Starting phenix.real_space_refine on Wed Feb 4 07:55:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v2a_64722/02_2026/9v2a_64722.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v2a_64722/02_2026/9v2a_64722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v2a_64722/02_2026/9v2a_64722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v2a_64722/02_2026/9v2a_64722.map" model { file = "/net/cci-nas-00/data/ceres_data/9v2a_64722/02_2026/9v2a_64722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v2a_64722/02_2026/9v2a_64722.cif" } resolution = 2.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.117 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 85 5.16 5 C 6135 2.51 5 N 1485 2.21 5 O 1645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9350 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1870 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} Restraints were copied for chains: B, C, D, E Time building chain proxies: 1.47, per 1000 atoms: 0.16 Number of scatterers: 9350 At special positions: 0 Unit cell: (95.996, 94.132, 66.172, 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 85 16.00 O 1645 8.00 N 1485 7.00 C 6135 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: 0.70 Conformation dependent library (CDL) restraints added in 254.3 milliseconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 0 sheets defined 87.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 76 through 93 removed outlier: 3.639A pdb=" N ASN A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 122 Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.656A pdb=" N VAL A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 157 through 171 removed outlier: 4.638A pdb=" N MET A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR A 166 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 205 removed outlier: 3.537A pdb=" N GLY A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 Processing helix chain 'A' and resid 224 through 247 Processing helix chain 'A' and resid 251 through 270 Proline residue: A 261 - end of helix removed outlier: 3.645A pdb=" N PHE A 266 " --> pdb=" O CYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.692A pdb=" N PHE A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 292 through 298 Processing helix chain 'A' and resid 300 through 314 Processing helix chain 'A' and resid 316 through 325 removed outlier: 3.735A pdb=" N SER A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 93 removed outlier: 3.639A pdb=" N ASN B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 131 through 143 removed outlier: 3.657A pdb=" N VAL B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 157 through 171 removed outlier: 4.637A pdb=" N MET B 163 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR B 166 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 205 removed outlier: 3.537A pdb=" N GLY B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 224 through 247 Processing helix chain 'B' and resid 251 through 270 Proline residue: B 261 - end of helix removed outlier: 3.646A pdb=" N PHE B 266 " --> pdb=" O CYS B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.693A pdb=" N PHE B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Proline residue: B 282 - end of helix Processing helix chain 'B' and resid 292 through 298 Processing helix chain 'B' and resid 300 through 314 Processing helix chain 'B' and resid 316 through 325 removed outlier: 3.734A pdb=" N SER B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 93 removed outlier: 3.638A pdb=" N ASN C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 122 Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 131 through 143 removed outlier: 3.656A pdb=" N VAL C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 157 through 171 removed outlier: 4.638A pdb=" N MET C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR C 166 " --> pdb=" O THR C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 205 removed outlier: 3.537A pdb=" N GLY C 205 " --> pdb=" O VAL C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 224 through 247 Processing helix chain 'C' and resid 251 through 270 Proline residue: C 261 - end of helix removed outlier: 3.645A pdb=" N PHE C 266 " --> pdb=" O CYS C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.693A pdb=" N PHE C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Proline residue: C 282 - end of helix Processing helix chain 'C' and resid 292 through 298 Processing helix chain 'C' and resid 300 through 314 Processing helix chain 'C' and resid 316 through 325 removed outlier: 3.735A pdb=" N SER C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 93 removed outlier: 3.639A pdb=" N ASN