Starting phenix.real_space_refine on Sat Apr 4 22:34:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ma0_63745/04_2026/9ma0_63745.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ma0_63745/04_2026/9ma0_63745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ma0_63745/04_2026/9ma0_63745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ma0_63745/04_2026/9ma0_63745.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ma0_63745/04_2026/9ma0_63745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ma0_63745/04_2026/9ma0_63745.map" } resolution = 3.33 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= 0.002 sd= 0.029 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 24 5.16 5 C 3152 2.51 5 N 831 2.21 5 O 982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4989 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3158 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 27, 'TRANS': 386} Chain: "B" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 978 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "C" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 853 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Time building chain proxies: 1.29, per 1000 atoms: 0.26 Number of scatterers: 4989 At special positions: 0 Unit cell: (79.05, 68, 123.25, 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 24 16.00 O 982 8.00 N 831 7.00 C 3152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 313.2 milliseconds 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1192 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 10 sheets defined 0.8% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'B' and resid 29 through 33 removed outlier: 3.884A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 6.373A pdb=" N ILE A 3 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLU A 136 " --> pdb=" O ILE A 3 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER A 5 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N GLN A 138 " --> pdb=" O SER A 5 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N MET A 137 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N GLU A 117 " --> pdb=" O MET A 137 " (cutoff:3.500A) removed outlier: 11.230A pdb=" N ASN A 139 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N SER A 115 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU A 116 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASP A 44 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 118 " --> pdb=" O ASN A 42 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A 122 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN A 38 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 21 removed outlier: 6.507A pdb=" N GLU A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 88 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 220 removed outlier: 3.934A pdb=" N LEU A 257 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 172 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 164 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA A 163 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 270 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 3.741A pdb=" N SER A 188 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 310 through 314 removed outlier: 3.659A pdb=" N THR A 406 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 398 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 394 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 319 through 324 removed outlier: 3.816A pdb=" N PHE A 380 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 381 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.516A pdb=" N VAL B 18 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 11 removed outlier: 7.526A pdb=" N GLU B 10 " --> pdb=" O SER B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.709A pdb=" N ARG B 38 " --> pdb=" O GLU B 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.827A pdb=" N SER C 39 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR C 92 " --> pdb=" O TYR C 41 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 252 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: 0.63 Time building geometry restraints manager: 0.50 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: 1613 1.34 - 1.46: 1202 1.46 - 1.58: 2264 1.58 - 1.70: 0 1.70 - 1.81: 35 Bond restraints: 5114 Sorted by residual: bond pdb=" N