Starting phenix.real_space_refine on Sat Apr 4 22:20:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wb3_65832/04_2026/9wb3_65832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wb3_65832/04_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_65832/04_2026/9wb3_65832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wb3_65832/04_2026/9wb3_65832.map" model { file = "/net/cci-nas-00/data/ceres_data/9wb3_65832/04_2026/9wb3_65832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wb3_65832/04_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-2.1rc1-6017/lib/python3.9/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: 1.20, per 1000 atoms: 0.25 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: 0.34 Conformation dependent library (CDL) restraints added in 324.6 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: 0.73 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: 0.79 Time building geometry restraints manager: 0.48 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: 6706 1.71 - 3.41: 321 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=" 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 angle pdb=" O THR C 104 " pdb=" C THR C 104 " pdb=" N VAL C 105 " ideal model delta sigma weight residual 123.30 120.08 3.22 1.19e+00 7.06e-01 7.31e+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: 688 0.101 - 0.203: 158 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.390 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5088 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= 0.318 Angle : 0.817 8.537 7079 Z= 0.430 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 covalent geometry : bond 0.00547 ( 4966) covalent geometry : angle 0.81705 ( 7079) hydrogen bonds : bond 0.14654 ( 185) hydrogen bonds : angle 5.01367 ( 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 : 0.130 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: 0.0750 time to fit residues: 5.5851 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 : 0.105 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 31 HIS B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.226986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.189398 restraints weight = 7107.517| |-----------------------------------------------------------------------------| r_work (start): 0.4340 rms_B_bonded: 2.30 r_work: 0.4225 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4966 Z= 0.170 Angle : 0.644 7.221 7079 Z= 0.328 Chirality : 0.040 0.205 857 Planarity : 0.005 0.047 632 Dihedral : 20.467 115.492 1622 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.62 % Allowed : 16.62 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.41), residues: 405 helix: 2.47 (1.45), residues: 11 sheet: 1.13 (0.42), residues: 153 loop : -1.14 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 74 TYR 0.014 0.002 TYR A 139 PHE 0.016 0.002 PHE A 25 TRP 0.021 0.003 TRP B 38 HIS 0.007 0.002 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 4966) covalent geometry : angle 0.64446 ( 7079) hydrogen bonds : bond 0.04346 ( 185) hydrogen bonds : angle 4.61866 ( 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 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 35 CYS cc_start: 0.7261 (p) cc_final: 0.6989 (p) REVERT: C 9 SER cc_start: 0.7508 (p) cc_final: 0.7183 (m) outliers start: 9 outliers final: 6 residues processed: 58 average time/residue: 0.0596 time to fit residues: 4.5739 Evaluate side-chains 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU 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 23 SER Chi-restraints excluded: chain C residue 47 ILE 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: 9.9990 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 104 HIS A 106 ASN B 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.210988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.172037 restraints weight = 6603.434| |-----------------------------------------------------------------------------| r_work (start): 0.4146 rms_B_bonded: 2.25 r_work: 0.4027 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4966 Z= 0.211 Angle : 0.685 7.552 7079 Z= 0.358 Chirality : 0.043 0.233 857 Planarity : 0.005 0.041 632 Dihedral : 20.351 125.545 1622 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.37 % Allowed : 18.95 % Favored : 76.68 % 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: -0.40 (0.40), residues: 405 helix: 2.35 (1.60), residues: 11 sheet: 0.92 (0.40), residues: 157 loop : -1.31 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 69 TYR 0.022 0.003 TYR A 60 PHE 0.021 0.003 PHE A 25 TRP 0.018 0.003 TRP B 38 HIS 0.007 0.002 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 4966) covalent geometry : angle 0.68508 ( 7079) hydrogen bonds : bond 0.05302 ( 185) hydrogen bonds : angle 4.75467 ( 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 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.118 Fit side-chains REVERT: B 65 