D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 122 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 131 through 143 removed outlier: 3.656A pdb=" N VAL D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 157 through 171 removed outlier: 4.638A pdb=" N MET D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR D 166 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 205 removed outlier: 3.537A pdb=" N GLY D 205 " --> pdb=" O VAL D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 224 through 247 Processing helix chain 'D' and resid 251 through 270 Proline residue: D 261 - end of helix removed outlier: 3.645A pdb=" N PHE D 266 " --> pdb=" O CYS D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 287 removed outlier: 3.693A pdb=" N PHE D 279 " --> pdb=" O VAL D 275 " (cutoff:3.500A) Proline residue: D 282 - end of helix Processing helix chain 'D' and resid 292 through 298 Processing helix chain 'D' and resid 300 through 314 Processing helix chain 'D' and resid 316 through 325 removed outlier: 3.735A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 93 removed outlier: 3.638A pdb=" N ASN E 86 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 122 Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 131 through 143 removed outlier: 3.657A pdb=" N VAL E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 153 Processing helix chain 'E' and resid 157 through 171 removed outlier: 4.638A pdb=" N MET E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR E 166 " --> pdb=" O THR E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 205 removed outlier: 3.537A pdb=" N GLY E 205 " --> pdb=" O VAL E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 221 Processing helix chain 'E' and resid 224 through 247 Processing helix chain 'E' and resid 251 through 270 Proline residue: E 261 - end of helix removed outlier: 3.645A pdb=" N PHE E 266 " --> pdb=" O CYS E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 287 removed outlier: 3.693A pdb=" N PHE E 279 " --> pdb=" O VAL E 275 " (cutoff:3.500A) Proline residue: E 282 - end of helix Processing helix chain 'E' and resid 292 through 298 Processing helix chain 'E' and resid 300 through 314 Processing helix chain 'E' and resid 316 through 325 removed outlier: 3.734A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) 760 hydrogen bonds defined for protein. 2280 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: 1.51 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2703 1.34 - 1.45: 1574 1.45 - 1.57: 5148 1.57 - 1.69: 5 1.69 - 1.81: 135 Bond restraints: 9565 Sorted by residual: bond pdb=" C PHE C 143 " pdb=" N PRO C 144 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 6.00e+00 bond pdb=" C PHE D 143 " pdb=" N PRO D 144 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.82e+00 bond pdb=" C PHE B 143 " pdb=" N PRO B 144 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.81e+00 bond pdb=" C PHE A 143 " pdb=" N PRO A 144 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.78e+00 bond pdb=" C PHE E 143 " pdb=" N PRO E 144 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.73e+00 ... (remaining 9560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 12409 1.75 - 3.50: 526 3.50 - 5.26: 95 5.26 - 7.01: 10 7.01 - 8.76: 40 Bond angle restraints: 13080 Sorted by residual: angle pdb=" CB GLU C 290 " pdb=" CG GLU C 290 " pdb=" CD GLU C 290 " ideal model delta sigma weight residual 112.60 120.10 -7.50 1.70e+00 3.46e-01 1.95e+01 angle pdb=" CB GLU D 290 " pdb=" CG GLU D 290 " pdb=" CD GLU D 290 " ideal model delta sigma weight residual 112.60 120.10 -7.50 1.70e+00 3.46e-01 1.95e+01 angle pdb=" CB GLU E 290 " pdb=" CG GLU E 290 " pdb=" CD GLU E 290 " ideal model delta sigma weight residual 112.60 120.09 -7.49 1.70e+00 3.46e-01 1.94e+01 angle pdb=" CB GLU B 290 " pdb=" CG GLU B 290 " pdb=" CD GLU B 290 " ideal model delta sigma weight residual 112.60 120.06 -7.46 1.70e+00 3.46e-01 1.92e+01 angle pdb=" CB GLU A 290 " pdb=" CG GLU A 290 " pdb=" CD GLU A 290 " ideal model delta sigma weight residual 112.60 120.04 -7.44 1.70e+00 3.46e-01 1.92e+01 ... (remaining 13075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 4995 16.39 - 32.79: 380 32.79 - 49.18: 100 49.18 - 65.57: 5 65.57 - 81.97: 15 Dihedral angle restraints: 5495 sinusoidal: 1885 harmonic: 3610 Sorted by residual: dihedral pdb=" CA ASN C 300 " pdb=" C ASN C 300 " pdb=" N LEU C 301 " pdb=" CA LEU C 301 " ideal model delta harmonic sigma weight residual -180.00 -157.79 -22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ASN E 300 " pdb=" C ASN E 300 " pdb=" N LEU E 301 " pdb=" CA LEU E 301 " ideal model delta harmonic sigma weight residual 180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ASN