Starting phenix.real_space_refine on Fri Aug 22 13:19:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8esa_28573/08_2025/8esa_28573.cif Found real_map, /net/cci-nas-00/data/ceres_data/8esa_28573/08_2025/8esa_28573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8esa_28573/08_2025/8esa_28573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8esa_28573/08_2025/8esa_28573.map" model { file = "/net/cci-nas-00/data/ceres_data/8esa_28573/08_2025/8esa_28573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8esa_28573/08_2025/8esa_28573.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 72 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 1970 2.51 5 N 563 2.21 5 O 593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3140 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2223 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "B" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 828 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 89 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 0.97, per 1000 atoms: 0.31 Number of scatterers: 3140 At special positions: 0 Unit cell: (84.15, 65.45, 67.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 593 8.00 N 563 7.00 C 1970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS C 12 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 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: 0.24 Conformation dependent library (CDL) restraints added in 125.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 716 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 7 sheets defined 17.4% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 56 through 85 removed outlier: 3.820A pdb=" N TRP A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 148 removed outlier: 3.699A pdb=" N HIS A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 3.511A pdb=" N GLN A 155 " --> pdb=" O HIS A 151 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 34 removed outlier: 6.965A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 101 " --> pdb=" O MET A 5 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 99 " --> pdb=" O TYR A 7 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR A 94 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR A 118 " --> pdb=" O THR A 94 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLN A 96 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TYR A 116 " --> pdb=" O GLN A 96 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET A 98 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HIS A 114 " --> pdb=" O MET A 98 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY A 100 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLY A 112 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP A 102 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N HIS A 114 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA A 125 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TYR A 116 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 190 removed outlier: 4.072A pdb=" N ARG A 202 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 201 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 190 removed outlier: 4.072A pdb=" N ARG A 202 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 201 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 3.801A pdb=" N GLU A 222 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 214 " --> pdb=" O GLN A 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11 Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 56 removed outlier: 3.981A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 63 " --> pdb=" O SER B 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 134 hydrogen bonds defined for protein. 