Starting phenix.real_space_refine on Tue Mar 3 12:34:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dkx_27493/03_2026/8dkx_27493.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dkx_27493/03_2026/8dkx_27493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dkx_27493/03_2026/8dkx_27493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dkx_27493/03_2026/8dkx_27493.map" model { file = "/net/cci-nas-00/data/ceres_data/8dkx_27493/03_2026/8dkx_27493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dkx_27493/03_2026/8dkx_27493.cif" } resolution = 3.0 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= 0.004 sd= 0.084 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: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2863 2.51 5 N 704 2.21 5 O 788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4370 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "B" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2680 Classifications: {'peptide': 334} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 15, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 1.07, per 1000 atoms: 0.24 Number of scatterers: 4370 At special positions: 0 Unit cell: (76.36, 63.91, 122.01, 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 15 16.00 O 788 8.00 N 704 7.00 C 2863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " 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: 0.29 Conformation dependent library (CDL) restraints added in 155.4 milliseconds 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 9 sheets defined 35.8% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.794A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 139 removed outlier: 3.914A pdb=" N SER P 124 " --> pdb=" O SER P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 153 removed outlier: 4.187A pdb=" N GLN P 145 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 182 Processing helix chain 'P' and resid 183 through 194 Processing helix chain 'P' and resid 202 through 226 removed outlier: 3.591A pdb=" N VAL P 206 " --> pdb=" O ASN P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 234 through 258 Processing helix chain 'P' and resid 263 through 291 Proline residue: P 283 - end of helix removed outlier: 3.751A pdb=" N PHE P 289 " --> pdb=" O ALA P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 323 removed outlier: 3.554A pdb=" N PHE P 311 " --> pdb=" O THR P 307 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET P 316 " --> pdb=" O SER P 312 " (cutoff:3.500A) Processing helix chain 'P' and resid 338 through 356 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.423A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET A 34 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ALA A 33 " --> pdb=" O TYR A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 6 removed outlier: 3.928A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 67 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.696A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.418A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 26 through 27 Processing sheet with id=AA7, first strand: chain 'P' and resid 31 through 35 removed outlier: 6.805A pdb=" N VAL P 32 " --> pdb=" O LEU P 116 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE P 118 " --> pdb=" O VAL P 32 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU P 34 " --> pdb=" O ILE P 118 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR P 98 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 39 through 43 removed outlier: 3.513A pdb=" N THR P 90 " --> pdb=" O GLU P 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 54 through 56 218 hydrogen bonds defined for protein. 621 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: 0.51 Time building geometry restraints manager: 0.44 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: 1343 1.34 - 1.46: 1039 1.46 - 1.58: 2086 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4490 Sorted by residual: bond pdb=" N GLY P 258 " pdb=" CA GLY P 258 " ideal model delta sigma weight residual 1.445 1.478 -0.033 8.30e-03 1.45e+04 1.60e+01 bond pdb=" N ILE P 260 " pdb=" CA ILE P 260 " ideal model delta sigma weight residual 1.456 1.500 -0.043 1.19e-02 7.06e+03 1.33e+01 bond pdb=" N VAL P 259 " pdb=" CA VAL P 259 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.17e+00 bond pdb=" N THR P 261 " pdb=" CA THR P 261 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.32e-02 5.74e+03 4.56e+00 bond pdb=" N TRP P 262 " pdb=" CA TRP P 262 " ideal