D 300 " pdb=" C ASN D 300 " pdb=" N LEU D 301 " pdb=" CA LEU D 301 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 962 0.039 - 0.078: 470 0.078 - 0.117: 118 0.117 - 0.156: 49 0.156 - 0.195: 6 Chirality restraints: 1605 Sorted by residual: chirality pdb=" CG LEU E 147 " pdb=" CB LEU E 147 " pdb=" CD1 LEU E 147 " pdb=" CD2 LEU E 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" CG LEU C 147 " pdb=" CB LEU C 147 " pdb=" CD1 LEU C 147 " pdb=" CD2 LEU C 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CG LEU A 147 " pdb=" CB LEU A 147 " pdb=" CD1 LEU A 147 " pdb=" CD2 LEU A 147 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.31e-01 ... (remaining 1602 not shown) Planarity restraints: 1610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO E 77 " -0.051 5.00e-02 4.00e+02 7.57e-02 9.18e+00 pdb=" N PRO E 78 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO E 78 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 78 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 77 " 0.051 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO B 78 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 78 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 78 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 77 " -0.051 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO A 78 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " -0.043 5.00e-02 4.00e+02 ... (remaining 1607 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3160 2.83 - 3.35: 9171 3.35 - 3.87: 17064 3.87 - 4.38: 20845 4.38 - 4.90: 34598 Nonbonded interactions: 84838 Sorted by model distance: nonbonded pdb=" O TRP E 260 " pdb=" OG1 THR E 264 " model vdw 2.318 3.040 nonbonded pdb=" O TRP A 260 " pdb=" OG1 THR A 264 " model vdw 2.318 3.040 nonbonded pdb=" O TRP C 260 " pdb=" OG1 THR C 264 " model vdw 2.318 3.040 nonbonded pdb=" O TRP D 260 " pdb=" OG1 THR D 264 " model vdw 2.318 3.040 nonbonded pdb=" O TRP B 260 " pdb=" OG1 THR B 264 " model vdw 2.319 3.040 ... (remaining 84833 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.010 Normalize map: mean=0, sd=1: 1.470 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.040 Find NCS groups from input model: 0.070 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:8.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.007 0.062 9565 Z= 0.284 Angle : 0.936 8.760 13080 Z= 0.536 Chirality : 0.051 0.195 1605 Planarity : 0.008 0.076 1610 Dihedral : 13.324 81.968 3185 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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: -5.23 (0.14), residues: 1270 helix: -3.18 (0.09), residues: 1105 sheet: None (None), residues: 0 loop : -3.20 (0.30), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 255 TYR 0.008 0.002 TYR B 81 PHE 0.031 0.003 PHE E 112 TRP 0.018 0.002 TRP B 244 HIS 0.001 0.000 HIS C 273 Details of bonding type rmsd covalent geometry : bond 0.00692 ( 9565) covalent geometry : angle 0.93631 (13080) hydrogen bonds : bond 0.24724 ( 760) hydrogen bonds : angle 9.16046 ( 2280) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.358 Fit side-chains REVERT: A 82 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7246 (tp30) REVERT: A 286 MET cc_start: 0.7279 (mmp) cc_final: 0.7068 (mmm) REVERT: A 316 MET cc_start: 0.8714 (mmm) cc_final: 0.8320 (mmm) REVERT: B 164 MET cc_start: 0.8773 (mmt) cc_final: 0.8111 (mmt) REVERT: B 286 MET cc_start: 0.7384 (mmp) cc_final: 0.7180 (mmm) REVERT: C 172 LYS cc_start: 0.8474 (mmtm) cc_final: 0.8201 (mmtt) REVERT: C 219 LEU cc_start: 0.7591 (mt) cc_final: 0.7105 (pp) REVERT: C 316 MET cc_start: 0.8691 (mmm) cc_final: 0.8264 (mmm) REVERT: D 164 MET cc_start: 0.8835 (mmt) cc_final: 0.8620 (mmt) REVERT: D 172 LYS cc_start: 0.8460 (mmtm) cc_final: 0.8229 (mptt) REVERT: D 219 LEU cc_start: 0.7449 (mt) cc_final: 0.7045 (pp) REVERT: D 227 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7662 (mt-10) REVERT: E 164 MET cc_start: 0.8753 (mmt) cc_final: 0.8002 (mmt) REVERT: E 219 LEU cc_start: 0.7431 (mt) cc_final: 0.6972 (pp) REVERT: E 278 MET cc_start: 0.8875 (mtt) cc_final: 0.8475 (mtt) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.6475 time to fit residues: 96.4318 Evaluate side-chains 114 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 152 ASN A 308 ASN B 105 GLN B 152 ASN B 308 ASN C 105 GLN C 152 ASN C 308 ASN D 105 GLN D 152 ASN D 308 ASN E 105 GLN E 152 ASN E 308 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.099018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.087895 restraints weight = 10378.165| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.01 r_work: 0.2912 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9565 Z= 0.137 Angle : 0.602 5.746 13080 Z= 0.317 