ILE A 290 " pdb=" CA ILE A 290 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.24e-02 6.50e+03 8.83e+00 bond pdb=" N TYR A 288 " pdb=" CA TYR A 288 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.23e-02 6.61e+03 8.54e+00 bond pdb=" N LEU A 194 " pdb=" CA LEU A 194 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.26e-02 6.30e+03 6.24e+00 bond pdb=" N MET A 193 " pdb=" CA MET A 193 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.22e-02 6.72e+03 6.15e+00 bond pdb=" C ASP B 99 " pdb=" N PRO B 100 " ideal model delta sigma weight residual 1.331 1.362 -0.031 1.27e-02 6.20e+03 5.94e+00 ... (remaining 5109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 6767 2.30 - 4.61: 175 4.61 - 6.91: 23 6.91 - 9.21: 8 9.21 - 11.52: 6 Bond angle restraints: 6979 Sorted by residual: angle pdb=" CA ASN A 78 " pdb=" CB ASN A 78 " pdb=" CG ASN A 78 " ideal model delta sigma weight residual 112.60 116.31 -3.71 1.00e+00 1.00e+00 1.38e+01 angle pdb=" CA GLN B 43 " pdb=" CB GLN B 43 " pdb=" CG GLN B 43 " ideal model delta sigma weight residual 114.10 121.25 -7.15 2.00e+00 2.50e-01 1.28e+01 angle pdb=" CG LYS A 218 " pdb=" CD LYS A 218 " pdb=" CE LYS A 218 " ideal model delta sigma weight residual 111.30 119.06 -7.76 2.30e+00 1.89e-01 1.14e+01 angle pdb=" C ARG B 87 " pdb=" N SER B 88 " pdb=" CA SER B 88 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.09e+01 angle pdb=" CA LEU C 11 " pdb=" CB LEU C 11 " pdb=" CG LEU C 11 " ideal model delta sigma weight residual 116.30 127.82 -11.52 3.50e+00 8.16e-02 1.08e+01 ... (remaining 6974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 2542 17.35 - 34.69: 342 34.69 - 52.04: 88 52.04 - 69.39: 29 69.39 - 86.73: 5 Dihedral angle restraints: 3006 sinusoidal: 1142 harmonic: 1864 Sorted by residual: dihedral pdb=" CA ASP B 99 " pdb=" CB ASP B 99 " pdb=" CG ASP B 99 " pdb=" OD1 ASP B 99 " ideal model delta sinusoidal sigma weight residual -30.00 -89.50 59.50 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA LEU B 119 " pdb=" C LEU B 119 " pdb=" N VAL B 120 " pdb=" CA VAL B 120 " ideal model delta harmonic sigma weight residual 180.00 162.84 17.16 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA GLY B 117 " pdb=" C GLY B 117 " pdb=" N THR B 118 " pdb=" CA THR B 118 " ideal model delta harmonic sigma weight residual 180.00 -162.84 -17.16 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 3003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 567 0.046 - 0.093: 147 0.093 - 0.139: 62 0.139 - 0.185: 9 0.185 - 0.232: 2 Chirality restraints: 787 Sorted by residual: chirality pdb=" CA ILE A 290 " pdb=" N ILE A 290 " pdb=" C ILE A 290 " pdb=" CB ILE A 290 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CG LEU A 213 " pdb=" CB LEU A 213 " pdb=" CD1 LEU A 213 " pdb=" CD2 LEU A 213 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ASN A 78 " pdb=" N ASN A 78 " pdb=" C ASN A 78 " pdb=" CB ASN A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 784 not shown) Planarity restraints: 904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 60 " 0.054 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO A 61 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 61 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 61 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 21 " 0.053 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO A 22 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 349 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C THR A 349 " 0.056 2.00e-02 2.50e+03 pdb=" O THR A 349 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 350 " -0.019 2.00e-02 2.50e+03 ... (remaining 901 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 847 2.78 - 3.31: 3986 3.31 - 3.84: 7784 3.84 - 4.37: 8015 4.37 - 4.90: 14520 Nonbonded interactions: 35152 Sorted by model distance: nonbonded pdb=" CE1 PHE A 275 " pdb=" SG CYS A 289 " model vdw 2.244 3.700 nonbonded pdb=" O THR C 72 " pdb=" OG1 THR C 72 " model vdw 2.321 3.040 nonbonded pdb=" OD1 ASP A 331 " pdb=" OG SER A 334 " model vdw 2.321 3.040 nonbonded pdb=" OG1 THR C 12 " pdb=" OE1 GLU C 110 " model vdw 2.322 3.040 nonbonded pdb=" OH TYR B 60 " pdb=" O ARG B 67 " model vdw 2.329 3.040 ... (remaining 35147 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.380 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 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 