Starting phenix.real_space_refine on Tue Aug 4 21:55:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9okr_70573/08_2026/9okr_70573.cif Found real_map, /net/cci-nas-00/data/ceres_data/9okr_70573/08_2026/9okr_70573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9okr_70573/08_2026/9okr_70573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9okr_70573/08_2026/9okr_70573.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9okr_70573/08_2026/9okr_70573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9okr_70573/08_2026/9okr_70573.map" } resolution = 4.1 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= 0.016 sd= 0.077 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 44 5.16 5 C 4510 2.51 5 N 1176 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6936 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1917 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain: "D" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1551 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 10, 'TRANS': 191} Restraints were copied for chains: C, E Time building chain proxies: 1.81, per 1000 atoms: 0.26 Number of scatterers: 6936 At special positions: 0 Unit cell: (73.26, 85.248, 99.9, 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 44 16.00 O 1206 8.00 N 1176 7.00 C 4510 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: 0.61 Conformation dependent library (CDL) restraints added in 405.1 milliseconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 64.4% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 1 through 30 Proline residue: B 7 - end of helix removed outlier: 3.589A pdb=" N ALA B 18 " --> pdb=" O MET B 14 " (cutoff:3.500A) Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 41 through 53 removed outlier: 3.944A pdb=" N GLY B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 75 Processing helix chain 'B' and resid 82 through 104 removed outlier: 4.832A pdb=" N LEU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N SER B 95 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 117 Processing helix chain 'B' and resid 123 through 144 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 154 through 162 Processing helix chain 'B' and resid 164 through 184 removed outlier: 3.741A pdb=" N VAL B 168 " --> pdb=" O LYS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 205 Proline residue: B 199 - end of helix removed outlier: 4.159A pdb=" N ARG B 205 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 235 Processing helix chain 'B' and resid 239 through 255 removed outlier: 3.633A pdb=" N VAL B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 30 Proline residue: C 7 - end of helix removed outlier: 3.589A pdb=" N ALA C 18 " --> pdb=" O MET C 14 " (cutoff:3.500A) Proline residue: C 21 - end of helix Processing helix chain 'C' and resid 31 through 41 Processing helix chain 'C' and resid 41 through 53 removed outlier: 3.944A pdb=" N GLY C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 75 Processing helix chain 'C' and resid 82 through 104 removed outlier: 4.832A pdb=" N LEU C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER C 95 " --> pdb=" O HIS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 117 Processing helix chain 'C' and resid 123 through 144 Processing helix chain 'C' and resid 145 through 154 Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 164 through 184 removed outlier: 3.741A pdb=" N VAL C 168 " --> pdb=" O LYS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 205 Proline residue: C 199 - end of helix removed outlier: 4.159A pdb=" N ARG C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 235 Processing helix chain 'C' and resid 239 through 255 removed outlier: 3.633A pdb=" N VAL C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 244 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 51 Processing helix chain 'D' and resid 85 through 91 Processing helix chain 'D' and resid 97 through 99 No H-bonds generated for 'chain 'D' and resid 97 through 99' Processing helix chain 'D' and resid 100 through 108 removed outlier: 3.947A pdb=" N ALA D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.848A pdb=" N ILE D 114 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 removed outlier: 3.970A pdb=" N ASN D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 171 Processing helix chain 'E' and resid 42 through 51 Processing helix chain 'E' and resid 85 through 91 Processing helix chain 'E' and resid 97 through 99 No H-bonds generated for 'chain 'E' and resid 97 through 99' Processing helix chain 'E' and resid 100 through 108 removed outlier: 3.948A pdb=" N ALA E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 114 removed outlier: 3.849A pdb=" N ILE E 114 " --> pdb=" O GLY E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 137 removed outlier: 3.969A pdb=" N ASN E 137 " --> pdb=" O ARG E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 171 Processing sheet with id=AA1, first strand: chain 'D' and resid 23 through 26 removed outlier: 7.394A pdb=" N LEU D 25 " --> pdb=" O GLU D 8 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU D 8 " --> pdb=" O LEU D 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AA3, first strand: chain 'D' and resid 69 through 72 removed outlier: 6.636A pdb=" N ILE D 32 