Chirality : 0.040 0.153 1605 Planarity : 0.006 0.047 1610 Dihedral : 4.604 21.329 1310 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.41 % Allowed : 5.92 % Favored : 93.67 % 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: -1.09 (0.21), residues: 1270 helix: -0.26 (0.14), residues: 1115 sheet: None (None), residues: 0 loop : -3.16 (0.34), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 255 TYR 0.006 0.001 TYR D 320 PHE 0.022 0.002 PHE B 266 TRP 0.013 0.001 TRP B 244 HIS 0.002 0.001 HIS C 273 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9565) covalent geometry : angle 0.60186 (13080) hydrogen bonds : bond 0.04511 ( 760) hydrogen bonds : angle 4.99588 ( 2280) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.356 Fit side-chains REVERT: A 82 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7554 (tp30) REVERT: B 164 MET cc_start: 0.8670 (mmt) cc_final: 0.8315 (mmt) REVERT: B 286 MET cc_start: 0.7836 (mmp) cc_final: 0.7585 (mmm) REVERT: C 172 LYS cc_start: 0.8488 (mmtm) cc_final: 0.8279 (mptt) REVERT: C 278 MET cc_start: 0.8904 (mtt) cc_final: 0.8430 (mtt) REVERT: C 286 MET cc_start: 0.8000 (mmt) cc_final: 0.7737 (mmm) REVERT: C 316 MET cc_start: 0.8763 (mmm) cc_final: 0.8384 (mmm) REVERT: D 164 MET cc_start: 0.8635 (mmt) cc_final: 0.8214 (mmt) REVERT: E 164 MET cc_start: 0.8592 (mmt) cc_final: 0.8174 (mmt) outliers start: 4 outliers final: 2 residues processed: 118 average time/residue: 0.7263 time to fit residues: 90.6418 Evaluate side-chains 116 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 209 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 94 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 38 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 47 optimal weight: 0.0050 chunk 30 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.0058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.097501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.086232 restraints weight = 10369.459| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.02 r_work: 0.2895 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9565 Z= 0.144 Angle : 0.595 5.590 13080 Z= 0.310 Chirality : 0.041 0.154 1605 Planarity : 0.005 0.041 1610 Dihedral : 4.455 20.175 1310 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.61 % Allowed : 6.73 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.23), residues: 1270 helix: 0.83 (0.15), residues: 1110 sheet: None (None), residues: 0 loop : -2.84 (0.34), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 255 TYR 0.007 0.001 TYR B 81 PHE 0.024 0.002 PHE B 266 TRP 0.014 0.001 TRP B 244 HIS 0.002 0.001 HIS C 273 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9565) covalent geometry : angle 0.59495 (13080) hydrogen bonds : bond 0.04232 ( 760) hydrogen bonds : angle 4.72526 ( 2280) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.353 Fit side-chains REVERT: A 82 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7465 (tp30) REVERT: A 219 LEU cc_start: 0.7593 (mt) cc_final: 0.7198 (tt) REVERT: B 164 MET cc_start: 0.8629 (mmt) cc_final: 0.8287 (mmt) REVERT: B 286 MET cc_start: 0.7797 (mmp) cc_final: 0.7541 (mmm) REVERT: C 286 MET cc_start: 0.7997 (mmt) cc_final: 0.7756 (mmm) REVERT: C 316 MET cc_start: 0.8757 (mmm) cc_final: 0.8375 (mmm) REVERT: D 164 MET cc_start: 0.8621 (mmt) cc_final: 0.8242 (mmt) REVERT: E 164 MET cc_start: 0.8588 (mmt) cc_final: 0.8289 (mmt) outliers start: 6 outliers final: 3 residues processed: 116 average time/residue: 0.7557 time to fit residues: 92.6390 Evaluate side-chains 117 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain E residue 209 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.096855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.085790 restraints weight = 10508.235| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.01 r_work: 0.2892 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9565 Z= 0.171 Angle : 0.622 5.920 13080 Z= 0.324 Chirality : 0.043 0.161 1605 Planarity : 0.005 0.044 1610 Dihedral : 4.511 20.579 1310 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.33 % Allowed : 6.53 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.23), residues: 1270 helix: 1.14 (0.15), residues: 1110 sheet: None (None), residues: 0 loop : -2.61 (0.36), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 255 TYR 0.008 0.002 TYR D 81 PHE 0.028 0.002 PHE B 266 TRP 0.013 0.001 TRP B 244 HIS 0.002 0.001 HIS C 273 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9565) covalent geometry : angle 0.62206 (13080) hydrogen bonds : bond 0.04497 ( 760) hydrogen bonds : angle 4.77588 ( 2280) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.365 Fit side-chains REVERT: A 82 