0.057 5114 Z= 0.202 Angle : 0.875 11.518 6979 Z= 0.436 Chirality : 0.052 0.232 787 Planarity : 0.008 0.083 904 Dihedral : 17.726 86.733 1814 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 0.00 % Allowed : 34.53 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.32), residues: 644 helix: None (None), residues: 0 sheet: -0.52 (0.34), residues: 245 loop : -2.34 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 66 TYR 0.011 0.001 TYR B 94 PHE 0.012 0.002 PHE A 219 TRP 0.023 0.002 TRP B 47 HIS 0.002 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 5114) covalent geometry : angle 0.87465 ( 6979) hydrogen bonds : bond 0.30512 ( 94) hydrogen bonds : angle 11.26502 ( 252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: A 223 CYS cc_start: 0.8037 (t) cc_final: 0.7742 (m) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.0645 time to fit residues: 7.9242 Evaluate side-chains 90 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 220 ASN A 309 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.187396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.159877 restraints weight = 6861.886| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 3.86 r_work: 0.4005 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5114 Z= 0.105 Angle : 0.567 6.160 6979 Z= 0.282 Chirality : 0.043 0.156 787 Planarity : 0.006 0.070 904 Dihedral : 4.225 17.503 692 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 3.22 % Allowed : 30.95 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.32), residues: 644 helix: None (None), residues: 0 sheet: -0.39 (0.33), residues: 250 loop : -2.14 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 66 TYR 0.007 0.001 TYR A 276 PHE 0.009 0.001 PHE A 123 TRP 0.010 0.001 TRP A 131 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 5114) covalent geometry : angle 0.56704 ( 6979) hydrogen bonds : bond 0.04171 ( 94) hydrogen bonds : angle 7.07625 ( 252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 223 CYS cc_start: 0.8118 (t) cc_final: 0.7844 (m) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 0.0619 time to fit residues: 9.0744 Evaluate side-chains 110 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 0.0070 chunk 46 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A 304 GLN A 309 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.183265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.156074 restraints weight = 6789.413| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 3.75 r_work: 0.3954 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5114 Z= 0.135 Angle : 0.583 6.722 6979 Z= 0.292 Chirality : 0.043 0.148 787 Planarity : 0.005 0.059 904 Dihedral : 4.412 16.138 692 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 5.19 % Allowed : 31.48 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.32), residues: 644 helix: None (None), residues: 0 sheet: -0.24 (0.33), residues: 249 loop : -2.04 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 108 TYR 0.012 0.001 TYR A 276 PHE 0.016 0.002 PHE A 123 TRP 0.014 0.002 TRP A 131 HIS 0.002 0.000 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5114) covalent geometry : angle 0.58310 ( 6979) hydrogen bonds : bond 0.03933 ( 94) hydrogen bonds : angle 6.01255 ( 252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 223 CYS cc_start: 0.8059 (t) cc_final: 0.7835 (m) REVERT: C 101 PHE cc_start: 0.4415 (OUTLIER) cc_final: 0.4170 (t80) outliers start: 29 outliers final: 20 residues processed: 118 average time/residue: 0.0592 time to fit residues: 9.3315 Evaluate side-chains 115 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 46 optimal weight: 0.0970 chunk 15 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 220 ASN A 309 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.181951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.155006 restraints weight = 6803.329| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 3.70 r_work: 0.3938 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5114 Z= 0.139 Angle : 0.594 9.439 6979 Z= 0.292 Chirality : 0.044 0.147 787 Planarity : 0.005 0.057 904 Dihedral : 4.466 17.017 692 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 6.44 % Allowed : 29.34 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.32), residues: 644 helix: None (None), residues: 0 sheet: -0.18 (0.33), residues: 248 loop : -1.99 