model delta sigma weight residual 1.460 1.485 -0.025 1.83e-02 2.99e+03 1.87e+00 ... (remaining 4485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 6042 2.73 - 5.46: 66 5.46 - 8.19: 10 8.19 - 10.92: 3 10.92 - 13.64: 1 Bond angle restraints: 6122 Sorted by residual: angle pdb=" N THR P 261 " pdb=" CA THR P 261 " pdb=" C THR P 261 " ideal model delta sigma weight residual 113.02 121.82 -8.80 1.20e+00 6.94e-01 5.38e+01 angle pdb=" N TRP P 262 " pdb=" CA TRP P 262 " pdb=" C TRP P 262 " ideal model delta sigma weight residual 113.20 99.56 13.64 2.08e+00 2.31e-01 4.30e+01 angle pdb=" N GLY P 258 " pdb=" CA GLY P 258 " pdb=" C GLY P 258 " ideal model delta sigma weight residual 111.20 119.74 -8.54 1.39e+00 5.18e-01 3.77e+01 angle pdb=" N VAL A 65 " pdb=" CA VAL A 65 " pdb=" C VAL A 65 " ideal model delta sigma weight residual 113.20 109.16 4.04 9.60e-01 1.09e+00 1.77e+01 angle pdb=" CA VAL P 259 " pdb=" C VAL P 259 " pdb=" O VAL P 259 " ideal model delta sigma weight residual 121.17 117.07 4.10 1.06e+00 8.90e-01 1.50e+01 ... (remaining 6117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 2312 17.22 - 34.44: 228 34.44 - 51.66: 37 51.66 - 68.88: 4 68.88 - 86.10: 2 Dihedral angle restraints: 2583 sinusoidal: 986 harmonic: 1597 Sorted by residual: dihedral pdb=" C ILE P 260 " pdb=" N ILE P 260 " pdb=" CA ILE P 260 " pdb=" CB ILE P 260 " ideal model delta harmonic sigma weight residual -122.00 -135.90 13.90 0 2.50e+00 1.60e-01 3.09e+01 dihedral pdb=" N ILE P 260 " pdb=" C ILE P 260 " pdb=" CA ILE P 260 " pdb=" CB ILE P 260 " ideal model delta harmonic sigma weight residual 123.40 135.21 -11.81 0 2.50e+00 1.60e-01 2.23e+01 dihedral pdb=" CA LYS P 335 " pdb=" C LYS P 335 " pdb=" N PHE P 336 " pdb=" CA PHE P 336 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 2580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 609 0.073 - 0.145: 80 0.145 - 0.218: 2 0.218 - 0.291: 0 0.291 - 0.363: 2 Chirality restraints: 693 Sorted by residual: chirality pdb=" CA THR P 261 " pdb=" N THR P 261 " pdb=" C THR P 261 " pdb=" CB THR P 261 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA ILE P 260 " pdb=" N ILE P 260 " pdb=" C ILE P 260 " pdb=" CB ILE P 260 " both_signs ideal model delta sigma weight residual False 2.43 2.08 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB VAL P 259 " pdb=" CA VAL P 259 " pdb=" CG1 VAL P 259 " pdb=" CG2 VAL P 259 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.96e-01 ... (remaining 690 not shown) Planarity restraints: 764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP P 297 " 0.012 2.00e-02 2.50e+03 1.05e-02 2.75e+00 pdb=" CG TRP P 297 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP P 297 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP P 297 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP P 297 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP P 297 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 297 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 297 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 297 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP P 297 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 259 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.64e+00 pdb=" C VAL P 259 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL P 259 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE P 260 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 43 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO B 44 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " -0.019 5.00e-02 4.00e+02 ... (remaining 761 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 70 2.66 - 3.22: 4081 3.22 - 3.78: 6520 3.78 - 4.34: 9227 4.34 - 4.90: 15449 Nonbonded interactions: 35347 Sorted by model distance: nonbonded pdb=" OH TYR P 134 " pdb=" OD1 ASP P 205 " model vdw 2.099 3.040 nonbonded pdb=" O SER A 52 " pdb=" NH1 ARG A 73 " model vdw 2.187 3.120 nonbonded pdb=" OE1 GLN B 6 " pdb=" OG1 THR B 102 " model vdw 2.198 3.040 nonbonded pdb=" OG1 THR A 40 " pdb=" O GLU A 42 " model vdw 2.205 3.040 nonbonded pdb=" OH TYR P 281 " pdb=" OD2 ASP P 305 " model vdw 2.245 3.040 ... (remaining 35342 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.850 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 0.043 4492 Z= 0.216 Angle : 0.748 13.644 6126 Z= 0.436 Chirality : 0.049 0.363 693 Planarity : 0.004 0.033 764 Dihedral : 13.282 86.102 1557 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.62 % Allowed : 6.43 % Favored : 92.95 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 