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7623 (tp30) REVERT: B 164 MET cc_start: 0.8646 (mmt) cc_final: 0.8250 (mmt) REVERT: B 286 MET cc_start: 0.7828 (mmp) cc_final: 0.7587 (mmm) REVERT: C 286 MET cc_start: 0.8066 (mmt) cc_final: 0.7838 (mmm) REVERT: C 315 MET cc_start: 0.8840 (mpt) cc_final: 0.8240 (mpt) REVERT: C 316 MET cc_start: 0.8730 (mmm) cc_final: 0.8346 (mmm) REVERT: D 164 MET cc_start: 0.8657 (mmt) cc_final: 0.8259 (mmt) outliers start: 13 outliers final: 9 residues processed: 118 average time/residue: 0.7205 time to fit residues: 90.0026 Evaluate side-chains 122 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 73 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.097888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.086640 restraints weight = 10431.983| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.02 r_work: 0.2895 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9565 Z= 0.134 Angle : 0.575 5.528 13080 Z= 0.299 Chirality : 0.041 0.150 1605 Planarity : 0.004 0.041 1610 Dihedral : 4.388 19.412 1310 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.33 % Allowed : 7.24 % Favored : 91.43 % 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: 1.38 (0.23), residues: 1270 helix: 1.40 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.43 (0.38), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 255 TYR 0.007 0.001 TYR A 320 PHE 0.022 0.002 PHE B 266 TRP 0.015 0.001 TRP B 244 HIS 0.002 0.001 HIS C 273 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9565) covalent geometry : angle 0.57515 (13080) hydrogen bonds : bond 0.03915 ( 760) hydrogen bonds : angle 4.57968 ( 2280) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.372 Fit side-chains REVERT: A 82 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7560 (tp30) REVERT: A 219 LEU cc_start: 0.7725 (mt) cc_final: 0.7222 (tt) REVERT: B 164 MET cc_start: 0.8651 (mmt) cc_final: 0.8262 (mmt) REVERT: B 286 MET cc_start: 0.7730 (mmp) cc_final: 0.7482 (mmm) REVERT: C 286 MET cc_start: 0.7997 (mmt) cc_final: 0.7770 (mmm) REVERT: C 315 MET cc_start: 0.8788 (mpt) cc_final: 0.8326 (mpt) REVERT: C 316 MET cc_start: 0.8750 (mmm) cc_final: 0.8372 (mmm) REVERT: D 164 MET cc_start: 0.8611 (mmt) cc_final: 0.8213 (mmt) outliers start: 13 outliers final: 5 residues processed: 123 average time/residue: 0.7065 time to fit residues: 92.0320 Evaluate side-chains 120 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain E residue 209 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 46 optimal weight: 0.0670 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.098734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.087514 restraints weight = 10489.017| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.02 r_work: 0.2914 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9565 Z= 0.123 Angle : 0.559 5.491 13080 Z= 0.290 Chirality : 0.040 0.144 1605 Planarity : 0.004 0.040 1610 Dihedral : 4.313 18.478 1310 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 1.33 % Allowed : 7.55 % Favored : 91.12 % 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 (0.24), residues: 1270 helix: 1.58 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.26 (0.39), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 255 TYR 0.006 0.001 TYR B 320 PHE 0.020 0.001 PHE D 266 TRP 0.015 0.001 TRP B 244 HIS 0.001 0.001 HIS A 273 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9565) covalent geometry : angle 0.55929 (13080) hydrogen bonds : bond 0.03699 ( 760) hydrogen bonds : angle 4.47724 ( 2280) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.367 Fit side-chains REVERT: A 219 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7311 (tt) REVERT: B 164 MET cc_start: 0.8613 (mmt) cc_final: 0.8293 (mmt) REVERT: B 172 LYS cc_start: 0.8206 (mptp) cc_final: 0.7682 (mptt) REVERT: B 286 MET cc_start: 0.7661 (mmp) cc_final: 0.7442 (mmm) REVERT: C 266 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7246 (p90) REVERT: C 286 MET cc_start: 0.7929 (mmt) cc_final: 0.7714 (mmm) REVERT: C 315 MET cc_start: 0.8787 (mpt) cc_final: 0.8357 (mpt) REVERT: C 316 MET cc_start: 0.8729 (mmm) cc_final: 0.8340 (mmm) REVERT: D 164 MET cc_start: 0.8574 (mmt) cc_final: 0.8212 (mmt) outliers start: 13 outliers final: 6 residues processed: 123 average time/residue: 0.7415 time to fit residues: 96.4823 Evaluate side-chains 124 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain E residue 209 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 95 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 0.0370 chunk 10 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN C 123 ASN E 123 ASN E 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.096248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.085400 