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 108 TYR 0.011 0.001 TYR A 276 PHE 0.016 0.001 PHE A 123 TRP 0.015 0.001 TRP A 131 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5114) covalent geometry : angle 0.59379 ( 6979) hydrogen bonds : bond 0.03572 ( 94) hydrogen bonds : angle 5.52816 ( 252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: A 121 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8078 (m) REVERT: A 223 CYS cc_start: 0.8045 (t) cc_final: 0.7812 (m) REVERT: B 23 LYS cc_start: 0.8285 (mmtp) cc_final: 0.7991 (mttm) REVERT: B 80 TYR cc_start: 0.6361 (OUTLIER) cc_final: 0.6044 (m-80) REVERT: C 101 PHE cc_start: 0.4300 (OUTLIER) cc_final: 0.4097 (t80) outliers start: 36 outliers final: 26 residues processed: 129 average time/residue: 0.0632 time to fit residues: 10.9447 Evaluate side-chains 133 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 309 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.179161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.152400 restraints weight = 6876.534| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 3.67 r_work: 0.3917 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5114 Z= 0.171 Angle : 0.633 8.456 6979 Z= 0.314 Chirality : 0.045 0.145 787 Planarity : 0.005 0.057 904 Dihedral : 4.766 18.329 692 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 6.08 % Allowed : 31.48 % Favored : 62.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.32), residues: 644 helix: None (None), residues: 0 sheet: -0.29 (0.33), residues: 250 loop : -1.95 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 66 TYR 0.014 0.002 TYR B 32 PHE 0.021 0.002 PHE A 123 TRP 0.018 0.002 TRP A 131 HIS 0.003 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 5114) covalent geometry : angle 0.63277 ( 6979) hydrogen bonds : bond 0.03721 ( 94) hydrogen bonds : angle 5.45472 ( 252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.6738 (p0) cc_final: 0.6458 (p0) REVERT: A 137 MET cc_start: 0.7018 (mpp) cc_final: 0.6616 (mpp) REVERT: A 223 CYS cc_start: 0.8096 (t) cc_final: 0.7834 (m) REVERT: A 268 ASN cc_start: 0.7064 (OUTLIER) cc_final: 0.6798 (t0) REVERT: A 269 ASN cc_start: 0.8015 (m-40) cc_final: 0.7807 (m110) REVERT: B 12 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7758 (tttt) REVERT: B 23 LYS cc_start: 0.8351 (mmtp) cc_final: 0.8048 (mttm) REVERT: B 80 TYR cc_start: 0.6510 (OUTLIER) cc_final: 0.6178 (m-80) outliers start: 34 outliers final: 25 residues processed: 135 average time/residue: 0.0581 time to fit residues: 10.6853 Evaluate side-chains 137 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.180060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.152067 restraints weight = 6898.887| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 3.75 r_work: 0.3911 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5114 Z= 0.150 Angle : 0.608 7.624 6979 Z= 0.303 Chirality : 0.045 0.150 787 Planarity : 0.005 0.064 904 Dihedral : 4.696 17.943 692 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 6.62 % Allowed : 30.95 % Favored : 62.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.32), residues: 644 helix: None (None), residues: 0 sheet: -0.29 (0.33), residues: 251 loop : -1.91 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 66 TYR 0.012 0.001 TYR A 276 PHE 0.016 0.002 PHE A 123 TRP 0.013 0.001 TRP A 131 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5114) covalent geometry : angle 0.60814 ( 6979) hydrogen bonds : bond 0.03444 ( 94) hydrogen bonds : angle 5.38426 ( 252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.6788 (p0) cc_final: 0.6500 (p0) REVERT: A 121 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8103 (m) REVERT: A 176 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7041 (pt) REVERT: A 223 CYS cc_start: 0.8121 (t) cc_final: 0.7889 (m) REVERT: A 268 ASN cc_start: 0.7022 (OUTLIER) cc_final: 0.6819 (t0) REVERT: B 12 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7391 (tmmt) REVERT: B 23 LYS cc_start: 0.8370 (mmtp) cc_final: 0.8099 (mttm) REVERT: B 67 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6383 (ptm160) REVERT: B 80 TYR cc_start: 0.6495 (OUTLIER) cc_final: 0.6139 (m-80) outliers start: 37 outliers final: 22 residues processed: 133 average time/residue: 0.0571 time to fit residues: 10.2843 Evaluate side-chains 132 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 12 LYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 48 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 ASN A 309 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.179815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.152867 restraints weight = 6854.587| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 3.69 r_work: 0.3929 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5114 Z= 0.122 Angle : 0.585 6.375 6979 Z= 0.290 Chirality : 0.044 0.151 787 Planarity : 0.006 0.092 904 Dihedral : 4.477 18.155 692 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 5.55 % Allowed : 32.38 % Favored : 62.