0.017 0.002 TRP C 90 HIS 0.007 0.002 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.25 ( 4966) covalent geometry : angle 0.71923 / 0.41 ( 7079) hydrogen bonds : bond 0.08005 / 5.35 ( 185) hydrogen bonds : angle 4.74809 / 3.34 ( 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 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.142 Fit side-chains REVERT: A 100 THR cc_start: 0.7964 (m) cc_final: 0.7763 (m) REVERT: A 134 MET cc_start: 0.5648 (mmt) cc_final: 0.5425 (mmp) REVERT: A 172 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.5922 (tp40) REVERT: B 65 SER cc_start: 0.7262 (OUTLIER) cc_final: 0.6961 (t) REVERT: C 42 SER cc_start: 0.8183 (p) cc_final: 0.7869 (m) outliers start: 20 outliers final: 16 residues processed: 60 average time/residue: 0.0462 time to fit residues: 3.9378 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 34 VAL 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 138 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 19 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 3 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 0.0040 chunk 42 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 = 0.4409 r_free = 0.4409 target = 0.190720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.171378 restraints weight = 7631.166| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 1.99 r_work: 0.4082 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.7583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4966 Z= 0.129 Angle : 0.574 6.929 7079 Z= 0.331 Chirality : 0.042 0.236 857 Planarity : 0.005 0.036 632 Dihedral : 20.494 135.718 1622 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.92 % Allowed : 26.24 % 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: -0.25 (0.42), residues: 405 helix: 3.55 (1.67), residues: 11 sheet: 0.63 (0.38), residues: 173 loop : -1.04 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 69 TYR 0.016 0.002 TYR B 82 PHE 0.014 0.001 PHE A 25 TRP 0.012 0.001 TRP C 90 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 4966) covalent geometry : angle 0.57445 / 0.33 ( 7079) hydrogen bonds : bond 0.05875 / 3.87 ( 185) hydrogen bonds : angle 4.55535 / 3.22 ( 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 51 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.132 Fit side-chains REVERT: A 100 THR cc_start: 0.7932 (m) cc_final: 0.7726 (m) REVERT: B 65 SER cc_start: 0.7079 (p) cc_final: 0.6739 (t) REVERT: C 42 SER cc_start: 0.8179 (p) cc_final: 0.7794 (m) outliers start: 10 outliers final: 7 residues processed: 48 average time/residue: 0.0620 time to fit residues: 3.9656 Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 2.9990 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 0.0020 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.189574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.170518 restraints weight = 7538.682| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 1.99 r_work: 0.4075 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.7755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4966 Z= 0.155 Angle : 0.572 6.755 7079 Z= 0.329 Chirality : 0.041 0.231 857 Planarity : 0.005 0.035 632 Dihedral : 20.433 136.756 1622 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.50 % Allowed : 26.82 % 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: -0.25 (0.42), residues: 405 helix: 3.41 (1.62), residues: 11 sheet: 0.61 (0.39), residues: 166 loop : -0.98 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.014 0.002 TYR A 139 PHE 0.018 0.002 PHE A 25 TRP 0.012 0.001 TRP C 90 HIS 0.007 0.002 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 4966) covalent geometry : angle 0.57158 / 0.33 ( 7079) hydrogen bonds : bond 0.05818 / 3.85 ( 185) hydrogen bonds : angle 4.42651 / 3.11 ( 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 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.133 Fit side-chains REVERT: A 134 MET cc_start: 0.5605 (mmt) cc_final: 0.5395 (mmp) REVERT: B 47 LEU cc_start: 0.8035 (mt) cc_final: 0.7738 (mt) REVERT: B 65 SER cc_start: 0.7053 (p) cc_final: 0.6734 (t) REVERT: B 93 THR cc_start: 0.7315 (m) cc_final: 0.7027 (p) REVERT: C 42 SER cc_start: 0.8149 (p) cc_final: 0.7772 (m) outliers start: 12 outliers final: 9 residues processed: 51 average time/residue: 0.0627 time to fit residues: 4.2947 Evaluate side-chains 50 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.0040 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 = 0.4404 r_free = 0.4404 target = 0.190178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.171290 restraints weight = 7521.817| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 1.97 r_work: 0.4084 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.7895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4966 Z= 0.144 Angle : 0.560 7.018 7079 Z= 0.323 Chirality : 0.041 0.234 857 Planarity : 0.004 0.034 632 Dihedral : 20.380 136.512 1622 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.50 % Allowed : 26.82 % 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: -0.23 (0.42), residues: 405 helix: 3.50 (1.63), residues: 11 sheet: 0.51 (0.38), residues: 178 loop : -0.94 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.014 0.002 TYR B 97 PHE 0.016 0.002 PHE A 25 TRP 0.012 0.001 TRP C 90 HIS 0.008 0.003 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4966) covalent geometry : angle 0.56004 / 0.32 ( 7079) hydrogen bonds : bond 0.05433 / 3.61 ( 185) hydrogen bonds : angle 4.43096 / 3.12 ( 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 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.130 Fit side-chains REVERT: A 134 MET cc_start: 0.5598 (mmt) cc_final: 0.5373 (mmp) REVERT: A 172 GLN cc_start: 0.6538 (OUTLIER) cc_final: 0.5899 (tp40) REVERT: B 47 LEU cc_start: 0.8077 (mt) cc_final: 0.7768 (mt) REVERT: B 93 THR cc_start: 0.7319 (m) cc_final: 0.7041 (p) outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 0.0601 time to fit residues: 4.4982 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 : 0.092 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 15 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.0770 chunk 2 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.0470 overall best weight: 0.4236 ------------------------------------------------------------------------------- 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 = 0.4399 r_free = 0.4399 target = 0.189773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.170981 restraints weight = 7527.789| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 1.95 r_work: 0.4079 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.7893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.264 4966 Z= 0.317 Angle : 1.120 59.178 7079 Z= 0.671 Chirality : 0.045 0.559 857 Planarity : 0.004 0.033 632 Dihedral : 20.384 136.524 1622 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.21 % Allowed : 26.82 % Favored : 69.97 % Cbeta Deviations : 0.27 % 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: -0.22 (0.42), residues: 405 helix: 3.48 (1.62), residues: 11 sheet: 0.52 (0.38), residues: 178 loop : -0.92 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.013 0.002 TYR B 97 PHE 0.016 0.002 PHE A 25 TRP 0.012 0.001 TRP C 90 HIS 0.007 0.002 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.32 ( 4966) covalent geometry : angle 1.12043 / 0.67 ( 7079) hydrogen bonds : bond 0.05424 / 3.61 ( 185) hydrogen bonds : angle 4.42925 / 3.12 ( 435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1105.39 seconds wall clock time: 19 minutes 41.31 seconds (1181.31 seconds total)