SER cc_start: 0.7190 (OUTLIER) cc_final: 0.6927 (t) REVERT: C 9 SER cc_start: 0.7119 (p) cc_final: 0.6800 (m) REVERT: C 49 GLN cc_start: 0.7073 (mm110) cc_final: 0.6781 (mp10) outliers start: 15 outliers final: 7 residues processed: 57 average time/residue: 0.0612 time to fit residues: 4.6511 Evaluate side-chains 51 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 159 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 19 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: 20.0000 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN B 8 GLN B 84 GLN C 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.209368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.171889 restraints weight = 6638.281| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.14 r_work: 0.4037 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.7196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4966 Z= 0.192 Angle : 0.636 8.105 7079 Z= 0.329 Chirality : 0.040 0.230 857 Planarity : 0.005 0.041 632 Dihedral : 20.192 128.723 1622 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.54 % Allowed : 21.28 % Favored : 73.18 % 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: -0.11 (0.41), residues: 405 helix: 2.91 (1.68), residues: 11 sheet: 0.89 (0.40), residues: 166 loop : -1.01 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 69 TYR 0.017 0.002 TYR A 139 PHE 0.017 0.003 PHE A 25 TRP 0.012 0.002 TRP C 90 HIS 0.008 0.002 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 4966) covalent geometry : angle 0.63562 ( 7079) hydrogen bonds : bond 0.04595 ( 185) hydrogen bonds : angle 4.47226 ( 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 71 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 73 THR cc_start: 0.7019 (m) cc_final: 0.6783 (p) REVERT: B 65 SER cc_start: 0.7015 (OUTLIER) cc_final: 0.6795 (t) REVERT: B 93 THR cc_start: 0.7557 (m) cc_final: 0.7293 (p) REVERT: C 9 SER cc_start: 0.7476 (p) cc_final: 0.7228 (m) outliers start: 19 outliers final: 12 residues processed: 65 average time/residue: 0.0621 time to fit residues: 5.4265 Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 70 LEU 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 92 ASP Chi-restraints excluded: chain C residue 10 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 10.0000 chunk 23 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.210643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.173673 restraints weight = 6638.289| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.14 r_work: 0.4058 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.7452 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= 0.131 Angle : 0.565 8.187 7079 Z= 0.293 Chirality : 0.038 0.229 857 Planarity : 0.004 0.037 632 Dihedral : 20.089 131.175 1622 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.79 % Allowed : 26.24 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.42), residues: 405 helix: 3.15 (1.63), residues: 11 sheet: 0.87 (0.40), residues: 168 loop : -0.79 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 53 TYR 0.010 0.001 TYR A 60 PHE 0.013 0.002 PHE A 25 TRP 0.010 0.001 TRP C 90 HIS 0.007 0.002 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4966) covalent geometry : angle 0.56487 ( 7079) hydrogen bonds : bond 0.03956 ( 185) hydrogen bonds : angle 4.26759 ( 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 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.122 Fit side-chains REVERT: A 46 ASP cc_start: 0.6465 (t0) cc_final: 0.6164 (t0) REVERT: A 55 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7549 (ttt-90) REVERT: B 47 LEU cc_start: 0.8036 (mt) cc_final: 0.7729 (mt) REVERT: B 93 THR cc_start: 0.7519 (m) cc_final: 0.7304 (p) outliers start: 13 outliers final: 10 residues processed: 61 average time/residue: 0.0575 time to fit residues: 4.6958 Evaluate side-chains 62 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 54 ILE Chi-restraints excluded: chain A residue 115 VAL 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 21 THR 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: 4.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.0050 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.207331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.170758 restraints weight = 6714.562| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 2.13 r_work: 0.4021 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.7889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4966 Z= 0.186 Angle : 0.654 9.001 7079 Z= 0.337 Chirality : 0.041 0.234 857 Planarity : 0.005 0.052 632 Dihedral : 20.175 132.674 1622 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.25 % Allowed : 25.36 % 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: -0.17 (0.41), residues: 405 helix: 3.14 (1.67), residues: 11 sheet: 0.71 (0.40), residues: 168 loop : -0.96 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 40 TYR 0.013 0.002 TYR A 60 PHE 0.020 