4.17 % 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: -3.42 (0.31), residues: 547 helix: -1.19 (0.31), residues: 204 sheet: -2.45 (0.37), residues: 161 loop : -3.10 (0.36), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 61 TYR 0.011 0.001 TYR B 49 PHE 0.020 0.001 PHE P 269 TRP 0.029 0.001 TRP P 297 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 4490) covalent geometry : angle 0.74813 ( 6122) SS BOND : bond 0.00182 ( 2) SS BOND : angle 0.43122 ( 4) hydrogen bonds : bond 0.15624 ( 218) hydrogen bonds : angle 7.66482 ( 621) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.161 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: B 82 ASP cc_start: 0.7840 (m-30) cc_final: 0.7598 (m-30) outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.4458 time to fit residues: 27.5677 Evaluate side-chains 51 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain P residue 259 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN A 111 GLN B 6 GLN B 38 GLN P 96 GLN P 149 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.155127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.121586 restraints weight = 5047.201| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.08 r_work: 0.3280 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4492 Z= 0.139 Angle : 0.608 10.300 6126 Z= 0.309 Chirality : 0.044 0.143 693 Planarity : 0.004 0.045 764 Dihedral : 5.750 56.357 599 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.28 % Allowed : 13.69 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.93 (0.33), residues: 547 helix: 0.25 (0.35), residues: 206 sheet: -1.68 (0.41), residues: 147 loop : -2.54 (0.37), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 112 TYR 0.014 0.001 TYR P 134 PHE 0.020 0.001 PHE A 69 TRP 0.016 0.001 TRP P 297 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4490) covalent geometry : angle 0.60824 ( 6122) SS BOND : bond 0.00242 ( 2) SS BOND : angle 0.73672 ( 4) hydrogen bonds : bond 0.04032 ( 218) hydrogen bonds : angle 5.28072 ( 621) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.130 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 71 GLU cc_start: 0.8336 (tt0) cc_final: 0.7719 (tm-30) REVERT: P 269 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.6069 (m-10) REVERT: P 325 GLN cc_start: 0.7265 (pt0) cc_final: 0.7056 (pt0) outliers start: 11 outliers final: 4 residues processed: 58 average time/residue: 0.4353 time to fit residues: 26.4464 Evaluate side-chains 52 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 0.0020 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 204 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.157582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.124048 restraints weight = 4980.282| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.05 r_work: 0.3336 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4492 Z= 0.115 Angle : 0.569 9.741 6126 Z= 0.287 Chirality : 0.042 0.135 693 Planarity : 0.003 0.027 764 Dihedral : 5.445 52.438 599 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.90 % Allowed : 15.15 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.17 (0.35), residues: 547 helix: 0.89 (0.36), residues: 206 sheet: -1.17 (0.43), residues: 146 loop : -2.22 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 24 TYR 0.012 0.001 TYR P 134 PHE 0.024 0.001 PHE A 69 TRP 0.015 0.001 TRP P 297 HIS 0.001 0.000 HIS P 211 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 4490) covalent geometry : angle 0.56882 ( 6122) SS BOND : bond 0.00311 ( 2) SS BOND : angle 0.48756 ( 4) hydrogen bonds : bond 0.03492 ( 218) hydrogen bonds : angle 4.78198 ( 621) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.155 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 4 LEU cc_start: 0.7341 (mp) cc_final: 0.6972 (mt) REVERT: B 79 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7894 (mm-40) REVERT: P 71 GLU cc_start: 0.8282 (tt0) cc_final: 0.7693 (tm-30) REVERT: P 204 ASN cc_start: 0.8154 (p0) cc_final: 0.7588 (p0) REVERT: P 269 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.5859 (m-10) REVERT: P 282 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.7058 (m-10) REVERT: P 318 LEU cc_start: 0.7494 (pp) cc_final: 0.7105 (tp) REVERT: P 325 GLN cc_start: 0.7238 (pt0) cc_final: 0.7028 (pt0) outliers start: 14 outliers final: 6 residues processed: 60 average time/residue: 0.4643 time to fit residues: 29.0799 Evaluate side-chains 61 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 1 