Starting phenix.real_space_refine on Tue Feb 3 17:04:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jeh_61417/02_2026/9jeh_61417.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jeh_61417/02_2026/9jeh_61417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jeh_61417/02_2026/9jeh_61417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jeh_61417/02_2026/9jeh_61417.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jeh_61417/02_2026/9jeh_61417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jeh_61417/02_2026/9jeh_61417.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.028 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 3462 2.51 5 N 908 2.21 5 O 1015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s 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: 5409 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2699 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 327} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2710 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 327} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.02, per 1000 atoms: 0.19 Number of scatterers: 5409 At special positions: 0 Unit cell: (63.51, 73.73, 96.36, 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 1015 8.00 N 908 7.00 C 3462 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: 0.25 Conformation dependent library (CDL) restraints added in 204.6 milliseconds 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 5 sheets defined 52.6% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 21 through 41 removed outlier: 3.815A pdb=" N THR A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.852A pdb=" N TYR A 50 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE A 51 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 69 Processing helix chain 'A' and resid 72 through 88 removed outlier: 4.390A pdb=" N THR A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 108 through 120 removed outlier: 4.152A pdb=" N LEU A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.677A pdb=" N LEU A 129 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 258 through 284 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 311 through 333 Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.606A pdb=" N ARG A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 46 through 51 removed outlier: 4.101A pdb=" N TYR B 50 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 51 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 72 through 88 removed outlier: 4.941A pdb=" N THR B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 108 through 120 removed outlier: 4.080A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.633A pdb=" N LEU B 129 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 172 removed outlier: 3.539A pdb=" N ALA B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 258 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 311 through 333 Processing helix chain 'B' and resid 333 through 339 removed outlier: 3.709A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 removed outlier: 7.684A pdb=" N VAL A 291 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL A 226 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 56 removed outlier: 6.410A pdb=" N ILE A 54 " --> pdb=" O MET A 134 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N THR A 136 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLY A 56 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL A 138 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 56 removed outlier: 6.410A pdb=" N ILE A 54 " --> pdb=" O MET A 134 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N THR A 136 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLY A 56 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N VAL A 138 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 188 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.349A pdb=" N ILE B 10 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU B 227 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 12 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE B 229 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER B 14 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N VAL B 291 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 226 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE B 293 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASN B 228 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 145 through 149 removed outlier: 3.504A pdb=" N ASN B 188 " --> pdb=" O ILE B 183 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 717 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: 0.50 Time building geometry restraints manager: 0.35 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: 1749 1.34 - 1.46: 734 1.46 - 1.57: 2984 1.57 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 5509 Sorted by residual: bond pdb=" CB ASP B 235 " pdb=" CG ASP B 235 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.22e+00 bond pdb=" SD MET B 134 " pdb=" CE MET B 134 " ideal model delta sigma weight residual 1.791 1.765 0.026 2.50e-02 1.60e+03 1.09e+00 bond pdb=" CB ILE A 135 " pdb=" CG2 ILE A 135 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.18e-01 bond pdb=" C LEU B 140 " pdb=" O LEU B 140 " ideal model delta sigma weight residual 1.235 1.224 0.011 1.26e-02 6.30e+03 7.54e-01 bond pdb=" CB GLU B 184 " pdb=" CG GLU B 184 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.37e-01 ... (remaining 5504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 7166 1.17 - 2.34: 187 2.34 - 3.51: 59 3.51 - 4.69: 10 4.69 - 5.86: 3 Bond angle restraints: 7425 Sorted by residual: angle pdb=" CA GLU B 287 " pdb=" CB GLU B 287 " pdb=" CG GLU B 287 " ideal model delta sigma weight residual 114.10 119.96 -5.86 2.00e+00 2.50e-01 8.58e+00 angle pdb=" C TYR B 251 " pdb=" N LEU B 252 " pdb=" CA LEU B 252 " ideal model delta sigma weight residual 121.54 126.57 -5.03 1.91e+00 2.74e-01 6.94e+00 angle pdb=" CA ASP B 235 " pdb=" CB ASP B 235 " pdb=" CG ASP B 235 " ideal model delta sigma weight residual 112.60 115.09 -2.49 1.00e+00 1.00e+00 6.21e+00 angle pdb=" C ASN B 16 " pdb=" N GLY B 17 " pdb=" CA GLY B 17 " ideal model delta sigma weight residual 122.73 120.67 2.06 9.30e-01 1.16e+00 4.92e+00 angle pdb=" CA TRP A 98 " pdb=" CB TRP A 98 " pdb=" CG TRP A 98 " ideal model delta sigma weight residual 113.60 117.76 -4.16 1.90e+00 2.77e-01 4.80e+00 ... (remaining 7420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 2855 17.39 - 34.79: 357 34.79 - 52.18: 125 52.18 - 69.57: 32 69.57 - 86.96: 6 Dihedral angle restraints: 3375 sinusoidal: 1391 harmonic: 1984 Sorted by residual: dihedral pdb=" CA MET B 134 " pdb=" C MET B 134 " pdb=" N ILE B 135 " pdb=" CA ILE B 135 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ARG B 21 " pdb=" C ARG B 21 " pdb=" N GLY B 22 " pdb=" CA GLY B 22 " ideal model delta harmonic sigma weight residual 180.00 163.12 16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ASN A 309 " pdb=" CB ASN A 309 " pdb=" CG ASN A 309 " pdb=" OD1 ASN A 309 " ideal model delta sinusoidal sigma weight residual -90.00 -164.26 74.26 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 3372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 522 0.033 - 0.066: 217 0.066 - 0.100: 54 0.100 - 0.133: 38 0.133 - 0.166: 1 Chirality restraints: 832 Sorted by residual: chirality pdb=" CA ASP B 235 " pdb=" N ASP B 235 " pdb=" C ASP B 235 " pdb=" CB ASP B 235 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA ILE A 12 " pdb=" N ILE A 12 " pdb=" C ILE A 12 " pdb=" CB ILE A 12 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE B 135 " pdb=" N ILE B 135 " pdb=" C ILE B 135 " pdb=" CB ILE B 135 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 829 not shown) Planarity restraints: 950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 235 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" C ASP B 235 " -0.043 2.00e-02 2.50e+03 pdb=" O ASP B 235 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR B 236 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 235 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" CG ASP B 235 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASP B 235 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP B 235 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 157 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.08e+00 pdb=" C THR A 157 " 0.035 2.00e-02 2.50e+03 pdb=" O THR A 157 " -0.013 2.00e-02 2.50e+03 pdb=" N MET A 158 " -0.012 2.00e-02 2.50e+03 ... (remaining 947 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 222 2.72 - 3.26: 5396 3.26 - 3.81: 9077 3.81 - 4.35: 11773 4.35 - 4.90: 19895 Nonbonded interactions: 46363 Sorted by model distance: nonbonded pdb=" O ARG B 260 " pdb=" OG SER B 264 " model vdw 2.173 3.040 nonbonded pdb=" OG SER B 105 " pdb=" O THR B 176 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR B 107 " pdb=" OD2 ASP B 308 " model vdw 2.299 3.040 nonbonded pdb=" NE2 HIS B 152 " pdb=" OE2 GLU B 207 " model vdw 2.300 3.120 nonbonded pdb=" NE1 TRP A 255 " pdb=" O PRO B 175 " model vdw 2.304 3.120 ... (remaining 46358 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 245 or (resid 246 and (name N or name CA or name \ C or name O or name CB )) or resid 247 through 248 or (resid 249 and (name N or \ name CA or name C or name O or name CB )) or resid 250 through 349)) selection = (chain 'B' and (resid 8 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 through 102 or (resid 103 and (name N or na \ me CA or name C or name O or name CB )) or resid 104 through 294 or (resid 295 a \ nd (name N or name CA or name C or name O or name CB )) or resid 296 through 303 \ or (resid 304 and (name N or name CA or name C or name O or name CB )) or resid \ 305 through 349)) } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.930 