Starting phenix.real_space_refine on Tue Aug 4 16:17:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u5q_63879/08_2026/9u5q_63879.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u5q_63879/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9u5q_63879/08_2026/9u5q_63879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u5q_63879/08_2026/9u5q_63879.map" model { file = "/net/cci-nas-00/data/ceres_data/9u5q_63879/08_2026/9u5q_63879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u5q_63879/08_2026/9u5q_63879.cif" } 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-2.2rc3-6140/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: 1.39, per 1000 atoms: 0.29 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: 0.45 Conformation dependent library (CDL) restraints added in 131.2 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: 0.72 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: 0.63 Time building geometry restraints manager: 0.57 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=" O5' A R 13 " ideal model delta sigma weight residual 1.593 1.620 -0.027 1.00e-02 1.00e+04 7.37e+00 bond pdb=" O3' U R 60 " pdb=" P G R 61 " ideal model delta sigma weight residual 1.607 1.579 0.028 1.20e-02 6.94e+03 5.48e+00 bond pdb=" P G R 12 " pdb=" O5' G R 12 " ideal model delta sigma weight residual 1.593 1.616 -0.023 1.00e-02 1.00e+04 5.31e+00 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 ... (remaining 4961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 6674 1.71 - 3.41: 352 3.41 - 5.12: 37 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=" C3' U R 14 " pdb=" O3' U R 14 " pdb=" P G R 15 " ideal model delta sigma weight residual 119.70 124.29 -4.59 1.20e+00 6.94e-01 1.46e+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=" C2' A R 56 " pdb=" C1' A R 56 " pdb=" N9 A R 56 " ideal model delta sigma weight residual 112.00 115.35 -3.35 1.10e+00 8.26e-01 9.30e+00 angle pdb=" C2' G R 53 " pdb=" C1' G R 53 " pdb=" N9 G R 53 " ideal model delta sigma weight residual 112.00 115.29 -3.29 1.10e+00 8.26e-01 8.94e+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: 685 0.101 - 0.203: 161 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: 2.130 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.240 Find NCS groups from input model: 0.030 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.710 ------------------------------------------------------------------------------- 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= 0.394 Angle : 0.829 8.537 7079 Z= 0.519 Chirality : 0.083 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 0.00545 / 0.39 ( 4966) covalent geometry : angle 0.82859 / 0.52 ( 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 : 0.147 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: 0.0590 time to fit residues: 4.1494 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 : 0.130 ------------------------------------------------------------------------------- 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 = 0.4718 r_free = 0.4718 target = 0.223236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.201849 restraints weight = 8531.031| |-----------------------------------------------------------------------------| r_work (start): 0.4497 rms_B_bonded: 2.32 r_work: 0.4400 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 4966 Z= 0.185 Angle : 0.633 6.429 7079 Z= 0.349 Chirality : 0.044 0.240 857 Planarity : 0.006 0.055 632 Dihedral : 20.666 125.888 1622 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.04 % Allowed : 18.66 % Favored : 79.30 % 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: 3.26 (1.63), residues: 11 sheet: 1.05 (0.39), residues: 169 loop : -1.21 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 74 TYR 0.014 0.002 TYR A 60 PHE 0.020 0.003 PHE A 25 TRP 0.013 0.002 TRP C 90 HIS 0.010 0.003 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 ( 4966) covalent geometry : angle 0.63321 / 0.35 ( 7079) hydrogen bonds : bond 0.06054 / 3.93 ( 185) hydrogen bonds : angle 4.49623 / 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 56 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.081 Fit side-chains REVERT: B 103 LYS cc_start: 0.8247 (mmpt) cc_final: 0.7946 (mmtt) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.0445 time to fit residues: 3.1780 Evaluate side-chains 51 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.076 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 64 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 0.0170 chunk 32 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 HIS 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 = 0.4576 r_free = 0.4576 target = 0.208672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.186417 restraints weight = 7975.669| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 2.17 r_work: 0.4240 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 4966 Z= 0.203 Angle : 0.709 12.868 7079 Z= 0.369 Chirality : 0.045 0.264 857 Planarity : 0.006 0.045 632 Dihedral : 20.628 130.213 1622 