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.153291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.120491 restraints weight = 4989.044| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.96 r_work: 0.3253 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4492 Z= 0.167 Angle : 0.602 10.214 6126 Z= 0.302 Chirality : 0.044 0.148 693 Planarity : 0.003 0.027 764 Dihedral : 5.475 45.006 599 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.11 % Allowed : 16.39 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.97 (0.35), residues: 547 helix: 1.04 (0.36), residues: 206 sheet: -1.02 (0.43), residues: 146 loop : -2.13 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 112 TYR 0.016 0.001 TYR P 134 PHE 0.019 0.001 PHE A 69 TRP 0.017 0.001 TRP P 297 HIS 0.002 0.001 HIS P 211 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 4490) covalent geometry : angle 0.60240 ( 6122) SS BOND : bond 0.00379 ( 2) SS BOND : angle 0.55914 ( 4) hydrogen bonds : bond 0.03924 ( 218) hydrogen bonds : angle 4.74576 ( 621) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.112 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 31 ASN cc_start: 0.8099 (m-40) cc_final: 0.7812 (m110) REVERT: B 79 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7931 (mm-40) REVERT: P 71 GLU cc_start: 0.8360 (tt0) cc_final: 0.7770 (tm-30) REVERT: P 269 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6069 (m-10) REVERT: P 325 GLN cc_start: 0.7364 (pt0) cc_final: 0.7131 (pt0) outliers start: 15 outliers final: 8 residues processed: 63 average time/residue: 0.4285 time to fit residues: 28.1945 Evaluate side-chains 59 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.154685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122027 restraints weight = 5019.903| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.95 r_work: 0.3288 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4492 Z= 0.147 Angle : 0.586 10.875 6126 Z= 0.292 Chirality : 0.044 0.146 693 Planarity : 0.003 0.026 764 Dihedral : 5.294 37.816 599 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.53 % Allowed : 16.80 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.79 (0.35), residues: 547 helix: 1.20 (0.36), residues: 206 sheet: -0.90 (0.43), residues: 146 loop : -2.08 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.015 0.001 TYR P 134 PHE 0.015 0.001 PHE A 69 TRP 0.015 0.001 TRP P 297 HIS 0.001 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4490) covalent geometry : angle 0.58622 ( 6122) SS BOND : bond 0.00339 ( 2) SS BOND : angle 0.48809 ( 4) hydrogen bonds : bond 0.03627 ( 218) hydrogen bonds : angle 4.60850 ( 621) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.148 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 31 ASN cc_start: 0.8097 (m-40) cc_final: 0.7806 (m110) REVERT: B 9 SER cc_start: 0.8282 (m) cc_final: 0.7887 (m) REVERT: B 79 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8025 (mm-40) REVERT: P 71 GLU cc_start: 0.8291 (tt0) cc_final: 0.7735 (tm-30) REVERT: P 269 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.6150 (m-10) REVERT: P 282 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7100 (m-10) REVERT: P 318 LEU cc_start: 0.7677 (pp) cc_final: 0.7200 (tp) outliers start: 17 outliers final: 10 residues processed: 64 average time/residue: 0.3964 time to fit residues: 26.7314 Evaluate side-chains 63 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.154633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.121737 restraints weight = 5171.641| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.02 r_work: 0.3304 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4492 Z= 0.150 Angle : 0.588 10.527 6126 Z= 0.292 Chirality : 0.044 0.147 693 Planarity : 0.003 0.026 764 Dihedral : 5.220 31.939 599 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.32 % Allowed : 17.43 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.87 (0.35), residues: 547 helix: 1.26 (0.36), residues: 206 sheet: -1.11 (0.41), residues: 149 loop : -2.12 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 24 TYR 0.015 0.001 TYR P 134 PHE 0.014 0.001 PHE A 69 TRP 0.014 0.001 TRP P 297 HIS 0.001 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4490) covalent geometry : angle 0.58758 ( 6122) SS BOND : bond 0.00392 ( 2) SS BOND : angle 0.53459 ( 4) hydrogen bonds : bond 0.03635 ( 218) hydrogen bonds : angle 4.57783 ( 621) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.157 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 31 ASN cc_start: 0.8206 (m-40) cc_final: 