Find NCS groups from input model: 0.050 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 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 : 0.003 0.032 5509 Z= 0.142 Angle : 0.518 5.857 7425 Z= 0.280 Chirality : 0.042 0.166 832 Planarity : 0.004 0.026 950 Dihedral : 17.957 86.962 2095 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.23 % Allowed : 30.99 % Favored : 66.78 % 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: -0.46 (0.32), residues: 680 helix: 0.64 (0.30), residues: 330 sheet: -1.04 (0.61), residues: 76 loop : -1.19 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 131 TYR 0.005 0.001 TYR A 330 PHE 0.008 0.001 PHE B 275 TRP 0.017 0.002 TRP A 98 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5509) covalent geometry : angle 0.51848 ( 7425) hydrogen bonds : bond 0.13029 ( 248) hydrogen bonds : angle 6.40571 ( 717) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.238 Fit side-chains REVERT: A 85 THR cc_start: 0.8172 (m) cc_final: 0.7676 (p) REVERT: A 184 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7819 (mm-30) REVERT: A 218 ASP cc_start: 0.8337 (p0) cc_final: 0.7927 (p0) REVERT: A 287 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7747 (mt-10) REVERT: B 85 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7767 (p) REVERT: B 94 LYS cc_start: 0.8416 (tttt) cc_final: 0.8099 (mtpt) REVERT: B 279 ARG cc_start: 0.8544 (mmt180) cc_final: 0.8327 (mmt90) REVERT: B 334 GLU cc_start: 0.7517 (tt0) cc_final: 0.7291 (tm-30) outliers start: 13 outliers final: 9 residues processed: 94 average time/residue: 0.4689 time to fit residues: 46.3829 Evaluate side-chains 87 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 102 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.0470 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN B 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.161046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135878 restraints weight = 6074.018| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.24 r_work: 0.3436 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5509 Z= 0.151 Angle : 0.512 4.998 7425 Z= 0.275 Chirality : 0.042 0.135 832 Planarity : 0.004 0.034 950 Dihedral : 5.880 55.703 756 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.79 % Allowed : 27.40 % Favored : 67.81 % 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: -0.59 (0.32), residues: 680 helix: 0.54 (0.29), residues: 336 sheet: -1.25 (0.57), residues: 76 loop : -1.24 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.005 0.001 TYR A 330 PHE 0.008 0.001 PHE B 275 TRP 0.013 0.002 TRP A 98 HIS 0.002 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 5509) covalent geometry : angle 0.51205 ( 7425) hydrogen bonds : bond 0.04364 ( 248) hydrogen bonds : angle 5.37140 ( 717) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 85 THR cc_start: 0.8181 (m) cc_final: 0.7720 (p) REVERT: A 218 ASP cc_start: 0.8350 (p0) cc_final: 0.7982 (p0) REVERT: A 287 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7770 (mt-10) REVERT: A 314 CYS cc_start: 0.8360 (m) cc_final: 0.7834 (m) REVERT: B 31 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: B 94 LYS cc_start: 0.8382 (tttt) cc_final: 0.8089 (mtpp) REVERT: B 279 ARG cc_start: 0.8572 (mmt180) cc_final: 0.8250 (mmt90) REVERT: B 282 GLU cc_start: 0.7678 (tt0) cc_final: 0.7114 (mt-10) REVERT: B 334 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7261 (tm-30) outliers start: 28 outliers final: 15 residues processed: 112 average time/residue: 0.4453 time to fit residues: 52.7164 Evaluate side-chains 98 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 334 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 31 optimal weight: 0.9990 chunk 55 optimal weight: 0.0040 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 43 optimal weight: 0.0370 chunk 2 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.4670 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.165916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141261 restraints weight = 5970.507| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.21 r_work: 0.3502 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5509 Z= 0.102 Angle : 0.463 4.686 7425 Z= 0.250 Chirality : 0.041 0.135 832 Planarity : 0.003 0.033 950 Dihedral : 4.728 54.604 743 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.94 % Allowed : 28.08 % Favored : 67.98 % 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: -0.15 (0.32), residues: 680 helix: 0.92 (0.29), residues: 324 sheet: -1.08 (0.58), residues: 76 loop : -0.95 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.004 0.001 TYR B 236 PHE 0.005 0.001 PHE B 275 TRP 0.014 0.002 TRP A 98 HIS 0.001 0.000 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 5509) covalent geometry : angle 0.46294 ( 7425) hydrogen bonds : bond 0.03541 ( 248) hydrogen bonds : angle 5.12064 ( 717) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 218 ASP cc_start: 0.8374 (p0) cc_final: 0.8029 (p0) REVERT: A 287 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7859 (mt-10) REVERT: A 314 CYS cc_start: 0.8364 (m) cc_final: 0.7822 (m) REVERT: A 338 ASN cc_start: 0.8157 (m-40) cc_final: 0.7656 (m110) REVERT: B 94 LYS cc_start: 0.8389 (tttt) cc_final: 0.8078 (mtpp) REVERT: B 112 LEU cc_start: 0.8086 (tp) cc_final: 0.7834 (tp) REVERT: B 279 ARG cc_start: 0.8602 (mmt180) cc_final: 0.8290 (mmt90) REVERT: B 282 GLU cc_start: 0.7693 (tt0) cc_final: 0.7152 (mt-10) outliers start: 23 outliers final: 13 residues processed: 112 average time/residue: 0.4369 time to fit residues: 51.8291 Evaluate side-chains 98 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 54 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 67 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.163907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139261 restraints weight = 5991.410| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.20 r_work: 0.3473 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5509 Z= 0.122 Angle : 0.487 4.743 7425 Z= 0.259 Chirality : 0.041 0.135 832 Planarity : 0.003 0.030 950 Dihedral : 4.671 53.414 743 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 4.45 % Allowed : 27.23 % Favored : 68.32 % 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: -0.14 (0.32), residues: 680 helix: 0.91 (0.29), residues: 324 sheet: -0.97 (0.58), residues: 76 loop : -0.96 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 92 TYR 0.005 0.001 TYR A 330 PHE 0.008 0.001 PHE B 275 TRP 0.013 0.002 TRP A 98 HIS 0.001 0.000 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 5509) covalent geometry : angle 0.48674 ( 7425) hydrogen bonds : bond 0.03723 ( 248) hydrogen bonds : angle 5.09128 ( 717) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 287 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7889 (mt-10) REVERT: A 307 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8138 (tt) REVERT: A 314 CYS cc_start: 0.8394 (m) cc_final: 0.7848 (m) REVERT: A 338 ASN cc_start: 0.8168 (m-40) cc_final: 0.7662 (m110) REVERT: B 31 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: B 94 LYS cc_start: 0.8377 (tttt) cc_final: 0.8073 (mtpp) REVERT: B 279 ARG cc_start: 0.8625 (mmt180) cc_final: 0.8313 (mmt90) REVERT: B 282 GLU cc_start: 0.7707 (tt0) cc_final: 0.7169 (mt-10) outliers start: 26 outliers final: 16 residues processed: 112 average time/residue: 0.4580 time to fit residues: 54.1098 Evaluate side-chains 97 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.163696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.138866 restraints weight = 6049.426| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.23 r_work: 0.3469 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5509 Z= 0.126 Angle : 0.494 4.986 7425 Z= 0.263 Chirality : 0.041 0.136 832 Planarity : 0.003 0.030 950 Dihedral : 4.556 53.139 741 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.28 % Allowed : 28.77 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.32), residues: 680 helix: 0.90 (0.29), residues: 324 sheet: -1.04 (0.58), residues: 76 loop : -0.97 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 104 TYR 0.004 0.001 TYR A 330 PHE 0.008 0.001 PHE B 275 TRP 0.013 0.002 TRP A 98 HIS 0.001 0.000 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5509) covalent geometry : angle 0.49407 ( 7425) hydrogen bonds : bond 0.03762 ( 248) hydrogen bonds : angle 5.11339 ( 717) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 287 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7885 (mt-10) REVERT: A 307 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8101 (tt) REVERT: A 314 CYS cc_start: 0.8364 (m) cc_final: 0.7783 (m) REVERT: A 338 ASN cc_start: 0.8179 (m-40) cc_final: 0.7645 (m110) REVERT: B 94 LYS cc_start: 0.8345 (tttt) cc_final: 0.8036 (mtpp) REVERT: B 279 ARG cc_start: 0.8575 (mmt180) cc_final: 0.8246 (mmt90) REVERT: B 282 GLU cc_start: 0.7675 (tt0) cc_final: 0.7098 (mt-10) REVERT: B 334 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7278 (tm-30) outliers start: 25 outliers final: 15 residues processed: 102 average time/residue: 0.4639 time to fit residues: 49.8478 Evaluate side-chains 98 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 334 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 15 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 0.0050 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.165045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140214 restraints weight = 6055.450| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.23 r_work: 0.3484 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5509 Z= 0.111 Angle : 0.481 5.188 7425 Z= 0.257 Chirality : 0.041 0.134 832 Planarity : 0.003 0.030 950 Dihedral : 4.507 53.705 741 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.94 % Allowed : 