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.32), residues: 644 helix: None (None), residues: 0 sheet: -0.21 (0.33), residues: 249 loop : -1.87 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.011 0.001 TYR A 276 PHE 0.012 0.001 PHE A 123 TRP 0.010 0.001 TRP A 131 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 5114) covalent geometry : angle 0.58484 ( 6979) hydrogen bonds : bond 0.03189 ( 94) hydrogen bonds : angle 5.19187 ( 252) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 121 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8098 (m) REVERT: A 223 CYS cc_start: 0.8070 (t) cc_final: 0.7857 (m) REVERT: A 268 ASN cc_start: 0.6998 (OUTLIER) cc_final: 0.6795 (t0) REVERT: A 342 PHE cc_start: 0.6632 (p90) cc_final: 0.6309 (p90) REVERT: B 43 GLN cc_start: 0.7757 (mp10) cc_final: 0.7529 (mp10) REVERT: B 48 MET cc_start: 0.4768 (pmm) cc_final: 0.4396 (pmm) REVERT: B 67 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6292 (ptm160) REVERT: B 80 TYR cc_start: 0.6442 (OUTLIER) cc_final: 0.6143 (m-80) outliers start: 31 outliers final: 21 residues processed: 131 average time/residue: 0.0624 time to fit residues: 10.8837 Evaluate side-chains 132 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 54 optimal weight: 0.0370 chunk 44 optimal weight: 0.0770 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.181493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.154052 restraints weight = 6864.309| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.78 r_work: 0.3930 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6543 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5114 Z= 0.104 Angle : 0.585 6.335 6979 Z= 0.289 Chirality : 0.044 0.152 787 Planarity : 0.005 0.078 904 Dihedral : 4.370 17.786 692 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 4.11 % Allowed : 34.35 % Favored : 61.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.33), residues: 644 helix: None (None), residues: 0 sheet: -0.15 (0.34), residues: 249 loop : -1.85 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.009 0.001 TYR A 276 PHE 0.009 0.001 PHE A 123 TRP 0.008 0.001 TRP B 114 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 5114) covalent geometry : angle 0.58514 ( 6979) hydrogen bonds : bond 0.02971 ( 94) hydrogen bonds : angle 5.20410 ( 252) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.6770 (p0) cc_final: 0.6489 (p0) REVERT: A 121 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8041 (m) REVERT: A 137 MET cc_start: 0.6989 (mpp) cc_final: 0.6525 (mpp) REVERT: A 223 CYS cc_start: 0.8141 (t) cc_final: 0.7922 (m) REVERT: A 268 ASN cc_start: 0.6975 (OUTLIER) cc_final: 0.6760 (t0) REVERT: A 342 PHE cc_start: 0.6567 (p90) cc_final: 0.6289 (p90) REVERT: B 43 GLN cc_start: 0.7738 (mp10) cc_final: 0.7492 (mp10) REVERT: B 67 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6272 (ptm160) REVERT: B 80 TYR cc_start: 0.6422 (OUTLIER) cc_final: 0.6105 (m-80) outliers start: 23 outliers final: 17 residues processed: 121 average time/residue: 0.0529 time to fit residues: 8.7472 Evaluate side-chains 123 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.0170 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 220 ASN A 309 ASN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.179541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.152625 restraints weight = 6844.007| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 3.67 r_work: 0.3911 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5114 Z= 0.158 Angle : 0.618 6.640 6979 Z= 0.309 Chirality : 0.045 0.149 787 Planarity : 0.006 0.076 904 Dihedral : 4.630 18.700 692 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.02 % Favored : 88.98 % Rotamer: Outliers : 5.01 % Allowed : 33.81 % Favored : 61.