0.002 PHE A 25 TRP 0.012 0.002 TRP C 90 HIS 0.009 0.003 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 4966) covalent geometry : angle 0.65431 ( 7079) hydrogen bonds : bond 0.04644 ( 185) hydrogen bonds : angle 4.52141 ( 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 67 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.125 Fit side-chains REVERT: A 172 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.5869 (tp40) REVERT: B 47 LEU cc_start: 0.8114 (mt) cc_final: 0.7853 (mt) outliers start: 18 outliers final: 13 residues processed: 59 average time/residue: 0.0560 time to fit residues: 4.4606 Evaluate side-chains 59 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.095 ------------------------------------------------------------------------------- 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 54 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 115 VAL 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 110 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 46 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.0020 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.207882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.171898 restraints weight = 6690.104| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 2.06 r_work: 0.4034 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.8163 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= 0.159 Angle : 0.595 7.935 7079 Z= 0.308 Chirality : 0.040 0.228 857 Planarity : 0.005 0.050 632 Dihedral : 20.166 134.328 1622 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.79 % Allowed : 26.82 % 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: -0.11 (0.42), residues: 405 helix: 3.28 (1.68), residues: 11 sheet: 0.64 (0.41), residues: 170 loop : -0.83 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 40 TYR 0.011 0.002 TYR A 60 PHE 0.019 0.002 PHE A 25 TRP 0.011 0.001 TRP C 90 HIS 0.007 0.002 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4966) covalent geometry : angle 0.59457 ( 7079) hydrogen bonds : bond 0.04246 ( 185) hydrogen bonds : angle 4.39045 ( 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 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.141 Fit side-chains REVERT: A 46 ASP cc_start: 0.6465 (t0) cc_final: 0.6163 (t0) REVERT: A 55 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7598 (ttt-90) REVERT: A 172 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.5850 (tp40) REVERT: B 47 LEU cc_start: 0.8017 (mt) cc_final: 0.7740 (mt) REVERT: B 93 THR cc_start: 0.7378 (m) cc_final: 0.7114 (p) outliers start: 13 outliers final: 11 residues processed: 56 average time/residue: 0.0539 time to fit residues: 4.2040 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 : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 22 LYS Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 115 VAL 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 C residue 21 THR Chi-restraints excluded: chain C residue 46 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 3 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 6 optimal weight: 0.0170 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.209487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.173468 restraints weight = 6723.110| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.10 r_work: 0.4054 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.8285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4966 Z= 0.118 Angle : 0.547 7.184 7079 Z= 0.287 Chirality : 0.039 0.233 857 Planarity : 0.004 0.033 632 Dihedral : 20.089 135.258 1622 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.37 % Allowed : 27.41 % Favored : 68.22 % 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: 0.10 (0.43), residues: 405 helix: 3.49 (1.68), residues: 11 sheet: 0.66 (0.41), residues: 169 loop : -0.57 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 40 TYR 0.009 0.001 TYR B 114 PHE 0.011 0.001 PHE A 25 TRP 0.010 0.001 TRP C 90 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 4966) covalent geometry : angle 0.54675 ( 7079) hydrogen bonds : bond 0.03825 ( 185) hydrogen bonds : angle 4.23631 ( 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 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.136 Fit side-chains REVERT: A 46 ASP cc_start: 0.6494 (t0) cc_final: 0.6243 (t0) REVERT: A 55 ARG cc_start: 0.7793 (ttp80) cc_final: 0.7571 (ttt-90) REVERT: A 172 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.5836 (tp40) REVERT: B 47 LEU cc_start: 0.7973 (mt) cc_final: 0.7678 (mt) REVERT: B 93 THR cc_start: 0.7301 (m) cc_final: 0.7087 (p) outliers start: 15 outliers final: 10 residues processed: 57 average time/residue: 0.0521 time to fit residues: 4.1689 Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 115 VAL 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 C residue 46 VAL Chi-restraints excluded: chain C residue 59 