29.45 % Favored : 66.61 % 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: -0.10 (0.32), residues: 680 helix: 0.95 (0.29), residues: 324 sheet: -0.97 (0.58), residues: 76 loop : -0.96 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 92 TYR 0.003 0.001 TYR A 330 PHE 0.007 0.001 PHE B 275 TRP 0.014 0.002 TRP A 98 HIS 0.001 0.000 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 5509) covalent geometry : angle 0.48134 ( 7425) hydrogen bonds : bond 0.03544 ( 248) hydrogen bonds : angle 5.06184 ( 717) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 307 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8139 (tt) REVERT: A 338 ASN cc_start: 0.8011 (m-40) cc_final: 0.7554 (m110) REVERT: B 94 LYS cc_start: 0.8316 (tttt) cc_final: 0.8036 (mtpt) REVERT: B 253 SER cc_start: 0.6853 (OUTLIER) cc_final: 0.6584 (m) REVERT: B 279 ARG cc_start: 0.8479 (mmt180) cc_final: 0.8171 (mmt90) REVERT: B 282 GLU cc_start: 0.7577 (tt0) cc_final: 0.7092 (mt-10) outliers start: 23 outliers final: 12 residues processed: 104 average time/residue: 0.4345 time to fit residues: 47.8213 Evaluate side-chains 91 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 27 optimal weight: 0.0870 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 62 optimal weight: 0.0570 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.166518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.141949 restraints weight = 6123.227| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.23 r_work: 0.3498 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5509 Z= 0.105 Angle : 0.488 6.296 7425 Z= 0.260 Chirality : 0.041 0.139 832 Planarity : 0.003 0.029 950 Dihedral : 4.444 54.046 741 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.42 % Allowed : 30.65 % Favored : 65.92 % 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: -0.07 (0.32), residues: 680 helix: 0.98 (0.29), residues: 324 sheet: -0.92 (0.59), residues: 76 loop : -0.95 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 92 TYR 0.005 0.001 TYR B 177 PHE 0.006 0.001 PHE B 275 TRP 0.010 0.001 TRP A 98 HIS 0.001 0.000 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 5509) covalent geometry : angle 0.48826 ( 7425) hydrogen bonds : bond 0.03423 ( 248) hydrogen bonds : angle 5.00151 ( 717) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 307 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8097 (tt) REVERT: A 314 CYS cc_start: 0.8152 (m) cc_final: 0.7636 (m) REVERT: A 338 ASN cc_start: 0.7971 (m-40) cc_final: 0.7516 (m110) REVERT: B 94 LYS cc_start: 0.8271 (tttt) cc_final: 0.7968 (mtpt) REVERT: B 279 ARG cc_start: 0.8447 (mmt180) cc_final: 0.8116 (mmt90) REVERT: B 282 GLU cc_start: 0.7524 (tt0) cc_final: 0.7003 (mt-10) outliers start: 20 outliers final: 11 residues processed: 100 average time/residue: 0.4455 time to fit residues: 47.0262 Evaluate side-chains 88 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 0.0870 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.158743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133758 restraints weight = 6066.765| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.21 r_work: 0.3410 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5509 Z= 0.218 Angle : 0.601 7.286 7425 Z= 0.316 Chirality : 0.045 0.152 832 Planarity : 0.004 0.028 950 Dihedral : 4.651 51.148 740 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.42 % Allowed : 31.34 % Favored : 65.24 % 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 (0.31), residues: 680 helix: 0.70 (0.29), residues: 322 sheet: -1.24 (0.56), residues: 76 loop : -1.22 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 92 TYR 0.007 0.001 TYR B 330 PHE 0.012 0.002 PHE B 275 TRP 0.012 0.002 TRP B 255 HIS 0.003 0.001 HIS B 152 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 5509) covalent geometry : angle 0.60126 ( 7425) hydrogen bonds : bond 0.04533 ( 248) hydrogen bonds : angle 5.28855 ( 717) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 85 THR cc_start: 0.8200 (m) cc_final: 0.7718 (p) REVERT: A 184 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7829 (mm-30) REVERT: A 287 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: A 307 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8125 (tt) REVERT: A 314 CYS cc_start: 0.8304 (m) cc_final: 0.7798 (m) REVERT: B 94 LYS cc_start: 0.8380 (tttt) cc_final: 0.8074 (mtpp) REVERT: B 184 GLU cc_start: 0.7718 (mp0) cc_final: 0.7399 (pm20) REVERT: B 279 ARG cc_start: 0.8636 (mmt180) cc_final: 0.8339 (mmt90) REVERT: B 282 GLU cc_start: 0.7696 (tt0) cc_final: 0.7114 (mt-10) outliers start: 20 outliers final: 12 residues processed: 90 average time/residue: 0.4535 time to fit residues: 43.1191 Evaluate side-chains 88 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.0060 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 0.0670 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 0.0870 