354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.43 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1049 1.34 - 1.46: 794 1.46 - 1.58: 1365 1.58 - 1.70: 0 1.70 - 1.81: 20 Bond restraints: 3228 Sorted by residual: bond pdb=" CB PRO B 32 " pdb=" CG PRO B 32 " ideal model delta sigma weight residual 1.506 1.468 0.038 3.90e-02 6.57e+02 9.41e-01 bond pdb=" CB PRO A 210 " pdb=" CG PRO A 210 " ideal model delta sigma weight residual 1.506 1.468 0.038 3.90e-02 6.57e+02 9.38e-01 bond pdb=" CB VAL C 2 " pdb=" CG2 VAL C 2 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.64e-01 bond pdb=" CB ARG A 35 " pdb=" CG ARG A 35 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.39e-01 bond pdb=" CG PRO A 210 " pdb=" CD PRO A 210 " ideal model delta sigma weight residual 1.512 1.491 0.021 2.70e-02 1.37e+03 5.95e-01 ... (remaining 3223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 4137 0.97 - 1.95: 195 1.95 - 2.92: 35 2.92 - 3.89: 7 3.89 - 4.86: 1 Bond angle restraints: 4375 Sorted by residual: angle pdb=" C CYS A 164 " pdb=" N VAL A 165 " pdb=" CA VAL A 165 " ideal model delta sigma weight residual 120.42 117.04 3.38 1.42e+00 4.96e-01 5.66e+00 angle pdb=" CA TYR A 159 " pdb=" CB TYR A 159 " pdb=" CG TYR A 159 " ideal model delta sigma weight residual 113.90 110.50 3.40 1.80e+00 3.09e-01 3.56e+00 angle pdb=" C GLN A 72 " pdb=" N THR A 73 " pdb=" CA THR A 73 " ideal model delta sigma weight residual 120.68 118.37 2.31 1.70e+00 3.46e-01 1.85e+00 angle pdb=" C THR A 163 " pdb=" N CYS A 164 " pdb=" CA CYS A 164 " ideal model delta sigma weight residual 120.29 118.39 1.90 1.42e+00 4.96e-01 1.79e+00 angle pdb=" CA CYS A 164 " pdb=" C CYS A 164 " pdb=" N VAL A 165 " ideal model delta sigma weight residual 117.39 118.94 -1.55 1.24e+00 6.50e-01 1.57e+00 ... (remaining 4370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 1642 15.45 - 30.89: 200 30.89 - 46.33: 45 46.33 - 61.78: 12 61.78 - 77.22: 5 Dihedral angle restraints: 1904 sinusoidal: 788 harmonic: 1116 Sorted by residual: dihedral pdb=" CA TYR A 27 " pdb=" C TYR A 27 " pdb=" N VAL A 28 " pdb=" CA VAL A 28 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ARG B 81 " pdb=" CB ARG B 81 " pdb=" CG ARG B 81 " pdb=" CD ARG B 81 " ideal model delta sinusoidal sigma weight residual -60.00 -111.49 51.49 3 1.50e+01 4.44e-03 9.02e+00 dihedral pdb=" CA ARG A 256 " pdb=" CB ARG A 256 " pdb=" CG ARG A 256 " pdb=" CD ARG A 256 " ideal model delta sinusoidal sigma weight residual -180.00 -129.33 -50.67 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 1901 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 245 0.028 - 0.056: 129 0.056 - 0.084: 45 0.084 - 0.111: 17 0.111 - 0.139: 8 Chirality restraints: 444 Sorted by residual: chirality pdb=" CA VAL A 261 " pdb=" N VAL A 261 " pdb=" C VAL A 261 " pdb=" CB VAL A 261 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE A 213 " pdb=" N ILE A 213 " pdb=" C ILE A 213 " pdb=" CB ILE A 213 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 chirality pdb=" CB VAL A 165 " pdb=" CA VAL A 165 " pdb=" CG1 VAL A 165 " pdb=" CG2 VAL A 165 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 441 not shown) Planarity restraints: 571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 160 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C LEU A 160 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU A 160 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 161 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 161 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C GLU A 161 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU A 161 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY A 162 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 49 " 0.016 5.00e-02 4.00e+02 2.42e-02 9.38e-01 pdb=" N PRO A 50 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " 0.014 5.00e-02 4.00e+02 ... (remaining 568 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 588 2.77 - 3.31: 2685 3.31 - 3.84: 4624 3.84 - 4.37: 5574 4.37 - 4.90: 10145 Nonbonded interactions: 23616 Sorted by model distance: nonbonded pdb=" OH TYR A 59 " pdb=" OH TYR A 171 " model vdw 2.243 3.040 nonbonded pdb=" O GLN A 255 " pdb=" NH2 ARG A 273 " model vdw 2.351 3.120 nonbonded pdb=" O SER A 207 " pdb=" OG SER A 207 " model vdw 2.391 3.040 nonbonded pdb=" OE2 GLU B 36 " pdb=" NH1 ARG B 81 " model vdw 2.415 3.120 nonbonded pdb=" NH2 ARG A 14 " pdb=" O GLU A 19 " model vdw 2.459 3.120 ... (remaining 23611 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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.010 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3232 Z= 0.158 Angle : 0.493 4.865 4383 Z= 0.261 Chirality : 0.041 0.139 444 Planarity : 0.004 0.028 571 Dihedral : 14.826 77.222 1176 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 aren not related in a simple way. whole: -0.99 (0.43), residues: 376 helix: 1.18 (0.60), residues: 66 sheet: -0.23 (0.52), residues: 110 loop : -1.58 