restraints weight = 10530.001| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.00 r_work: 0.2864 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9565 Z= 0.195 Angle : 0.639 6.173 13080 Z= 0.334 Chirality : 0.045 0.167 1605 Planarity : 0.005 0.045 1610 Dihedral : 4.514 20.278 1310 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.22 % Allowed : 7.96 % Favored : 90.82 % 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: 1.33 (0.23), residues: 1270 helix: 1.34 (0.15), residues: 1110 sheet: None (None), residues: 0 loop : -2.20 (0.40), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 231 TYR 0.010 0.002 TYR A 81 PHE 0.032 0.002 PHE D 266 TRP 0.010 0.001 TRP B 244 HIS 0.002 0.001 HIS C 273 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 9565) covalent geometry : angle 0.63935 (13080) hydrogen bonds : bond 0.04642 ( 760) hydrogen bonds : angle 4.77775 ( 2280) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.364 Fit side-chains REVERT: A 82 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7516 (tp30) REVERT: A 219 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7377 (tt) REVERT: B 164 MET cc_start: 0.8653 (mmt) cc_final: 0.8262 (mmt) REVERT: B 286 MET cc_start: 0.7870 (mmp) cc_final: 0.7621 (mmm) REVERT: C 82 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7487 (tp30) REVERT: C 286 MET cc_start: 0.8090 (mmt) cc_final: 0.7852 (mmm) REVERT: C 315 MET cc_start: 0.8828 (mpt) cc_final: 0.8460 (mpt) REVERT: D 164 MET cc_start: 0.8662 (mmt) cc_final: 0.8257 (mmt) outliers start: 12 outliers final: 7 residues processed: 120 average time/residue: 0.7368 time to fit residues: 93.4980 Evaluate side-chains 124 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain E residue 209 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 0.0050 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN E 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.099072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.087925 restraints weight = 10360.474| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.01 r_work: 0.2921 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9565 Z= 0.120 Angle : 0.555 5.454 13080 Z= 0.288 Chirality : 0.040 0.142 1605 Planarity : 0.004 0.041 1610 Dihedral : 4.311 18.595 1310 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.12 % Allowed : 8.16 % Favored : 90.71 % 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 (0.24), residues: 1270 helix: 1.64 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.07 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 231 TYR 0.006 0.001 TYR B 320 PHE 0.019 0.001 PHE C 266 TRP 0.017 0.001 TRP B 244 HIS 0.001 0.001 HIS D 273 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9565) covalent geometry : angle 0.55494 (13080) hydrogen bonds : bond 0.03616 ( 760) hydrogen bonds : angle 4.45453 ( 2280) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.465 Fit side-chains REVERT: A 82 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7467 (tp30) REVERT: A 219 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7395 (tt) REVERT: A 266 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7165 (p90) REVERT: B 164 MET cc_start: 0.8644 (mmt) cc_final: 0.8312 (mmt) REVERT: B 266 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7160 (p90) REVERT: B 286 MET cc_start: 0.7662 (mmp) cc_final: 0.7452 (mmm) REVERT: C 266 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7171 (p90) REVERT: C 286 MET cc_start: 0.7926 (mmt) cc_final: 0.7708 (mmm) REVERT: C 315 MET cc_start: 0.8786 (mpt) cc_final: 0.8421 (mpt) REVERT: D 164 MET cc_start: 0.8572 (mmt) cc_final: 0.8188 (mmt) outliers start: 11 outliers final: 5 residues processed: 124 average time/residue: 0.7317 time to fit residues: 95.9531 Evaluate side-chains 124 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain E residue 209 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 20 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN E 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.096527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.085399 restraints weight = 10359.231| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.00 r_work: 0.2884 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9565 Z= 0.149 Angle : 0.592 5.589 13080 Z= 0.308 Chirality : 0.042 0.156 1605 Planarity : 0.004 0.042 1610 Dihedral : 4.388 19.291 1310 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.12 % Allowed : 8.27 % Favored : 90.61 % 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: 1.67 (0.24), residues: 1270 helix: 1.57 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.09 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 231 TYR 0.007 0.001 