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.6314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.164725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139887 restraints weight = 6006.369| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.21 r_work: 0.3488 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5509 Z= 0.117 Angle : 0.510 6.437 7425 Z= 0.272 Chirality : 0.042 0.170 832 Planarity : 0.003 0.030 950 Dihedral : 4.497 54.402 740 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.74 % Allowed : 32.02 % Favored : 65.24 % 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: -0.09 (0.32), residues: 680 helix: 1.10 (0.29), residues: 310 sheet: -1.06 (0.57), residues: 76 loop : -1.00 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.004 0.001 TYR B 330 PHE 0.007 0.001 PHE A 275 TRP 0.015 0.002 TRP A 98 HIS 0.001 0.000 HIS B 181 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 5509) covalent geometry : angle 0.50999 ( 7425) hydrogen bonds : bond 0.03676 ( 248) hydrogen bonds : angle 5.11218 ( 717) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 254 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7676 (tp) REVERT: A 307 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8064 (tt) REVERT: A 314 CYS cc_start: 0.8259 (m) cc_final: 0.7741 (m) REVERT: A 338 ASN cc_start: 0.8176 (m-40) cc_final: 0.7659 (m110) REVERT: B 94 LYS cc_start: 0.8329 (tttt) cc_final: 0.7992 (mtpt) REVERT: B 184 GLU cc_start: 0.7681 (mp0) cc_final: 0.7331 (pm20) REVERT: B 253 SER cc_start: 0.6984 (OUTLIER) cc_final: 0.6711 (m) REVERT: B 282 GLU cc_start: 0.7664 (tt0) cc_final: 0.7104 (mt-10) outliers start: 16 outliers final: 10 residues processed: 91 average time/residue: 0.4360 time to fit residues: 41.9289 Evaluate side-chains 86 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 23 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 55 optimal weight: 0.0070 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.166286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141554 restraints weight = 6063.440| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.23 r_work: 0.3503 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5509 Z= 0.111 Angle : 0.509 7.108 7425 Z= 0.272 Chirality : 0.041 0.165 832 Planarity : 0.004 0.030 950 Dihedral : 4.411 55.422 740 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.23 % Allowed : 32.19 % Favored : 65.58 % 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: 0.02 (0.32), residues: 680 helix: 1.16 (0.29), residues: 310 sheet: -0.88 (0.58), residues: 76 loop : -0.94 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.004 0.001 TYR B 330 PHE 0.009 0.001 PHE B 275 TRP 0.011 0.002 TRP A 98 HIS 0.001 0.000 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 5509) covalent geometry : angle 0.50928 ( 7425) hydrogen bonds : bond 0.03524 ( 248) hydrogen bonds : angle 5.01426 ( 717) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1360 Ramachandran restraints generated. 680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 307 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8065 (tt) REVERT: A 314 CYS cc_start: 0.8256 (m) cc_final: 0.7715 (m) REVERT: A 338 ASN cc_start: 0.8134 (m-40) cc_final: 0.7628 (m110) REVERT: B 94 LYS cc_start: 0.8321 (tttt) cc_final: 0.8006 (mtpt) REVERT: B 184 GLU cc_start: 0.7657 (mp0) cc_final: 0.7295 (pm20) REVERT: B 253 SER cc_start: 0.7020 (OUTLIER) cc_final: 0.6752 (m) REVERT: B 279 ARG cc_start: 0.8494 (mmt180) cc_final: 0.7912 (mmm160) REVERT: B 282 GLU cc_start: 0.7650 (tt0) cc_final: 0.7102 (mt-10) outliers start: 13 outliers final: 10 residues processed: 89 average time/residue: 0.4096 time to fit residues: 38.7382 Evaluate side-chains 91 residues out of total 590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 64 optimal weight: 0.0050 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.166832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142073 restraints weight = 6067.084| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.23 r_work: 0.3507 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5509 Z= 0.113 Angle : 0.518 6.785 7425 Z= 0.275 Chirality : 0.041 0.172 832 Planarity : 0.004 0.030 950 Dihedral : 4.390 55.590 740 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.40 % Allowed : 32.19 % Favored : 65.41 % 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: 0.05 (0.32), residues: 680 helix: 1.17 (0.29), residues: 310 sheet: -0.79 (0.59), residues: 76 loop : -0.94 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 92 TYR 0.006 0.001 TYR A 330 PHE 0.007 0.001 PHE B 275 TRP 0.008 0.001 TRP A 98 HIS 0.001 0.000 HIS B 271 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 5509) covalent geometry : angle 0.51816 ( 7425) hydrogen bonds : bond 0.03495 ( 248) hydrogen bonds : angle 5.00464 ( 717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.43 seconds wall clock time: 32 minutes 51.45 seconds (1971.45 seconds total)