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.207167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.171433 restraints weight = 6614.681| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.08 r_work: 0.4032 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.8524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4966 Z= 0.169 Angle : 0.613 7.799 7079 Z= 0.321 Chirality : 0.040 0.226 857 Planarity : 0.005 0.060 632 Dihedral : 20.160 136.223 1622 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.08 % Allowed : 27.11 % Favored : 68.80 % 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: -0.06 (0.42), residues: 405 helix: 3.12 (1.68), residues: 11 sheet: 0.61 (0.40), residues: 168 loop : -0.70 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 40 TYR 0.013 0.002 TYR A 139 PHE 0.015 0.002 PHE A 25 TRP 0.013 0.002 TRP C 90 HIS 0.006 0.002 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 4966) covalent geometry : angle 0.61332 ( 7079) hydrogen bonds : bond 0.04395 ( 185) hydrogen bonds : angle 4.49099 ( 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 61 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.084 Fit side-chains REVERT: A 46 ASP cc_start: 0.6490 (t0) cc_final: 0.6193 (t0) REVERT: A 55 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7597 (ttt-90) REVERT: A 172 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.5862 (tp40) REVERT: B 47 LEU cc_start: 0.8028 (mt) cc_final: 0.7736 (mt) outliers start: 14 outliers final: 12 residues processed: 57 average time/residue: 0.0491 time to fit residues: 3.9647 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 : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 115 VAL 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 C residue 10 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 59 GLU 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: 1.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 7 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.207715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.171380 restraints weight = 6643.945| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 2.19 r_work: 0.4032 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.8653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4966 Z= 0.152 Angle : 0.589 7.492 7079 Z= 0.306 Chirality : 0.039 0.225 857 Planarity : 0.005 0.043 632 Dihedral : 20.112 136.812 1622 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.21 % Allowed : 27.70 % 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: 0.03 (0.43), residues: 405 helix: 3.21 (1.66), residues: 11 sheet: 0.68 (0.41), residues: 168 loop : -0.65 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 69 TYR 0.011 0.002 TYR A 139 PHE 0.015 0.002 PHE A 25 TRP 0.011 0.002 TRP C 90 HIS 0.008 0.002 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4966) covalent geometry : angle 0.58902 ( 7079) hydrogen bonds : bond 0.04184 ( 185) hydrogen bonds : angle 4.52087 ( 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: 11 poor density : 47 time to evaluate : 0.125 Fit side-chains REVERT: A 46 ASP cc_start: 0.6534 (t0) cc_final: 0.6258 (t0) REVERT: A 55 ARG cc_start: 0.7820 (ttp80) cc_final: 0.7592 (ttt-90) REVERT: A 172 GLN cc_start: 0.6661 (OUTLIER) cc_final: 0.5843 (tp40) REVERT: B 47 LEU cc_start: 0.7993 (mt) cc_final: 0.7701 (mt) REVERT: B 93 THR cc_start: 0.7391 (m) cc_final: 0.7109 (p) outliers start: 11 outliers final: 10 residues processed: 55 average time/residue: 0.0498 time to fit residues: 3.8718 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 : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 115 VAL 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 C residue 46 VAL Chi-restraints excluded: chain C residue 59 GLU 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: 0.9980 chunk 40 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.204900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.169269 restraints weight = 6601.299| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.07 r_work: 0.4013 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.8944 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= 0.210 Angle : 0.675 8.040 7079 Z= 0.350 Chirality : 0.041 0.223 857 Planarity : 0.006 0.079 632 Dihedral : 20.254 137.667 1622 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.79 % Allowed : 26.82 % 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: -0.20 (0.42), residues: 405 helix: 2.85 (1.69), residues: 11 sheet: 0.53 (0.41), residues: 168 loop : -0.80 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 69 TYR 0.018 0.002 TYR A 139 PHE 0.017 0.002 PHE A 25 TRP 0.014 0.002 TRP C 90 HIS 0.004 0.002 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 4966) covalent geometry : angle 0.67497 ( 7079) hydrogen bonds : bond 0.04900 ( 185) hydrogen bonds : angle 4.79391 ( 435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1296.33 seconds wall clock time: 22 minutes 53.95 seconds (1373.95 seconds total)