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU D 192 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR D 34 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU D 194 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU D 36 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS D 200 " --> pdb=" O CYS D 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 23 through 26 removed outlier: 7.393A pdb=" N LEU E 25 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU E 8 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AA6, first strand: chain 'E' and resid 69 through 72 removed outlier: 6.636A pdb=" N ILE E 32 " --> pdb=" O GLU E 190 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU E 192 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR E 34 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU E 194 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU E 36 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N CYS E 200 " --> pdb=" O CYS E 193 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1293 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: 1.04 Time building geometry restraints manager: 0.81 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: 2221 1.34 - 1.46: 1242 1.46 - 1.57: 3511 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 7050 Sorted by residual: bond pdb=" CG1 ILE B 140 " pdb=" CD1 ILE B 140 " ideal model delta sigma weight residual 1.513 1.427 0.086 3.90e-02 6.57e+02 4.89e+00 bond pdb=" CG1 ILE C 140 " pdb=" CD1 ILE C 140 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.76e+00 bond pdb=" CB VAL C 244 " pdb=" CG2 VAL C 244 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.27e+00 bond pdb=" CB VAL B 244 " pdb=" CG2 VAL B 244 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.25e+00 bond pdb=" CA ALA D 41 " pdb=" C ALA D 41 " ideal model delta sigma weight residual 1.523 1.487 0.037 1.80e-02 3.09e+03 4.18e+00 ... (remaining 7045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 9296 2.51 - 5.02: 258 5.02 - 7.53: 36 7.53 - 10.05: 2 10.05 - 12.56: 2 Bond angle restraints: 9594 Sorted by residual: angle pdb=" C PRO B 238 " pdb=" N ALA B 239 " pdb=" CA ALA B 239 " ideal model delta sigma weight residual 122.79 112.93 9.86 1.70e+00 3.46e-01 3.36e+01 angle pdb=" C PRO C 238 " pdb=" N ALA C 239 " pdb=" CA ALA C 239 " ideal model delta sigma weight residual 122.79 112.97 9.82 1.70e+00 3.46e-01 3.33e+01 angle pdb=" N ASP B 236 " pdb=" CA ASP B 236 " pdb=" C ASP B 236 " ideal model delta sigma weight residual 109.71 115.40 -5.69 1.41e+00 5.03e-01 1.63e+01 angle pdb=" N ASP C 236 " pdb=" CA ASP C 236 " pdb=" C ASP C 236 " ideal model delta sigma weight residual 109.71 115.39 -5.68 1.41e+00 5.03e-01 1.62e+01 angle pdb=" C LYS C 164 " pdb=" N LEU C 165 " pdb=" CA LEU C 165 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 ... (remaining 9589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 3906 16.61 - 33.22: 276 33.22 - 49.83: 44 49.83 - 66.43: 10 66.43 - 83.04: 6 Dihedral angle restraints: 4242 sinusoidal: 1630 harmonic: 2612 Sorted by residual: dihedral pdb=" CA ASP B 236 " pdb=" C ASP B 236 " pdb=" N THR B 237 " pdb=" CA THR B 237 " ideal model delta harmonic sigma weight residual 180.00 116.75 63.25 0 5.00e+00 4.00e-02 1.60e+02 dihedral pdb=" CA ASP C 236 " pdb=" C ASP C 236 " pdb=" N THR C 237 " pdb=" CA THR C 237 " ideal model delta harmonic sigma weight residual 180.00 116.79 63.21 0 5.00e+00 4.00e-02 1.60e+02 dihedral pdb=" CA ARG C 77 " pdb=" C ARG C 77 " pdb=" N PRO C 78 " pdb=" CA PRO C 78 " ideal model delta harmonic sigma weight residual -180.00 -124.06 -55.94 0 5.00e+00 4.00e-02 1.25e+02 ... (remaining 4239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1053 0.071 - 0.142: 151 0.142 - 0.212: 6 0.212 - 0.283: 4 0.283 - 0.354: 2 Chirality restraints: 1216 Sorted by residual: chirality pdb=" CB THR B 237 " pdb=" CA THR B 237 " pdb=" OG1 THR B 237 " pdb=" CG2 THR B 237 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CB THR C 237 " pdb=" CA THR C 237 " pdb=" OG1 THR C 237 " pdb=" CG2 THR C 237 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA PRO B 241 " pdb=" N PRO B 241 " pdb=" C PRO B 241 " pdb=" CB PRO B 241 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1213 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 237 " -0.079 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO C 238 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO C 238 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 238 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 237 " 0.079 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO B 238 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO B 238 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 238 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 236 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C ASP C 236 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP C 236 " -0.013 2.00e-02 2.50e+03 pdb=" N THR C 237 " -0.011 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 678 2.73 - 3.27: 7303 3.27 - 3.82: 11457 3.82 - 4.36: 12837 4.36 - 4.90: 22152 Nonbonded interactions: 54427 Sorted by model distance: nonbonded pdb=" OG SER D 3 " pdb=" O LEU D 27 " model vdw 2.191 3.040 nonbonded pdb=" OG SER E 3 " pdb=" O LEU E 27 " model vdw 2.191 3.040 nonbonded