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 219 TYR 0.010 0.001 TYR A 159 PHE 0.014 0.002 PHE B 56 TRP 0.006 0.001 TRP A 244 HIS 0.003 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 3228) covalent geometry : angle 0.49270 ( 4375) SS BOND : bond 0.00242 ( 4) SS BOND : angle 0.60554 ( 8) hydrogen bonds : bond 0.22007 ( 121) hydrogen bonds : angle 8.52704 ( 354) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.123 Fit side-chains REVERT: A 110 LEU cc_start: 0.7718 (tt) cc_final: 0.7508 (tt) REVERT: A 154 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6901 (pt0) REVERT: B 45 ARG cc_start: 0.7243 (ttp80) cc_final: 0.5821 (mmt90) outliers start: 1 outliers final: 0 residues processed: 52 average time/residue: 0.0858 time to fit residues: 5.2656 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.161769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125524 restraints weight = 3760.240| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.41 r_work: 0.3281 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3232 Z= 0.187 Angle : 0.568 5.926 4383 Z= 0.301 Chirality : 0.044 0.153 444 Planarity : 0.004 0.026 571 Dihedral : 4.419 16.756 429 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.60 % Allowed : 6.02 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 aren not related in a simple way. whole: -1.00 (0.43), residues: 376 helix: 0.72 (0.61), residues: 72 sheet: -0.53 (0.47), residues: 129 loop : -1.30 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 157 TYR 0.013 0.002 TYR A 159 PHE 0.016 0.002 PHE B 56 TRP 0.013 0.001 TRP A 204 HIS 0.004 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 3228) covalent geometry : angle 0.56781 ( 4375) SS BOND : bond 0.00443 ( 4) SS BOND : angle 0.81548 ( 8) hydrogen bonds : bond 0.05195 ( 121) hydrogen bonds : angle 5.73861 ( 354) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.119 Fit side-chains REVERT: A 110 LEU cc_start: 0.7983 (tt) cc_final: 0.7648 (tt) REVERT: A 154 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7174 (pt0) REVERT: A 157 ARG cc_start: 0.8147 (ttt-90) cc_final: 0.7759 (ptm-80) REVERT: A 222 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: B 45 ARG cc_start: 0.8030 (ttp80) cc_final: 0.5775 (mmt90) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.0830 time to fit residues: 5.0241 Evaluate side-chains 50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 4 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 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 = 0.3913 r_free = 0.3913 target = 0.162597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.127782 restraints weight = 3676.486| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.27 r_work: 0.3340 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3232 Z= 0.144 Angle : 0.506 5.512 4383 Z= 0.268 Chirality : 0.042 0.145 444 Planarity : 0.003 0.026 571 Dihedral : 4.174 16.201 429 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.90 % Allowed : 8.73 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 aren not related in a simple way. whole: -0.87 (0.42), residues: 376 helix: 1.03 (0.60), residues: 72 sheet: -0.63 (0.45), residues: 135 loop : -1.16 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 157 TYR 0.014 0.001 TYR A 159 PHE 0.012 0.002 PHE B 56 TRP 0.013 0.001 TRP A 204 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3228) covalent geometry : angle 0.50537 ( 4375) SS BOND : bond 0.00347 ( 4) SS BOND : angle 0.60792 ( 8) hydrogen bonds : bond 0.04435 ( 121) hydrogen bonds : angle 5.01457 ( 354) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.125 Fit side-chains REVERT: A 110 LEU cc_start: 0.7938 (tt) cc_final: 0.7564 (tt) REVERT: A 154 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7181 (pt0) REVERT: A 157 ARG cc_start: 0.8072 (ttt-90) cc_final: 0.7731 (ptm-80) REVERT: A 222 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: B 45 ARG cc_start: 0.7917 (ttp80) cc_final: 0.5750 (mmt90) outliers start: 3 outliers final: 0 residues processed: 49 average time/residue: 0.0959 time to fit residues: 5.5215 Evaluate side-chains 45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.161543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.126655 restraints weight = 3681.537| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.28 r_work: 0.3344 