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.08 % Allowed : 18.66 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.40), residues: 405 helix: 3.19 (1.51), residues: 11 sheet: 0.91 (0.42), residues: 152 loop : -1.31 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 74 TYR 0.019 0.003 TYR A 139 PHE 0.017 0.003 PHE B 31 TRP 0.020 0.003 TRP B 38 HIS 0.010 0.002 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 ( 4966) covalent geometry : angle 0.70928 / 0.37 ( 7079) hydrogen bonds : bond 0.07263 / 4.80 ( 185) hydrogen bonds : angle 4.70928 / 3.33 ( 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 64 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.131 Fit side-chains REVERT: A 35 CYS cc_start: 0.7293 (p) cc_final: 0.7026 (p) REVERT: B 103 LYS cc_start: 0.7890 (mtpt) cc_final: 0.7673 (mmtt) REVERT: C 9 SER cc_start: 0.7599 (p) cc_final: 0.7229 (m) outliers start: 14 outliers final: 8 residues processed: 60 average time/residue: 0.0550 time to fit residues: 4.4721 Evaluate side-chains 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 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 60 LYS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 46 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 28 optimal weight: 0.6980 chunk 12 optimal weight: 30.0000 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4568 r_free = 0.4568 target = 0.207221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.184932 restraints weight = 7931.505| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.29 r_work: 0.4220 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4966 Z= 0.136 Angle : 0.541 6.237 7079 Z= 0.301 Chirality : 0.040 0.267 857 Planarity : 0.004 0.035 632 Dihedral : 20.401 132.767 1622 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.50 % Allowed : 20.99 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.41), residues: 405 helix: 3.49 (1.58), residues: 11 sheet: 0.85 (0.40), residues: 171 loop : -1.12 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 18 TYR 0.020 0.002 TYR B 82 PHE 0.016 0.002 PHE A 25 TRP 0.013 0.002 TRP C 90 HIS 0.007 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 4966) covalent geometry : angle 0.54053 / 0.30 ( 7079) hydrogen bonds : bond 0.05415 / 3.55 ( 185) hydrogen bonds : angle 4.39667 / 3.09 ( 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: 12 poor density : 49 time to evaluate : 0.125 Fit side-chains REVERT: A 35 CYS cc_start: 0.7257 (p) cc_final: 0.7029 (p) REVERT: C 9 SER cc_start: 0.7557 (p) cc_final: 0.7148 (m) REVERT: C 42 SER cc_start: 0.7677 (OUTLIER) cc_final: 0.6970 (m) outliers start: 12 outliers final: 7 residues processed: 55 average time/residue: 0.0546 time to fit residues: 4.2217 Evaluate side-chains 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 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 C residue 23 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE 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: 0.5980 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4474 r_free = 0.4474 target = 0.197840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.176976 restraints weight = 7914.129| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 2.09 r_work: 0.4143 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6493 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4966 Z= 0.183 Angle : 0.646 7.836 7079 Z= 0.352 Chirality : 0.044 0.312 857 Planarity : 0.005 0.032 632 Dihedral : 20.482 137.532 1622 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.66 % Allowed : 21.28 % Favored : 74.05 % 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: -0.19 (0.41), residues: 405 helix: 3.49 (1.55), residues: 11 sheet: 0.71 (0.40), residues: 161 loop : -0.95 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 74 TYR 0.012 0.002 TYR A 60 PHE 0.018 0.003 PHE A 25 TRP 0.012 0.002 TRP C 90 HIS 0.007 0.002 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 ( 4966) covalent geometry : angle 0.64582 / 0.35 ( 7079) hydrogen bonds : bond 0.06540 / 4.35 ( 185) hydrogen bonds : angle 4.41247 / 3.16 ( 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 66 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 35 CYS cc_start: 0.7187 (p) cc_final: 0.6972 (p) REVERT: B 115 MET cc_start: 0.5943 (mpp) cc_final: 0.5628 (mtt) REVERT: C 9 SER cc_start: 0.7464 (p) cc_final: 0.7047 (m) REVERT: C 42 SER cc_start: 0.8151 (p) cc_final: 0.7753 (m) outliers start: 16 outliers final: 14 residues processed: 60 average time/residue: 0.0472 time to fit residues: 3.9362 Evaluate side-chains 63 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.4437 r_free = 0.4437 target = 0.193755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.172701 restraints weight = 7955.883| |-----------------------------------------------------------------------------| r_work (start): 0.4190 rms_B_bonded: 2.29 r_work: 0.4083 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.6619 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= 0.186 Angle : 0.619 7.449 7079 Z= 0.341 