pdb=" NH2 ARG C 146 " pdb=" O ARG E 93 " model vdw 2.197 3.120 nonbonded pdb=" O ARG B 77 " pdb=" NE ARG B 77 " model vdw 2.246 3.120 nonbonded pdb=" O ARG C 77 " pdb=" NE ARG C 77 " model vdw 2.247 3.120 ... (remaining 54422 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 'B' selection = chain 'C' } ncs_group { reference = 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.110 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.006 0.086 7050 Z= 0.307 Angle : 0.931 12.557 9594 Z= 0.525 Chirality : 0.049 0.354 1216 Planarity : 0.007 0.121 1180 Dihedral : 12.319 83.043 2558 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.66 % Allowed : 4.84 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.69 % 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: 1.71 (0.30), residues: 910 helix: 2.33 (0.22), residues: 552 sheet: 0.19 (0.52), residues: 92 loop : -1.14 (0.43), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 167 TYR 0.021 0.004 TYR D 160 PHE 0.023 0.002 PHE B 48 TRP 0.029 0.003 TRP C 143 HIS 0.006 0.002 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.31 ( 7050) covalent geometry : angle 0.93137 / 0.53 ( 9594) hydrogen bonds : bond 0.12998 / 8.86 ( 439) hydrogen bonds : angle 4.99121 / 3.59 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 HIS cc_start: 0.8296 (m-70) cc_final: 0.7959 (m90) REVERT: B 140 ILE cc_start: 0.8775 (mp) cc_final: 0.8501 (mp) REVERT: B 157 LEU cc_start: 0.9260 (mt) cc_final: 0.8993 (mm) REVERT: B 210 PRO cc_start: 0.9209 (Cg_exo) cc_final: 0.8978 (Cg_endo) REVERT: C 33 TYR cc_start: 0.7719 (m-80) cc_final: 0.7467 (m-80) REVERT: D 119 GLN cc_start: 0.8640 (mp10) cc_final: 0.8338 (pm20) REVERT: E 22 ASP cc_start: 0.9231 (t0) cc_final: 0.8991 (t0) REVERT: E 144 LEU cc_start: 0.9017 (mt) cc_final: 0.8514 (pp) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.0947 time to fit residues: 38.3561 Evaluate side-chains 202 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 179 HIS E 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.047099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.034921 restraints weight = 45302.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.036081 restraints weight = 29775.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.036932 restraints weight = 22278.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.037519 restraints weight = 17901.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.038032 restraints weight = 15290.413| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7050 Z= 0.216 Angle : 0.802 8.823 9594 Z= 0.406 Chirality : 0.045 0.174 1216 Planarity : 0.006 0.094 1180 Dihedral : 6.541 60.374 974 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.05 % Favored : 94.51 % Rotamer: Outliers : 0.39 % Allowed : 3.15 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.69 % 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: 1.29 (0.29), residues: 910 helix: 1.88 (0.22), residues: 554 sheet: 0.95 (0.56), residues: 82 loop : -1.38 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 167 TYR 0.013 0.002 TYR B 114 PHE 0.018 0.003 PHE C 25 TRP 0.032 0.002 TRP C 143 HIS 0.012 0.002 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 ( 7050) covalent geometry : angle 0.80203 / 0.41 ( 9594) hydrogen bonds : bond 0.04928 / 3.31 ( 439) hydrogen bonds : angle 4.95808 / 3.58 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 233 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 HIS cc_start: 0.9046 (m-70) cc_final: 0.8629 (m-70) REVERT: B 43 LEU cc_start: 0.9307 (tp) cc_final: 0.9050 (tp) REVERT: B 89 MET cc_start: 0.9548 (mmp) cc_final: 0.9269 (mmm) REVERT: B 104 MET cc_start: 0.9296 (tpt) cc_final: 0.8881 (tpp) REVERT: B 156 ASP cc_start: 0.9509 (p0) cc_final: 0.8801 (p0) REVERT: B 157 LEU cc_start: 0.9674 (mt) cc_final: 0.9360 (mm) REVERT: B 173 MET cc_start: 0.9359 (mmm) cc_final: 0.8685 (mmt) REVERT: B 213 MET cc_start: 0.9207 (ttt) cc_final: 0.8655 (ttm) REVERT: B 245 LEU cc_start: 0.9527 (tt) cc_final: 0.9033 (mm) REVERT: C 38 LEU cc_start: 0.9757 (OUTLIER) cc_final: 0.9526 (tt) REVERT: C 40 HIS cc_start: 0.9599 (m90) cc_final: 0.9343 (m90) REVERT: C 67 LEU cc_start: 0.9657 (mm) cc_final: 0.9281 (pp) REVERT: C 91 HIS cc_start: 0.9349 (m90) cc_final: 0.8988 (m90) REVERT: C 156 ASP cc_start: 0.9508 (p0) cc_final: 0.9302 (p0) REVERT: C 186 PHE cc_start: 0.9131 (p90) cc_final: 0.8742 (p90) REVERT: D 84 LEU cc_start: 0.9265 (tp) cc_final: 0.8942 (tp) REVERT: D 118 MET cc_start: 0.9584 (mmp) cc_final: 0.9086 (mmp) REVERT: D 125 GLU cc_start: 0.9760 (mp0) cc_final: 0.9556 (mp0) REVERT: D 144 LEU cc_start: 0.9488 (mt) cc_final: 0.8719 (pp) REVERT: D 176 MET cc_start: 0.9682 (tmm) cc_final: 0.9229 (tmm) REVERT: D 179 HIS cc_start: 0.9425 (t-90) cc_final: 0.9028 (t70) REVERT: D 187 LYS cc_start: 0.9568 (mmmt) cc_final: 0.9285 (tptp) REVERT: E 14 PHE cc_start: 0.9288 (m-80) cc_final: 0.8939 (m-80) REVERT: E 22 ASP cc_start: 0.9810 (t0) cc_final: 0.9432 (p0) REVERT: E 53 LEU cc_start: 0.9571 (tt) cc_final: 0.9242 (mp) REVERT: E 144 LEU cc_start: 0.9319 (mt) cc_final: 0.8681 (pp) REVERT: E 169 GLU cc_start: 0.9050 (tt0) cc_final: 0.8725 (tt0) REVERT: E 176 MET cc_start: 0.9390 (ptp) cc_final: 0.8877 (tmm) outliers start: 3 outliers final: 0 residues processed: 235 average time/residue: 0.0915 time to fit residues: 28.0067 Evaluate side-chains 188 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 53 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 65 optimal weight: 0.0170 chunk 32 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 overall best weight: 5.