TYR C 81 PHE 0.024 0.002 PHE D 266 TRP 0.013 0.001 TRP B 244 HIS 0.001 0.001 HIS D 273 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9565) covalent geometry : angle 0.59152 (13080) hydrogen bonds : bond 0.04128 ( 760) hydrogen bonds : angle 4.60933 ( 2280) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.361 Fit side-chains REVERT: A 82 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7523 (tp30) REVERT: A 219 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7414 (tt) REVERT: A 266 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7435 (p90) REVERT: B 266 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7293 (p90) REVERT: B 286 MET cc_start: 0.7739 (mmp) cc_final: 0.7523 (mmm) REVERT: C 82 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7353 (tp30) REVERT: C 286 MET cc_start: 0.7977 (mmt) cc_final: 0.7745 (mmm) REVERT: C 315 MET cc_start: 0.8808 (mpt) cc_final: 0.8470 (mpt) REVERT: D 164 MET cc_start: 0.8631 (mmt) cc_final: 0.8239 (mmt) outliers start: 11 outliers final: 7 residues processed: 120 average time/residue: 0.7024 time to fit residues: 89.1400 Evaluate side-chains 125 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 266 PHE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 266 PHE Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain E residue 209 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 1 optimal weight: 0.7980 chunk 105 optimal weight: 0.0570 chunk 71 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 110 optimal weight: 0.0030 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.4908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN E 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.099856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.088768 restraints weight = 10366.627| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.01 r_work: 0.2932 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9565 Z= 0.119 Angle : 0.552 5.472 13080 Z= 0.286 Chirality : 0.039 0.140 1605 Planarity : 0.004 0.041 1610 Dihedral : 4.267 18.211 1310 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.51 % Allowed : 9.29 % Favored : 90.20 % 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: 1.99 (0.24), residues: 1270 helix: 1.78 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -1.94 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 255 TYR 0.006 0.001 TYR C 187 PHE 0.018 0.001 PHE C 266 TRP 0.016 0.001 TRP B 244 HIS 0.001 0.000 HIS D 273 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 9565) covalent geometry : angle 0.55158 (13080) hydrogen bonds : bond 0.03555 ( 760) hydrogen bonds : angle 4.41051 ( 2280) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.363 Fit side-chains REVERT: A 219 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7448 (tt) REVERT: A 266 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7199 (p90) REVERT: B 286 MET cc_start: 0.7661 (mmp) cc_final: 0.7459 (mmm) REVERT: C 286 MET cc_start: 0.7915 (mmt) cc_final: 0.7700 (mmm) REVERT: C 315 MET cc_start: 0.8784 (mpt) cc_final: 0.8458 (mpt) REVERT: D 164 MET cc_start: 0.8575 (mmt) cc_final: 0.8199 (mmt) outliers start: 5 outliers final: 3 residues processed: 124 average time/residue: 0.6497 time to fit residues: 85.4321 Evaluate side-chains 121 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 266 PHE Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain E residue 316 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 24 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 45 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: D 102 GLN E 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.097960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.086924 restraints weight = 10335.272| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.00 r_work: 0.2901 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9565 Z= 0.137 Angle : 0.577 5.535 13080 Z= 0.300 Chirality : 0.041 0.151 1605 Planarity : 0.004 0.041 1610 Dihedral : 4.325 18.711 1310 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.92 % Allowed : 8.88 % Favored : 90.20 % 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: 1.91 (0.24), residues: 1270 helix: 1.73 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -1.97 (0.41), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 231 TYR 0.007 0.001 TYR B 320 PHE 0.022 0.002 PHE C 266 TRP 0.014 0.001 TRP B 244 HIS 0.001 0.001 HIS D 273 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9565) covalent geometry : angle 0.57701 (13080) hydrogen bonds : bond 0.03939 ( 760) hydrogen bonds : angle 4.52019 ( 2280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4017.21 seconds wall clock time: 69 minutes 20.16 seconds (4160.16 seconds total)