Chirality : 0.043 0.261 857 Planarity : 0.005 0.035 632 Dihedral : 20.420 138.772 1622 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.50 % Allowed : 24.49 % Favored : 72.01 % 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 (0.42), residues: 405 helix: 3.48 (1.62), residues: 11 sheet: 0.64 (0.39), residues: 166 loop : -0.80 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 18 TYR 0.016 0.002 TYR A 60 PHE 0.021 0.002 PHE A 25 TRP 0.013 0.002 TRP C 90 HIS 0.004 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 ( 4966) covalent geometry : angle 0.61940 / 0.34 ( 7079) hydrogen bonds : bond 0.06317 / 4.14 ( 185) hydrogen bonds : angle 4.49463 / 3.19 ( 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 51 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.134 Fit side-chains REVERT: A 35 CYS cc_start: 0.7399 (p) cc_final: 0.7154 (p) REVERT: A 172 GLN cc_start: 0.6534 (OUTLIER) cc_final: 0.5988 (tp40) REVERT: B 115 MET cc_start: 0.6024 (mpp) cc_final: 0.5758 (mtt) REVERT: C 9 SER cc_start: 0.7428 (p) cc_final: 0.7098 (m) REVERT: C 42 SER cc_start: 0.8149 (p) cc_final: 0.7782 (m) REVERT: C 49 GLN cc_start: 0.7187 (mm-40) cc_final: 0.6924 (mp10) outliers start: 12 outliers final: 9 residues processed: 48 average time/residue: 0.0470 time to fit residues: 3.3607 Evaluate side-chains 47 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU 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 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: 4.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 = 0.4407 r_free = 0.4407 target = 0.190335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.170877 restraints weight = 7673.227| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.97 r_work: 0.4086 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.7054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 4966 Z= 0.258 Angle : 0.700 6.608 7079 Z= 0.382 Chirality : 0.048 0.255 857 Planarity : 0.005 0.035 632 Dihedral : 20.620 139.458 1622 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.96 % Allowed : 23.91 % 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: -0.40 (0.42), residues: 405 helix: 3.15 (1.62), residues: 11 sheet: 0.57 (0.41), residues: 153 loop : -1.02 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 69 TYR 0.024 0.003 TYR A 139 PHE 0.028 0.003 PHE A 25 TRP 0.015 0.003 TRP C 90 HIS 0.007 0.002 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.26 ( 4966) covalent geometry : angle 0.70016 / 0.38 ( 7079) hydrogen bonds : bond 0.07707 / 5.17 ( 185) hydrogen bonds : angle 4.60178 / 3.28 ( 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 58 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 41 time to evaluate : 0.138 Fit side-chains REVERT: A 172 GLN cc_start: 0.6536 (OUTLIER) cc_final: 0.5944 (tp40) REVERT: C 9 SER cc_start: 0.7441 (p) cc_final: 0.7219 (m) REVERT: C 42 SER cc_start: 0.8151 (p) cc_final: 0.7855 (m) outliers start: 17 outliers final: 15 residues processed: 53 average time/residue: 0.0532 time to fit residues: 4.1278 Evaluate side-chains 53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 102 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 65 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 3 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.192895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.173595 restraints weight = 7717.832| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 1.93 r_work: 0.4119 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.7190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4966 Z= 0.136 Angle : 0.558 6.122 7079 Z= 0.315 Chirality : 0.042 0.288 857 Planarity : 0.004 0.035 632 Dihedral : 20.424 138.890 1622 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.50 % Allowed : 26.24 % Favored : 70.26 % 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: -0.24 (0.42), residues: 405 helix: 3.53 (1.65), residues: 11 sheet: 0.51 (0.39), residues: 166 loop : -0.87 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.012 0.002 TYR B 82 PHE 0.014 0.001 PHE A 25 TRP 0.013 0.001 TRP C 90 HIS 0.008 0.002 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 4966) covalent geometry : angle 0.55808 / 0.31 ( 7079) hydrogen bonds : bond 0.05694 / 3.77 ( 185) hydrogen bonds : angle 4.49376 / 3.17 ( 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 52 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.127 Fit side-chains REVERT: B 36 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6700 (ptp) REVERT: B 65 SER cc_start: 0.7157 (p) cc_final: 0.6776 (t) REVERT: C 9 SER cc_start: 0.7360 (p) cc_final: 0.7142 (m) REVERT: C 42 SER cc_start: 0.8131 (p) cc_final: 0.7809 (m) outliers start: 12 outliers final: 10 residues processed: 50 average time/residue: 0.0596 time to fit residues: 4.1409 Evaluate side-chains 49 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.130 ------------------------------------------------------------------------------- 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 102 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 