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 HIS ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN E 119 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.034464 restraints weight = 44840.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.035715 restraints weight = 28362.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.036633 restraints weight = 20667.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.037296 restraints weight = 16370.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.037753 restraints weight = 13711.586| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7050 Z= 0.204 Angle : 0.742 8.459 9594 Z= 0.376 Chirality : 0.044 0.237 1216 Planarity : 0.006 0.088 1180 Dihedral : 6.387 59.025 974 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.29 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.69 % 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: 1.14 (0.29), residues: 910 helix: 1.73 (0.22), residues: 554 sheet: 0.90 (0.55), residues: 92 loop : -1.46 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 48 TYR 0.018 0.002 TYR E 77 PHE 0.013 0.002 PHE C 159 TRP 0.015 0.001 TRP B 143 HIS 0.009 0.002 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 ( 7050) covalent geometry : angle 0.74201 / 0.38 ( 9594) hydrogen bonds : bond 0.04510 / 2.95 ( 439) hydrogen bonds : angle 4.87693 / 3.53 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 HIS cc_start: 0.9359 (m-70) cc_final: 0.8955 (m90) REVERT: B 104 MET cc_start: 0.9090 (tpt) cc_final: 0.8674 (tpp) REVERT: B 156 ASP cc_start: 0.9426 (p0) cc_final: 0.8789 (p0) REVERT: B 213 MET cc_start: 0.8117 (ttt) cc_final: 0.7848 (ttm) REVERT: B 245 LEU cc_start: 0.9100 (tt) cc_final: 0.8666 (mm) REVERT: C 67 LEU cc_start: 0.9461 (mm) cc_final: 0.9229 (pp) REVERT: C 91 HIS cc_start: 0.9297 (m90) cc_final: 0.8853 (m90) REVERT: C 184 MET cc_start: 0.9459 (ppp) cc_final: 0.9175 (ppp) REVERT: C 186 PHE cc_start: 0.9260 (p90) cc_final: 0.8807 (p90) REVERT: D 77 TYR cc_start: 0.9350 (t80) cc_final: 0.9056 (t80) REVERT: D 118 MET cc_start: 0.8752 (mmp) cc_final: 0.8494 (mmp) REVERT: D 144 LEU cc_start: 0.9427 (mt) cc_final: 0.8894 (pp) REVERT: D 176 MET cc_start: 0.9600 (tmm) cc_final: 0.9227 (tmm) REVERT: D 179 HIS cc_start: 0.9535 (t-90) cc_final: 0.9221 (t70) REVERT: E 14 PHE cc_start: 0.8724 (m-80) cc_final: 0.8516 (m-80) REVERT: E 22 ASP cc_start: 0.9852 (t0) cc_final: 0.9585 (p0) REVERT: E 144 LEU cc_start: 0.9276 (mt) cc_final: 0.8900 (pp) REVERT: E 169 GLU cc_start: 0.8844 (tt0) cc_final: 0.8538 (tt0) REVERT: E 176 MET cc_start: 0.9547 (ptp) cc_final: 0.9175 (tmm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.0867 time to fit residues: 24.8153 Evaluate side-chains 172 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 84 optimal weight: 0.0060 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 5 optimal weight: 0.0270 chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 HIS ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.047039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.034394 restraints weight = 44385.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.035538 restraints weight = 30222.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.036393 restraints weight = 22883.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.037044 restraints weight = 18561.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.037540 restraints weight = 15828.232| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7050 Z= 0.133 Angle : 0.772 9.044 9594 Z= 0.364 Chirality : 0.045 0.280 1216 Planarity : 0.006 0.086 1180 Dihedral : 6.192 57.363 974 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.69 % 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: 1.23 (0.29), residues: 910 helix: 1.65 (0.22), residues: 558 sheet: 1.24 (0.57), residues: 92 loop : -1.20 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 48 TYR 0.016 0.002 TYR B 114 PHE 0.017 0.002 PHE C 231 TRP 0.006 0.001 TRP C 145 HIS 0.012 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 7050) covalent geometry : angle 0.77197 / 0.36 ( 9594) hydrogen bonds : bond 0.03943 / 2.61 ( 439) hydrogen bonds : angle 4.54203 / 3.28 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 34 PHE cc_start: 0.9404 (m-80) cc_final: 0.9197 (m-80) REVERT: B 89 MET cc_start: 0.9546 (mmp) cc_final: 0.9286 (mmm) REVERT: B 91 HIS cc_start: 0.9510 (m-70) cc_final: 0.9070 (m90) REVERT: B 104 MET cc_start: 0.9373 (tpt) cc_final: 0.8915 (tpp) REVERT: B 186 PHE cc_start: 0.9087 (p90) cc_final: 0.8599 (p90) REVERT: B 231 PHE cc_start: 0.9478 (t80) cc_final: 0.9221 (t80) REVERT: B 245 LEU cc_start: 0.9564 (tt) cc_final: 0.8959 (mm) REVERT: C 40 HIS cc_start: 0.9575 (m90) cc_final: 0.9324 (m90) REVERT: C 67 LEU cc_start: 0.9675 (mm) cc_final: 0.9384 (pp) REVERT: C 91 HIS cc_start: 0.9364 (m90) cc_final: 0.9029 (m90) REVERT: C 104 MET cc_start: 0.8468 (mmp) cc_final: 0.7726 (tpp) REVERT: C 156 ASP cc_start: 0.9574 (p0) cc_final: 0.9341 (p0) REVERT: C 159 PHE cc_start: 0.9139 (t80) cc_final: 0.8888 (t80) REVERT: C 204 ARG cc_start: 0.9422 (tpt90) cc_final: 0.9001 (tpp-160) REVERT: C 222 MET cc_start: 0.9234 (ppp) cc_final: 0.8973 (ppp) REVERT: D 84 LEU cc_start: 0.9346 (tp) cc_final: 0.9009 (tp) REVERT: D 118 MET cc_start: 0.9488 (mmp) cc_final: 0.9180 (mmp) REVERT: D 142 LEU cc_start: 0.9794 (mm) cc_final: 0.9586 (pp) REVERT: D 144 LEU cc_start: 0.9511 (mt) cc_final: 0.8798 (pp) REVERT: D 176 MET cc_start: 0.9568 (tmm) cc_final: 0.8988 (tmm) REVERT: D 179 HIS cc_start: 0.9273 (t-90) cc_final: 0.8912 (t70) REVERT: E 22 ASP cc_start: 0.9773 (t0) cc_final: 0.9322 (p0) REVERT: E 51 LEU cc_start: 0.9754 (mt) cc_final: 0.9406 (pp) REVERT: E 144 LEU cc_start: 0.9501 (mt) cc_final: 0.9113 (pp) REVERT: E 161 ASP cc_start: 0.9585 (m-30) cc_final: 0.9308 (m-30) REVERT: E 169 GLU cc_start: 0.9033 (tt0) cc_final: 0.8664 (tt0) REVERT: E 176 MET cc_start: 0.9485 (ptp) cc_final: 0.9148 (ptp) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.0839 time to fit residues: 24.3796 Evaluate side-chains 177 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 52 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.046672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.033958 restraints weight = 45099.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.035052 restraints weight = 31064.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.035872 restraints weight = 23702.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.036505 restraints weight = 19342.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.036990 restraints weight = 16533.313| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7050 Z= 0.134 Angle : 0.727 8.356 9594 Z= 0.351 Chirality : 0.044 0.197 1216 Planarity : 0.006 0.084 1180 Dihedral : 6.075 56.594 974 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.26 % Allowed : 2.49 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.46 % 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: 1.16 (0.29), residues: 910 helix: 1.55 (0.22), residues: 558 sheet: 1.19 (0.57), residues: 92 loop : -1.09 (0.42), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 48 TYR 0.015 0.002 TYR C 114 PHE 0.010 0.002 PHE C 25 TRP 0.045 0.003 TRP B 143 HIS 0.003 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 7050) covalent geometry : angle 0.72694 / 0.35 ( 9594) hydrogen bonds : bond 0.03713 / 2.46 ( 439) hydrogen bonds : angle 4.46657 / 3.22 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 206 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 ASP cc_start: 0.9421 (m-30) cc_final: 0.9145 (m-30) REVERT: B 89 MET cc_start: 0.9552 (mmp) cc_final: 0.9324 (mmm) REVERT: B 91 HIS cc_start: 0.9554 (m-70) cc_final: 0.9128 (m90) REVERT: B 104 MET cc_start: 0.9357 (tpt) cc_final: 0.8912 (tpp) REVERT: B 151 MET cc_start: 0.9724 (tmm) cc_final: 0.9504 (tmm) REVERT: B 156 ASP cc_start: 0.9455 (p0) cc_final: 0.9124 (p0) REVERT: B 245 LEU cc_start: 0.9580 (tt) cc_final: 0.8996 (mm) REVERT: C 40 HIS cc_start: 0.9576 (m90) cc_final: 0.9306 (m90) REVERT: C 67 LEU cc_start: 0.9690 (mm) cc_final: 0.9395 (pp) REVERT: C 91 HIS cc_start: 0.9409 (m90) cc_final: 0.9067 (m90) REVERT: C 118 ASP cc_start: 0.9357 (t70) cc_final: 0.9078 (t0) REVERT: C 159 PHE cc_start: 0.9207 (t80) cc_final: 0.8900 (t80) REVERT: C 222 MET cc_start: 0.9249 (ppp) cc_final: 0.9010 (ppp) REVERT: D 84 LEU cc_start: 0.9380 (tp) cc_final: 0.9086 (tp) REVERT: D 118 MET cc_start: 0.9508 (mmp) cc_final: 0.9172 (mmp) REVERT: D 142 LEU cc_start: 0.9802 (mm) cc_final: 0.9567 (pp) REVERT: D 176 MET cc_start: 0.9507 (tmm) cc_final: 0.9162 (tmm) REVERT: D 179 HIS cc_start: 0.9238 (t-90) cc_final: 0.8900 (t70) REVERT: E 14 PHE cc_start: 0.9732 (t80) cc_final: 0.9402 (t80) REVERT: E 51 LEU cc_start: 0.9775 (mt) cc_final: 0.9458 (pp) REVERT: E 144 LEU cc_start: 0.9473 (mt) cc_final: 0.9073 (pp) REVERT: E 169 GLU cc_start: 0.9003 (tt0) cc_final: 0.8607 (tt0) REVERT: E 176 MET cc_start: 0.9468 (ptp) cc_final: 0.9226 (ptp) outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.0861 time to fit residues: 23.6348 Evaluate side-chains 172 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 81 optimal weight: 30.0000 chunk 37 optimal weight: 0.0000 chunk 1 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 HIS ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN E 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.053808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.037792 restraints weight = 44123.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.039329 restraints weight = 28313.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.040471 restraints weight = 20597.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.041360 restraints weight = 16230.