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.32), residues: 644 helix: None (None), residues: 0 sheet: -0.26 (0.33), residues: 250 loop : -1.88 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 66 TYR 0.012 0.001 TYR A 122 PHE 0.019 0.002 PHE A 123 TRP 0.016 0.002 TRP A 131 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 5114) covalent geometry : angle 0.61849 ( 6979) hydrogen bonds : bond 0.03409 ( 94) hydrogen bonds : angle 5.16934 ( 252) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7150 (pm20) cc_final: 0.6670 (pm20) REVERT: A 121 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8121 (m) REVERT: A 223 CYS cc_start: 0.8116 (t) cc_final: 0.7881 (m) REVERT: B 43 GLN cc_start: 0.7796 (mp10) cc_final: 0.7556 (mp10) REVERT: B 67 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6490 (ptm160) REVERT: B 80 TYR cc_start: 0.6546 (OUTLIER) cc_final: 0.6207 (m-80) REVERT: B 98 LYS cc_start: 0.2264 (OUTLIER) cc_final: 0.1907 (mttt) outliers start: 28 outliers final: 22 residues processed: 127 average time/residue: 0.0590 time to fit residues: 10.1853 Evaluate side-chains 133 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 60 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.180389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.153395 restraints weight = 6868.788| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 3.69 r_work: 0.3925 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5114 Z= 0.127 Angle : 0.602 7.167 6979 Z= 0.299 Chirality : 0.044 0.150 787 Planarity : 0.006 0.086 904 Dihedral : 4.529 17.675 692 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 4.65 % Allowed : 33.99 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.32), residues: 644 helix: None (None), residues: 0 sheet: -0.17 (0.34), residues: 249 loop : -1.88 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 66 TYR 0.010 0.001 TYR A 276 PHE 0.013 0.001 PHE A 123 TRP 0.010 0.001 TRP A 131 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5114) covalent geometry : angle 0.60205 ( 6979) hydrogen bonds : bond 0.03177 ( 94) hydrogen bonds : angle 5.11252 ( 252) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1288 Ramachandran restraints generated. 644 Oldfield, 0 Emsley, 644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.6778 (p0) cc_final: 0.6533 (p0) REVERT: A 121 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8086 (m) REVERT: A 137 MET cc_start: 0.6930 (mpp) cc_final: 0.6478 (mpp) REVERT: A 223 CYS cc_start: 0.8113 (t) cc_final: 0.7890 (m) REVERT: B 43 GLN cc_start: 0.7794 (mp10) cc_final: 0.7551 (mp10) REVERT: B 67 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6466 (ptm160) REVERT: B 80 TYR cc_start: 0.6544 (OUTLIER) cc_final: 0.6225 (m-80) REVERT: B 98 LYS cc_start: 0.2188 (OUTLIER) cc_final: 0.1818 (mttt) outliers start: 26 outliers final: 21 residues processed: 123 average time/residue: 0.0619 time to fit residues: 10.2811 Evaluate side-chains 127 residues out of total 559 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 80 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.0170 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 17 optimal weight: 0.0670 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 0.0970 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.181827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.154493 restraints weight = 6875.333| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 3.77 r_work: 0.3939 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5114 Z= 0.097 Angle : 0.586 7.607 6979 Z= 0.285 Chirality : 0.044 0.151 787 Planarity : 0.005 0.078 904 Dihedral : 4.223 16.590 692 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 3.76 % Allowed : 34.53 % Favored : 61.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.33), residues: 644 helix: None (None), residues: 0 sheet: -0.11 (0.34), residues: 249 loop : -1.85 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 66 TYR 0.008 0.001 TYR A 276 PHE 0.007 0.001 PHE C 103 TRP 0.008 0.001 TRP B 47 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 5114) covalent geometry : angle 0.58563 ( 6979) hydrogen bonds : bond 0.02745 ( 94) hydrogen bonds : angle 4.93687 ( 252) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1546.56 seconds wall clock time: 27 minutes 7.04 seconds (1627.04 seconds total)