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3232 Z= 0.165 Angle : 0.523 5.064 4383 Z= 0.275 Chirality : 0.042 0.135 444 Planarity : 0.003 0.027 571 Dihedral : 4.207 16.809 429 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.11 % Allowed : 9.94 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 aren not related in a simple way. whole: -0.83 (0.42), residues: 376 helix: 1.19 (0.60), residues: 72 sheet: -0.71 (0.45), residues: 140 loop : -1.09 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 157 TYR 0.015 0.001 TYR A 159 PHE 0.014 0.002 PHE B 56 TRP 0.009 0.001 TRP A 204 HIS 0.003 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 3228) covalent geometry : angle 0.52249 ( 4375) SS BOND : bond 0.00350 ( 4) SS BOND : angle 0.54564 ( 8) hydrogen bonds : bond 0.04475 ( 121) hydrogen bonds : angle 4.88649 ( 354) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.162 Fit side-chains REVERT: A 110 LEU cc_start: 0.7953 (tt) cc_final: 0.7561 (tt) REVERT: A 154 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7218 (pt0) REVERT: A 157 ARG cc_start: 0.8062 (ttt-90) cc_final: 0.7739 (ptm-80) REVERT: A 222 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: B 45 ARG cc_start: 0.7955 (ttp80) cc_final: 0.5861 (mmt90) outliers start: 7 outliers final: 3 residues processed: 52 average time/residue: 0.0932 time to fit residues: 5.6595 Evaluate side-chains 49 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain C residue 4 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 1 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.158259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122771 restraints weight = 3687.166| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.38 r_work: 0.3313 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3232 Z= 0.184 Angle : 0.534 5.318 4383 Z= 0.282 Chirality : 0.042 0.146 444 Planarity : 0.004 0.028 571 Dihedral : 4.286 17.315 429 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.11 % Allowed : 11.45 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 aren not related in a simple way. whole: -0.75 (0.42), residues: 376 helix: 1.12 (0.61), residues: 72 sheet: -0.37 (0.45), residues: 133 loop : -1.27 (0.44), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.011 0.002 TYR A 99 PHE 0.015 0.002 PHE B 56 TRP 0.008 0.001 TRP A 204 HIS 0.003 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 3228) covalent geometry : angle 0.53438 ( 4375) SS BOND : bond 0.00365 ( 4) SS BOND : angle 0.56687 ( 8) hydrogen bonds : bond 0.04651 ( 121) hydrogen bonds : angle 4.87780 ( 354) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.132 Fit side-chains REVERT: A 110 LEU cc_start: 0.7914 (tt) cc_final: 0.7495 (tt) REVERT: A 154 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7194 (pt0) REVERT: A 157 ARG cc_start: 0.8051 (ttt-90) cc_final: 0.7729 (ptm-80) REVERT: A 222 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: B 45 ARG cc_start: 0.7970 (ttp80) cc_final: 0.5879 (mmt-90) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.0982 time to fit residues: 5.5075 Evaluate side-chains 51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain C residue 4 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 8 optimal weight: 0.0470 chunk 31 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 21 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.165039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.129045 restraints weight = 3612.995| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.39 r_work: 0.3338 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3232 Z= 0.118 Angle : 0.467 4.600 4383 Z= 0.250 Chirality : 0.040 0.135 444 Planarity : 0.003 0.027 571 Dihedral : 3.945 15.540 429 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.81 % Allowed : 12.65 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 aren not related in a simple way. whole: -0.54 (0.43), residues: 376 helix: 1.55 (0.61), residues: 72 sheet: -0.51 (0.45), residues: 140 loop : -1.01 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 157 TYR 0.015 0.001 TYR A 159 PHE 0.011 0.001 PHE B 70 TRP 0.012 0.001 TRP A 204 HIS 0.003 0.001 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 3228) covalent geometry : angle 0.46732 ( 4375) SS BOND : bond 0.00354 ( 4) SS BOND : angle 0.48161 ( 8) hydrogen bonds : bond 0.03915 ( 121) hydrogen