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.042053 restraints weight = 13428.123| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7050 Z= 0.124 Angle : 0.737 8.433 9594 Z= 0.353 Chirality : 0.045 0.391 1216 Planarity : 0.006 0.085 1180 Dihedral : 6.051 55.352 974 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.46 % 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: 1.08 (0.29), residues: 910 helix: 1.49 (0.22), residues: 558 sheet: 1.30 (0.58), residues: 92 loop : -1.20 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 48 TYR 0.017 0.001 TYR C 114 PHE 0.016 0.002 PHE C 231 TRP 0.021 0.002 TRP B 143 HIS 0.008 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 7050) covalent geometry : angle 0.73685 / 0.35 ( 9594) hydrogen bonds : bond 0.03561 / 2.35 ( 439) hydrogen bonds : angle 4.42866 / 3.18 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 LEU cc_start: 0.9217 (tp) cc_final: 0.8985 (tp) REVERT: B 89 MET cc_start: 0.9501 (mmp) cc_final: 0.9298 (mmm) REVERT: B 91 HIS cc_start: 0.9548 (m-70) cc_final: 0.9165 (m90) REVERT: B 104 MET cc_start: 0.9476 (tpt) cc_final: 0.9000 (tpp) REVERT: B 156 ASP cc_start: 0.9525 (p0) cc_final: 0.9126 (p0) REVERT: B 213 MET cc_start: 0.9219 (ttt) cc_final: 0.8726 (ttm) REVERT: C 40 HIS cc_start: 0.9602 (m90) cc_final: 0.9311 (m90) REVERT: C 67 LEU cc_start: 0.9675 (mm) cc_final: 0.9378 (pp) REVERT: C 91 HIS cc_start: 0.9461 (m90) cc_final: 0.9050 (m90) REVERT: C 104 MET cc_start: 0.8348 (mmp) cc_final: 0.7580 (tpp) REVERT: C 112 MET cc_start: 0.9623 (tpt) cc_final: 0.9405 (tpp) REVERT: C 159 PHE cc_start: 0.9318 (t80) cc_final: 0.9025 (t80) REVERT: C 222 MET cc_start: 0.9144 (ppp) cc_final: 0.8924 (ppp) REVERT: D 77 TYR cc_start: 0.9355 (t80) cc_final: 0.9154 (t80) REVERT: D 118 MET cc_start: 0.9361 (mmp) cc_final: 0.9086 (mmm) REVERT: D 176 MET cc_start: 0.9475 (tmm) cc_final: 0.9144 (tmm) REVERT: D 179 HIS cc_start: 0.9342 (t-90) cc_final: 0.9020 (t70) REVERT: E 14 PHE cc_start: 0.9828 (t80) cc_final: 0.9527 (t80) REVERT: E 51 LEU cc_start: 0.9793 (mt) cc_final: 0.9488 (pp) REVERT: E 169 GLU cc_start: 0.8995 (tt0) cc_final: 0.8601 (tt0) REVERT: E 176 MET cc_start: 0.9570 (ptp) cc_final: 0.9271 (tmm) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.0856 time to fit residues: 23.6246 Evaluate side-chains 174 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 HIS E 39 ASN ** E 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.041474 restraints weight = 51886.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.042606 restraints weight = 35071.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.043471 restraints weight = 26304.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.044131 restraints weight = 21023.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.044556 restraints weight = 17620.541| |-----------------------------------------------------------------------------| r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7050 Z= 0.157 Angle : 0.744 8.040 9594 Z= 0.363 Chirality : 0.044 0.334 1216 Planarity : 0.006 0.082 1180 Dihedral : 5.982 54.844 974 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.46 % 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: 1.04 (0.29), residues: 910 helix: 1.42 (0.22), residues: 558 sheet: 1.37 (0.58), residues: 92 loop : -1.16 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 30 TYR 0.018 0.002 TYR B 114 PHE 0.014 0.002 PHE B 25 TRP 0.018 0.001 TRP C 143 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 7050) covalent geometry : angle 0.74362 / 0.36 ( 9594) hydrogen bonds : bond 0.03609 / 2.39 ( 439) hydrogen bonds : angle 4.63873 / 3.37 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 HIS cc_start: 0.9504 (m-70) cc_final: 0.9065 (m90) REVERT: B 104 MET cc_start: 0.9373 (tpt) cc_final: 0.8912 (tpp) REVERT: B 156 ASP cc_start: 0.9467 (p0) cc_final: 0.9136 (p0) REVERT: B 173 MET cc_start: 0.9127 (mtp) cc_final: 0.8600 (ttt) REVERT: B 213 MET cc_start: 0.9259 (ttt) cc_final: 0.8925 (ttt) REVERT: B 231 PHE cc_start: 0.9579 (t80) cc_final: 0.9356 (t80) REVERT: C 25 PHE cc_start: 0.9023 (m-80) cc_final: 0.8782 (m-80) REVERT: C 40 HIS cc_start: 0.9577 (m90) cc_final: 0.9320 (m90) REVERT: C 67 LEU cc_start: 0.9729 (mm) cc_final: 0.9478 (pp) REVERT: C 118 ASP cc_start: 0.9369 (t0) cc_final: 0.9030 (t0) REVERT: C 119 LEU cc_start: 0.9810 (mp) cc_final: 0.9571 (tp) REVERT: D 84 LEU cc_start: 0.9472 (tp) cc_final: 0.9262 (tp) REVERT: D 125 GLU cc_start: 0.9732 (mp0) cc_final: 0.9376 (pm20) REVERT: D 176 MET cc_start: 0.9521 (tmm) cc_final: 0.9129 (tmm) REVERT: D 179 HIS cc_start: 0.9250 (t-90) cc_final: 0.8953 (t70) REVERT: E 14 PHE cc_start: 0.9771 (t80) cc_final: 0.9466 (t80) REVERT: E 169 GLU cc_start: 0.9053 (tt0) cc_final: 0.8652 (tt0) REVERT: E 176 MET cc_start: 0.9498 (ptp) cc_final: 0.9246 (tmm) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.0797 time to fit residues: 20.6396 Evaluate side-chains 167 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 30 optimal weight: 0.0370 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 89 optimal weight: 0.0040 chunk 36 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 67 optimal weight: 50.0000 chunk 41 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 overall best weight: 1.8074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 HIS ** E 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.046300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.033781 restraints weight = 45753.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.034942 restraints weight = 30458.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.035818 restraints weight = 22759.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.036494 restraints weight = 18278.