0.7892 (m110) REVERT: B 9 SER cc_start: 0.8357 (m) cc_final: 0.8000 (m) REVERT: B 79 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8030 (mm-40) REVERT: P 71 GLU cc_start: 0.8282 (tt0) cc_final: 0.7783 (tm-30) REVERT: P 269 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.6176 (m-10) REVERT: P 282 PHE cc_start: 0.8017 (OUTLIER) cc_final: 0.7213 (m-10) REVERT: P 318 LEU cc_start: 0.7730 (pp) cc_final: 0.7261 (tp) outliers start: 16 outliers final: 10 residues processed: 63 average time/residue: 0.4109 time to fit residues: 27.1676 Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.152982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.120153 restraints weight = 5113.129| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.99 r_work: 0.3289 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4492 Z= 0.176 Angle : 0.606 10.807 6126 Z= 0.303 Chirality : 0.045 0.154 693 Planarity : 0.003 0.029 764 Dihedral : 5.145 23.800 597 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.94 % Allowed : 16.80 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.88 (0.35), residues: 547 helix: 1.17 (0.36), residues: 207 sheet: -1.11 (0.41), residues: 149 loop : -2.05 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 24 TYR 0.018 0.001 TYR P 134 PHE 0.015 0.001 PHE A 69 TRP 0.014 0.001 TRP P 297 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 4490) covalent geometry : angle 0.60610 ( 6122) SS BOND : bond 0.00401 ( 2) SS BOND : angle 0.56121 ( 4) hydrogen bonds : bond 0.03871 ( 218) hydrogen bonds : angle 4.62358 ( 621) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.171 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 31 ASN cc_start: 0.8321 (m-40) cc_final: 0.8008 (m110) REVERT: B 79 GLN cc_start: 0.8338 (mt0) cc_final: 0.7996 (mm-40) REVERT: P 71 GLU cc_start: 0.8324 (tt0) cc_final: 0.7838 (tm-30) REVERT: P 269 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.6209 (m-10) REVERT: P 282 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7277 (m-10) outliers start: 19 outliers final: 9 residues processed: 66 average time/residue: 0.4265 time to fit residues: 29.4719 Evaluate side-chains 60 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 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 = 0.3795 r_free = 0.3795 target = 0.156364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123983 restraints weight = 5063.032| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.02 r_work: 0.3311 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4492 Z= 0.147 Angle : 0.588 11.273 6126 Z= 0.292 Chirality : 0.044 0.149 693 Planarity : 0.003 0.031 764 Dihedral : 5.066 22.546 597 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.90 % Allowed : 18.46 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.78 (0.35), residues: 547 helix: 1.26 (0.36), residues: 207 sheet: -1.04 (0.41), residues: 149 loop : -2.03 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 24 TYR 0.015 0.001 TYR P 134 PHE 0.014 0.001 PHE A 69 TRP 0.012 0.001 TRP P 297 HIS 0.001 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4490) covalent geometry : angle 0.58791 ( 6122) SS BOND : bond 0.00409 ( 2) SS BOND : angle 0.51063 ( 4) hydrogen bonds : bond 0.03588 ( 218) hydrogen bonds : angle 4.54600 ( 621) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.167 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 31 ASN cc_start: 0.8277 (m-40) cc_final: 0.7976 (m110) REVERT: B 9 SER cc_start: 0.8469 (m) cc_final: 0.8265 (m) REVERT: B 79 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8013 (mm-40) REVERT: P 71 GLU cc_start: 0.8328 (tt0) cc_final: 0.7837 (tm-30) REVERT: P 269 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6111 (m-10) REVERT: P 282 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7237 (m-10) REVERT: P 318 LEU cc_start: 0.7765 (pp) cc_final: 0.7275 (tp) outliers start: 14 outliers final: 10 residues processed: 62 average time/residue: 0.4301 time to fit residues: 27.9189 Evaluate side-chains 63 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.0570 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.158728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126195 restraints weight = 5042.357| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.01 r_work: 0.3340 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4492 Z= 0.123 Angle : 0.566 10.839 6126 Z= 0.281 Chirality : 0.043 0.138 693 Planarity : 0.004 0.059 764 Dihedral : 4.909 22.502 597 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.11 % Allowed : 18.67 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.57 (0.35), residues: 547 helix: 1.39 (0.36), residues: 207 sheet: -0.86 (0.43), residues: 140 loop : -1.89 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 24 TYR 0.013 0.001 TYR P 134 PHE 0.012 0.001 PHE A 69 TRP 0.012 0.001 TRP P 297 HIS 0.001 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4490) covalent geometry : angle 0.56592 ( 6122) SS BOND : bond 0.00394 ( 2) SS BOND : angle 0.49128 ( 4) hydrogen bonds : bond 0.03343 ( 218) hydrogen bonds : angle 4.41916 ( 621) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.096 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 18 LEU cc_start: 0.8548 (mt) cc_final: 0.8315 (mp) REVERT: A 31 ASN cc_start: 0.8173 (m-40) cc_final: 0.7875 (m110) REVERT: B 79 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7852 (mm-40) REVERT: P 71 GLU cc_start: 0.8303 (tt0) cc_final: 0.7821 (tm-30) REVERT: P 180 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8062 (mp) REVERT: P 269 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6084 (m-10) REVERT: P 282 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7207 (m-10) REVERT: P 318 LEU cc_start: 0.7657 (pp) cc_final: 0.7293 (tp) outliers start: 15 outliers final: 11 residues processed: 63 average time/residue: 0.4062 time to fit residues: 26.8569 Evaluate side-chains 64 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 3 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.157369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124992 restraints weight = 5027.916| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.00 r_work: 0.3322 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4492 Z= 0.139 Angle : 0.581 10.981 6126 Z= 0.287 Chirality : 0.043 0.144 693 Planarity : 0.004 0.056 764 Dihedral : 4.933 22.577 597 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.32 % Allowed : 19.09 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.65 (0.35), residues: 547 helix: 1.40 (0.36), residues: 207 sheet: -1.00 (0.40), residues: 149 loop : -1.96 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 24 TYR 0.015 0.001 TYR P 134 PHE 0.010 0.001 PHE A 69 TRP 0.012 0.001 TRP P 297 HIS 0.001 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4490) covalent geometry : angle 0.58141 ( 6122) SS BOND : bond 0.00445 ( 2) SS BOND : angle 0.56973 ( 4) hydrogen bonds : bond 0.03491 ( 218) hydrogen bonds : angle 4.44172 ( 621) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.179 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 31 ASN cc_start: 0.8207 (m-40) cc_final: 0.7901 (m110) REVERT: B 79 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7831 (mm-40) REVERT: P 71 GLU cc_start: 0.8323 (tt0) cc_final: 0.7841 (tm-30) REVERT: P 180 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8049 (mp) REVERT: P 269 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.6114 (m-10) REVERT: P 282 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7226 (m-10) REVERT: P 318 LEU cc_start: 0.7702 (pp) cc_final: 0.7266 (tp) outliers start: 16 outliers final: 11 residues processed: 63 average time/residue: 0.4180 time to fit residues: 27.6454 Evaluate side-chains 61 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 276 VAL Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 16 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 189 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.157337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124663 restraints weight = 5111.366| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.03 r_work: 0.3341 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4492 Z= 0.148 Angle : 0.596 11.043 6126 Z= 0.294 Chirality : 0.044 0.147 693 Planarity : 0.004 0.054 764 Dihedral : 4.986 23.642 597 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.73 % Allowed : 19.09 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.66 (0.35), residues: 547 helix: 1.37 (0.36), residues: 207 sheet: -0.98 (0.40), residues: 149 loop : -1.98 (0.41), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 24 TYR 0.015 0.001 TYR P 134 PHE 0.025 0.001 PHE A 69 TRP 0.012 0.001 TRP P 297 HIS 0.001 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4490) covalent geometry : angle 0.59630 ( 6122) SS BOND : bond 0.00447 ( 2) SS BOND : angle 0.57868 ( 4) hydrogen bonds : bond 0.03586 ( 218) hydrogen bonds : angle 4.46352 ( 621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1533.49 seconds wall clock time: 26 minutes 55.45 seconds (1615.45 seconds total)