bonds : angle 4.65634 ( 354) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.122 Fit side-chains REVERT: A 72 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7885 (mm-40) REVERT: A 110 LEU cc_start: 0.7949 (tt) cc_final: 0.7555 (tt) REVERT: A 154 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7165 (pt0) REVERT: A 157 ARG cc_start: 0.7982 (ttt-90) cc_final: 0.7772 (ptm-80) REVERT: A 222 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: B 45 ARG cc_start: 0.7917 (ttp80) cc_final: 0.5894 (mmt-90) outliers start: 6 outliers final: 3 residues processed: 48 average time/residue: 0.0934 time to fit residues: 5.2708 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.163780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127619 restraints weight = 3717.260| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.42 r_work: 0.3334 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3232 Z= 0.147 Angle : 0.498 4.769 4383 Z= 0.264 Chirality : 0.041 0.136 444 Planarity : 0.003 0.026 571 Dihedral : 4.019 16.497 429 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.41 % Allowed : 12.65 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 aren not related in a simple way. whole: -0.46 (0.43), residues: 376 helix: 1.46 (0.61), residues: 72 sheet: -0.26 (0.45), residues: 135 loop : -1.06 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.016 0.001 TYR A 159 PHE 0.012 0.002 PHE B 30 TRP 0.009 0.001 TRP A 274 HIS 0.002 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 3228) covalent geometry : angle 0.49836 ( 4375) SS BOND : bond 0.00311 ( 4) SS BOND : angle 0.44691 ( 8) hydrogen bonds : bond 0.04093 ( 121) hydrogen bonds : angle 4.67547 ( 354) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.126 Fit side-chains REVERT: A 72 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7885 (mm-40) REVERT: A 77 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7543 (t70) REVERT: A 110 LEU cc_start: 0.7932 (tt) cc_final: 0.7519 (tt) REVERT: A 154 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7239 (pt0) REVERT: A 157 ARG cc_start: 0.8001 (ttt-90) cc_final: 0.7771 (ptm-80) REVERT: A 222 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: B 45 ARG cc_start: 0.7954 (ttp80) cc_final: 0.5891 (mmt-90) outliers start: 8 outliers final: 3 residues processed: 50 average time/residue: 0.0960 time to fit residues: 5.6319 Evaluate side-chains 49 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 30 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 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 = 0.3921 r_free = 0.3921 target = 0.163888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127679 restraints weight = 3738.161| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.42 r_work: 0.3348 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3232 Z= 0.145 Angle : 0.496 4.784 4383 Z= 0.264 Chirality : 0.041 0.135 444 Planarity : 0.003 0.027 571 Dihedral : 4.027 16.346 429 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.11 % Allowed : 12.95 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 aren not related in a simple way. whole: -0.47 (0.43), residues: 376 helix: 1.37 (0.62), residues: 73 sheet: -0.20 (0.45), residues: 135 loop : -1.12 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 219 TYR 0.019 0.002 TYR A 159 PHE 0.011 0.002 PHE B 30 TRP 0.010 0.001 TRP A 274 HIS 0.002 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3228) covalent geometry : angle 0.49619 ( 4375) SS BOND : bond 0.00329 ( 4) SS BOND : angle 0.47297 ( 8) hydrogen bonds : bond 0.04100 ( 121) hydrogen bonds : angle 4.64665 ( 354) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.134 Fit side-chains REVERT: A 110 LEU cc_start: 0.7960 (tt) cc_final: 0.7543 (tt) REVERT: A 154 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7226 (pt0) REVERT: A 157 ARG cc_start: 0.7998 (ttt-90) cc_final: 0.7789 (ptm-80) REVERT: A 222 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: B 45 ARG cc_start: 0.7998 (ttp80) cc_final: 0.5966 (mmt-90) outliers start: 7 outliers final: 5 residues processed: 48 average time/residue: 0.1032 time to fit residues: 5.7962 Evaluate side-chains 50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain C residue 10 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.162768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127519 