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.037006 restraints weight = 15395.666| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7050 Z= 0.122 Angle : 0.771 8.783 9594 Z= 0.364 Chirality : 0.046 0.310 1216 Planarity : 0.006 0.088 1180 Dihedral : 5.913 54.601 974 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.34 % 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: 1.04 (0.29), residues: 910 helix: 1.42 (0.22), residues: 558 sheet: 1.37 (0.57), residues: 92 loop : -1.15 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 204 TYR 0.019 0.001 TYR C 114 PHE 0.017 0.002 PHE C 231 TRP 0.015 0.001 TRP C 143 HIS 0.003 0.001 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 7050) covalent geometry : angle 0.77088 / 0.36 ( 9594) hydrogen bonds : bond 0.03470 / 2.29 ( 439) hydrogen bonds : angle 4.44722 / 3.23 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 HIS cc_start: 0.9416 (m90) cc_final: 0.9216 (m-70) REVERT: B 43 LEU cc_start: 0.9292 (tp) cc_final: 0.8929 (tp) REVERT: B 91 HIS cc_start: 0.9492 (m-70) cc_final: 0.9096 (m90) REVERT: B 104 MET cc_start: 0.9427 (tpt) cc_final: 0.8924 (tpp) REVERT: B 151 MET cc_start: 0.9768 (tmm) cc_final: 0.9407 (ptm) REVERT: B 156 ASP cc_start: 0.9520 (p0) cc_final: 0.9149 (p0) REVERT: B 173 MET cc_start: 0.9126 (mtp) cc_final: 0.8491 (ttt) REVERT: B 213 MET cc_start: 0.9273 (ttt) cc_final: 0.8775 (ttm) REVERT: B 231 PHE cc_start: 0.9614 (t80) cc_final: 0.9177 (t80) REVERT: B 245 LEU cc_start: 0.9574 (tt) cc_final: 0.8964 (mm) REVERT: C 25 PHE cc_start: 0.9151 (m-80) cc_final: 0.8926 (m-80) REVERT: C 40 HIS cc_start: 0.9546 (m90) cc_final: 0.9252 (m90) REVERT: C 67 LEU cc_start: 0.9735 (mm) cc_final: 0.9468 (pp) REVERT: C 91 HIS cc_start: 0.9489 (m-70) cc_final: 0.9068 (m90) REVERT: C 104 MET cc_start: 0.8396 (mmp) cc_final: 0.7674 (tpp) REVERT: C 112 MET cc_start: 0.9585 (tpt) cc_final: 0.9377 (tpp) REVERT: C 118 ASP cc_start: 0.9417 (t0) cc_final: 0.9143 (t0) REVERT: C 159 PHE cc_start: 0.9269 (t80) cc_final: 0.9019 (t80) REVERT: C 204 ARG cc_start: 0.9448 (tpt90) cc_final: 0.8940 (tpm170) REVERT: C 213 MET cc_start: 0.9403 (tpt) cc_final: 0.9103 (tpt) REVERT: D 84 LEU cc_start: 0.9402 (tp) cc_final: 0.9171 (tp) REVERT: D 118 MET cc_start: 0.9450 (mmp) cc_final: 0.9016 (mmp) REVERT: D 125 GLU cc_start: 0.9770 (mp0) cc_final: 0.9519 (mp0) REVERT: D 176 MET cc_start: 0.9464 (tmm) cc_final: 0.9116 (tmm) REVERT: D 179 HIS cc_start: 0.9223 (t-90) cc_final: 0.8923 (t70) REVERT: E 14 PHE cc_start: 0.9788 (t80) cc_final: 0.9492 (t80) REVERT: E 51 LEU cc_start: 0.9797 (mt) cc_final: 0.9496 (pp) REVERT: E 169 GLU cc_start: 0.9066 (tt0) cc_final: 0.8663 (tt0) REVERT: E 176 MET cc_start: 0.9551 (ptp) cc_final: 0.9211 (tmm) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.0838 time to fit residues: 21.8066 Evaluate side-chains 167 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 85 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 0.0980 chunk 81 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 91 HIS ** E 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.045915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.033576 restraints weight = 46623.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.034682 restraints weight = 31573.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.035537 restraints weight = 23896.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.036205 restraints weight = 19221.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.036712 restraints weight = 16218.909| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7050 Z= 0.141 Angle : 0.739 8.228 9594 Z= 0.356 Chirality : 0.045 0.289 1216 Planarity : 0.006 0.087 1180 Dihedral : 5.790 54.229 974 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.23 % 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: 0.93 (0.29), residues: 910 helix: 1.33 (0.22), residues: 560 sheet: 1.30 (0.57), residues: 92 loop : -1.20 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 204 TYR 0.018 0.002 TYR C 114 PHE 0.013 0.001 PHE C 34 TRP 0.014 0.001 TRP C 143 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 7050) covalent geometry : angle 0.73949 / 0.36 ( 9594) hydrogen bonds : bond 0.03439 / 2.29 ( 439) hydrogen bonds : angle 4.53473 / 3.31 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 PHE cc_start: 0.9428 (m-10) cc_final: 0.9192 (m-80) REVERT: B 30 ARG cc_start: 0.9452 (mtm-85) cc_final: 0.9000 (ptp90) REVERT: B 43 LEU cc_start: 0.9341 (tp) cc_final: 0.8992 (tp) REVERT: B 91 HIS cc_start: 0.9499 (m-70) cc_final: 0.9109 (m90) REVERT: B 104 MET cc_start: 0.9426 (tpt) cc_final: 0.8923 (tpp) REVERT: B 151 MET cc_start: 0.9788 (tmm) cc_final: 0.9378 (ptm) REVERT: B 156 ASP cc_start: 0.9523 (p0) cc_final: 0.9179 (p0) REVERT: B 173 MET cc_start: 0.9173 (mtp) cc_final: 0.8642 (ttt) REVERT: B 213 MET cc_start: 0.9304 (ttt) cc_final: 0.8989 (ttt) REVERT: B 222 MET cc_start: 0.9785 (ptp) cc_final: 0.9424 (ptp) REVERT: B 231 PHE cc_start: 0.9632 (t80) cc_final: 0.9177 (t80) REVERT: C 25 PHE cc_start: 0.9072 (m-80) cc_final: 0.8848 (m-80) REVERT: C 40 HIS cc_start: 0.9557 (m90) cc_final: 0.9259 (m90) REVERT: C 43 LEU cc_start: 0.9556 (tp) cc_final: 0.9341 (tp) REVERT: C 104 MET cc_start: 0.8449 (mmp) cc_final: 0.7715 (tpp) REVERT: D 118 MET cc_start: 0.9473 (mmp) cc_final: 0.9125 (mmp) REVERT: D 125 GLU cc_start: 0.9763 (mp0) cc_final: 0.9387 (pm20) REVERT: D 176 MET cc_start: 0.9450 (tmm) cc_final: 0.9121 (tmm) REVERT: D 179 HIS cc_start: 0.9209 (t-90) cc_final: 0.8916 (t70) REVERT: E 14 PHE cc_start: 0.9782 (t80) cc_final: 0.9492 (t80) REVERT: E 169 GLU cc_start: 0.9058 (tt0) cc_final: 0.8652 (tt0) REVERT: E 176 MET cc_start: 0.9514 (ptp) cc_final: 0.9203 (tmm) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.0732 time to fit residues: 18.7962 Evaluate side-chains 159 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 59 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 HIS C 91 HIS E 39 ASN ** E 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.045151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.033066 restraints weight = 47537.