62 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- 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: 0.9980 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 0.0570 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.190601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.171546 restraints weight = 7595.231| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 1.95 r_work: 0.4090 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.7620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4966 Z= 0.154 Angle : 0.566 6.455 7079 Z= 0.316 Chirality : 0.041 0.266 857 Planarity : 0.005 0.034 632 Dihedral : 20.361 139.392 1622 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.92 % Allowed : 26.53 % Favored : 70.55 % 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 (0.43), residues: 405 helix: 3.49 (1.60), residues: 11 sheet: 0.45 (0.39), residues: 171 loop : -0.74 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 100 TYR 0.013 0.002 TYR A 60 PHE 0.018 0.002 PHE A 25 TRP 0.013 0.001 TRP C 90 HIS 0.007 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 4966) covalent geometry : angle 0.56642 / 0.32 ( 7079) hydrogen bonds : bond 0.05643 / 3.80 ( 185) hydrogen bonds : angle 4.39436 / 3.08 ( 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 57 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.129 Fit side-chains REVERT: B 93 THR cc_start: 0.7230 (m) cc_final: 0.6973 (p) REVERT: C 42 SER cc_start: 0.8155 (p) cc_final: 0.7804 (m) REVERT: C 93 SER cc_start: 0.8256 (m) cc_final: 0.7987 (p) outliers start: 10 outliers final: 7 residues processed: 53 average time/residue: 0.0518 time to fit residues: 3.9012 Evaluate side-chains 48 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 MET Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 64 SER 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: 0.0980 chunk 25 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 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: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4409 r_free = 0.4409 target = 0.190461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.171701 restraints weight = 7581.817| |-----------------------------------------------------------------------------| r_work (start): 0.4193 rms_B_bonded: 1.94 r_work: 0.4094 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.7833 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= 0.144 Angle : 0.548 5.773 7079 Z= 0.308 Chirality : 0.041 0.282 857 Planarity : 0.004 0.035 632 Dihedral : 20.345 139.553 1622 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.21 % Allowed : 26.24 % Favored : 70.55 % 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: 3.42 (1.59), residues: 11 sheet: 0.54 (0.38), residues: 175 loop : -0.77 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 69 TYR 0.012 0.002 TYR B 97 PHE 0.015 0.002 PHE A 25 TRP 0.011 0.001 TRP C 90 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 ( 4966) covalent geometry : angle 0.54752 / 0.31 ( 7079) hydrogen bonds : bond 0.05441 / 3.63 ( 185) hydrogen bonds : angle 4.39280 / 3.08 ( 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 54 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.138 Fit side-chains REVERT: B 93 THR cc_start: 0.7288 (m) cc_final: 0.7024 (p) REVERT: C 42 SER cc_start: 0.8169 (p) cc_final: 0.7822 (m) outliers start: 11 outliers final: 10 residues processed: 51 average time/residue: 0.0531 time to fit residues: 3.8213 Evaluate side-chains 53 residues out of total 343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 62 SER 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: 0.4980 chunk 40 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.0970 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.0060 chunk 29 optimal weight: 0.0040 overall best weight: 0.3206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.190591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.171834 restraints weight = 7591.945| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 1.94 r_work: 0.4098 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.7834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.463 4966 Z= 0.402 Angle : 1.087 65.896 7079 Z= 0.687 Chirality : 0.041 0.281 857 Planarity : 0.011 0.253 632 Dihedral : 20.343 139.587 1622 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.62 % Allowed : 26.82 % Favored : 70.55 % 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: -0.11 (0.42), residues: 405 helix: 3.46 (1.60), residues: 11 sheet: 0.53 (0.39), residues: 175 loop : -0.76 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.011 0.002 TYR B 97 PHE 0.015 0.002 PHE A 25 TRP 0.011 0.001 TRP C 90 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00862 / 0.40 ( 4966) covalent geometry : angle 1.08665 / 0.69 ( 7079) hydrogen bonds : bond 0.05409 / 3.61 ( 185) hydrogen bonds : angle 4.39074 / 3.08 ( 435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1186.28 seconds wall clock time: 21 minutes 6.06 seconds (1266.06 seconds total)