restraints weight = 3656.748| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.26 r_work: 0.3331 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3232 Z= 0.174 Angle : 0.522 5.382 4383 Z= 0.278 Chirality : 0.042 0.137 444 Planarity : 0.004 0.027 571 Dihedral : 4.206 17.084 429 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.11 % Allowed : 12.65 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 aren not related in a simple way. whole: -0.49 (0.42), residues: 376 helix: 1.32 (0.61), residues: 73 sheet: -0.22 (0.45), residues: 135 loop : -1.10 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.016 0.002 TYR A 159 PHE 0.013 0.002 PHE B 30 TRP 0.011 0.001 TRP A 274 HIS 0.003 0.001 HIS B 84 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 3228) covalent geometry : angle 0.52219 ( 4375) SS BOND : bond 0.00353 ( 4) SS BOND : angle 0.53681 ( 8) hydrogen bonds : bond 0.04417 ( 121) hydrogen bonds : angle 4.77034 ( 354) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.093 Fit side-chains REVERT: A 110 LEU cc_start: 0.7968 (tt) cc_final: 0.7506 (tt) REVERT: A 154 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7222 (pt0) REVERT: A 222 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: B 45 ARG cc_start: 0.8006 (ttp80) cc_final: 0.5941 (mmt-90) outliers start: 7 outliers final: 3 residues processed: 51 average time/residue: 0.0855 time to fit residues: 5.0835 Evaluate side-chains 49 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 0.0370 chunk 16 optimal weight: 0.3980 chunk 19 optimal weight: 0.0670 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.168152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.132222 restraints weight = 3556.718| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.32 r_work: 0.3381 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3232 Z= 0.098 Angle : 0.454 4.325 4383 Z= 0.244 Chirality : 0.040 0.142 444 Planarity : 0.003 0.028 571 Dihedral : 3.785 15.108 429 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.51 % Allowed : 12.65 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 aren not related in a simple way. whole: -0.26 (0.43), residues: 376 helix: 1.53 (0.61), residues: 73 sheet: -0.08 (0.45), residues: 135 loop : -0.97 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.017 0.001 TYR A 159 PHE 0.011 0.001 PHE B 70 TRP 0.013 0.001 TRP A 204 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 3228) covalent geometry : angle 0.45424 ( 4375) SS BOND : bond 0.00307 ( 4) SS BOND : angle 0.39135 ( 8) hydrogen bonds : bond 0.03563 ( 121) hydrogen bonds : angle 4.49219 ( 354) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.122 Fit side-chains REVERT: A 110 LEU cc_start: 0.7953 (tt) cc_final: 0.7574 (tt) REVERT: A 154 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7191 (pt0) REVERT: A 222 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: B 45 ARG cc_start: 0.7909 (ttp80) cc_final: 0.5939 (mmt-90) REVERT: C 10 VAL cc_start: 0.8538 (p) cc_final: 0.8291 (m) outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.0854 time to fit residues: 4.9103 Evaluate side-chains 46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.167677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.131775 restraints weight = 3638.927| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.32 r_work: 0.3369 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3232 Z= 0.174 Angle : 1.244 59.196 4383 Z= 0.728 Chirality : 0.042 0.167 444 Planarity : 0.004 0.028 571 Dihedral : 3.905 18.953 429 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.51 % Allowed : 13.25 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 aren not related in a simple way. whole: -0.36 (0.43), residues: 376 helix: 1.21 (0.62), residues: 73 sheet: -0.06 (0.46), residues: 135 loop : -0.98 (0.45), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.018 0.002 TYR C 3 PHE 0.019 0.002 PHE A 33 TRP 0.012 0.001 TRP A 204 HIS 0.002 0.001 HIS A 3 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3228) covalent geometry : angle 1.24545 ( 4375) SS BOND : bond 0.00311 ( 4) SS BOND : angle 0.41617 ( 8) hydrogen bonds : bond 0.04117 ( 121) hydrogen bonds : angle 4.50449 ( 354) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1084.28 seconds wall clock time: 19 minutes 16.66 seconds (1156.66 seconds total)