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.034170 restraints weight = 32187.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.035011 restraints weight = 24123.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.035651 restraints weight = 19430.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.036140 restraints weight = 16384.362| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.7225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7050 Z= 0.177 Angle : 0.790 11.141 9594 Z= 0.388 Chirality : 0.048 0.441 1216 Planarity : 0.006 0.090 1180 Dihedral : 5.813 53.487 974 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.29), residues: 910 helix: 1.23 (0.22), residues: 560 sheet: 1.17 (0.56), residues: 92 loop : -1.27 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 48 TYR 0.018 0.002 TYR C 114 PHE 0.028 0.002 PHE C 159 TRP 0.014 0.002 TRP B 143 HIS 0.008 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.18 ( 7050) covalent geometry : angle 0.79001 / 0.39 ( 9594) hydrogen bonds : bond 0.03623 / 2.46 ( 439) hydrogen bonds : angle 4.66494 / 3.41 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 PHE cc_start: 0.9153 (m-10) cc_final: 0.8931 (m-80) REVERT: B 43 LEU cc_start: 0.9436 (tp) cc_final: 0.9179 (tp) REVERT: B 91 HIS cc_start: 0.9521 (m-70) cc_final: 0.9143 (m90) REVERT: B 104 MET cc_start: 0.9435 (tpt) cc_final: 0.8939 (tpp) REVERT: B 148 LEU cc_start: 0.9823 (tp) cc_final: 0.9582 (tp) REVERT: B 151 MET cc_start: 0.9730 (tmm) cc_final: 0.9444 (ptm) REVERT: B 156 ASP cc_start: 0.9529 (p0) cc_final: 0.9109 (p0) REVERT: B 173 MET cc_start: 0.9217 (mtp) cc_final: 0.8820 (ttm) REVERT: B 213 MET cc_start: 0.9322 (ttt) cc_final: 0.8986 (ttt) REVERT: B 231 PHE cc_start: 0.9694 (t80) cc_final: 0.9210 (t80) REVERT: C 25 PHE cc_start: 0.9073 (m-80) cc_final: 0.8844 (m-80) REVERT: C 40 HIS cc_start: 0.9577 (m90) cc_final: 0.9293 (m90) REVERT: C 43 LEU cc_start: 0.9556 (tp) cc_final: 0.9345 (tp) REVERT: C 159 PHE cc_start: 0.9317 (t80) cc_final: 0.9108 (t80) REVERT: C 204 ARG cc_start: 0.9544 (tpt90) cc_final: 0.8930 (tpm170) REVERT: C 213 MET cc_start: 0.9374 (tpt) cc_final: 0.8918 (tpt) REVERT: D 77 TYR cc_start: 0.9242 (t80) cc_final: 0.9007 (t80) REVERT: D 118 MET cc_start: 0.9522 (mmp) cc_final: 0.9272 (mmm) REVERT: D 125 GLU cc_start: 0.9783 (mp0) cc_final: 0.9409 (pm20) REVERT: D 176 MET cc_start: 0.9483 (tmm) cc_final: 0.9169 (tmm) REVERT: D 179 HIS cc_start: 0.9205 (t-90) cc_final: 0.8940 (t70) REVERT: E 14 PHE cc_start: 0.9771 (t80) cc_final: 0.9505 (t80) REVERT: E 53 LEU cc_start: 0.9500 (tt) cc_final: 0.9257 (mp) REVERT: E 169 GLU cc_start: 0.9066 (tt0) cc_final: 0.8667 (tt0) REVERT: E 176 MET cc_start: 0.9484 (ptp) cc_final: 0.9206 (tmm) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.0735 time to fit residues: 18.6611 Evaluate side-chains 155 residues out of total 762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 64 optimal weight: 30.0000 chunk 84 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 0.0670 chunk 83 optimal weight: 0.0770 chunk 21 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 88 optimal weight: 30.0000 chunk 65 optimal weight: 10.0000 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.047510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.034755 restraints weight = 45472.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.035975 restraints weight = 30299.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.036892 restraints weight = 22647.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.037585 restraints weight = 18136.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.038124 restraints weight = 15233.029| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.7359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7050 Z= 0.128 Angle : 0.816 9.516 9594 Z= 0.380 Chirality : 0.047 0.397 1216 Planarity : 0.006 0.093 1180 Dihedral : 5.647 53.894 974 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.23 % 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: 0.89 (0.29), residues: 910 helix: 1.32 (0.22), residues: 560 sheet: 1.28 (0.57), residues: 92 loop : -1.26 (0.42), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 48 TYR 0.021 0.002 TYR C 114 PHE 0.025 0.002 PHE C 159 TRP 0.015 0.001 TRP B 143 HIS 0.003 0.000 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 7050) covalent geometry : angle 0.81629 / 0.38 ( 9594) hydrogen bonds : bond 0.03384 / 2.25 ( 439) hydrogen bonds : angle 4.45383 / 3.24 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1229.19 seconds wall clock time: 21 minutes 54.87 seconds (1314.87 seconds total)