Starting phenix.real_space_refine on Sun Aug 24 09:11:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8odt_16816/08_2025/8odt_16816.cif Found real_map, /net/cci-nas-00/data/ceres_data/8odt_16816/08_2025/8odt_16816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8odt_16816/08_2025/8odt_16816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8odt_16816/08_2025/8odt_16816.map" model { file = "/net/cci-nas-00/data/ceres_data/8odt_16816/08_2025/8odt_16816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8odt_16816/08_2025/8odt_16816.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.016 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: 5 Type Number sf(0) Gaussians S 47 5.16 5 C 5998 2.51 5 N 1589 2.21 5 O 1670 1.98 5 H 9496 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18800 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3634 Classifications: {'peptide': 230} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 224} Chain: "B" Number of atoms: 3634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3634 Classifications: {'peptide': 230} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 224} Chain: "C" Number of atoms: 3634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3634 Classifications: {'peptide': 230} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 224} Chain: "D" Number of atoms: 3634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3634 Classifications: {'peptide': 230} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 224} Chain: "E" Number of atoms: 3634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3634 Classifications: {'peptide': 230} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 224} Chain: "F" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 349 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "G" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 281 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Time building chain proxies: 3.71, per 1000 atoms: 0.20 Number of scatterers: 18800 At special positions: 0 Unit cell: (88.192, 95.68, 128.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 O 1670 8.00 N 1589 7.00 C 5998 6.00 H 9496 1.00 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: 1.77 Conformation dependent library (CDL) restraints added in 653.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2226 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 92.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 14 through 57 Processing helix chain 'A' and resid 61 through 72 removed outlier: 3.764A pdb=" N LYS A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 removed outlier: 3.553A pdb=" N LEU A 76 " --> pdb=" O ARG A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 77 through 98 Processing helix chain 'A' and resid 100 through 125 Processing helix chain 'A' and resid 126 through 157 Proline residue: A 138 - end of helix removed outlier: 3.698A pdb=" N GLY A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 167 through 229 removed outlier: 4.467A pdb=" N ALA A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Proline residue: A 187 - end of helix Processing helix chain 'B' and resid 6 through 13 removed outlier: 3.875A pdb=" N PHE B 10 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 57 Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 72 through 76 removed outlier: 3.866A pdb=" N LEU B 76 " --> pdb=" O ARG B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 97 removed outlier: 3.599A pdb=" N GLN B 81 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 125 Processing helix chain 'B' and resid 126 through 157 Proline residue: B 138 - end of helix removed outlier: 3.613A pdb=" N GLY B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 229 removed outlier: 3.826A pdb=" N ILE B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Proline residue: B 187 - end of helix removed outlier: 3.606A pdb=" N LYS B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 13 removed outlier: 3.614A pdb=" N LYS C 12 " --> pdb=" O ASP C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 57 Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.988A pdb=" N LYS C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 77 through 98 Processing helix chain 'C' and resid 100 through 125 Processing helix chain 'C' and resid 126 through 158 Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 167 through 228 Proline residue: C 187 - end of helix removed outlier: 3.612A pdb=" N ASN C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 12 Processing helix chain 'D' and resid 14 through 57 Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 72 through 77 removed outlier: 7.457A pdb=" N THR D 77 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 98 Processing helix chain 'D' and resid 100 through 125 Processing helix chain 'D' and resid 126 through 157 Proline residue: D 138 - end of helix removed outlier: 3.709A pdb=" N GLY D 157 " --> pdb=" O PHE D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 166 removed outlier: 3.660A pdb=" N MET D 166 " --> pdb=" O THR D 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 163 through 166' Processing helix chain 'D' and resid 167 through 229 removed outlier: 3.718A pdb=" N ILE D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Proline residue: D 187 - end of helix removed outlier: 3.566A pdb=" N LYS D 229 " --> pdb=" O SER D 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 13 removed outlier: 3.825A pdb=" N LEU E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 58 Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 72 through 77 removed outlier: 3.607A pdb=" N LEU E 76 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR E 77 " --> pdb=" O ASP E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 98 Processing helix chain 'E' and resid 100 through 125 removed outlier: 3.525A pdb=" N THR E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 157 Proline residue: E 138 - end of helix Processing helix chain 'E' and resid 163 through 166 Processing helix chain 'E' and resid 167 through 229 Proline residue: E 187 - end of helix removed outlier: 3.555A pdb=" N LYS E 229 " --> pdb=" O SER E 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 35 removed outlier: 3.607A pdb=" N ILE F 31 " --> pdb=" O VAL F 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.683A pdb=" N LEU G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2562 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: 4.97 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 9496 1.03 - 1.23: 10 1.23 - 1.42: 3928 1.42 - 1.62: 5444 1.62 - 1.82: 94 Bond restraints: 18972 Sorted by residual: bond pdb=" CA ILE D 127 " pdb=" CB ILE D 127 " ideal model delta sigma weight residual 1.539 1.529 0.010 5.40e-03 3.43e+04 3.60e+00 bond pdb=" CA LEU B 164 " pdb=" CB LEU B 164 " ideal model delta sigma weight residual 1.523 1.544 -0.021 1.21e-02 6.83e+03 2.89e+00 bond pdb=" CA ILE E 127 " pdb=" CB ILE E 127 " ideal model delta sigma weight residual 1.539 1.530 0.009 5.40e-03 3.43e+04 2.79e+00 bond pdb=" CG LEU B 175 " pdb=" CD2 LEU B 175 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.26e+00 bond pdb=" C ILE C 186 " pdb=" O ILE C 186 " ideal model delta sigma weight residual 1.242 1.254 -0.012 8.60e-03 1.35e+04 1.94e+00 ... (remaining 18967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.19: 34295 6.19 - 12.38: 2 12.38 - 18.57: 0 18.57 - 24.75: 0 24.75 - 30.94: 5 Bond angle restraints: 34302 Sorted by residual: angle pdb=" NE ARG A 92 " pdb=" CD ARG A 92 " pdb=" HD2 ARG A 92 " ideal model delta sigma weight residual 108.00 77.06 30.94 3.00e+00 1.11e-01 1.06e+02 angle pdb=" CG ARG A 92 " pdb=" CD ARG A 92 " pdb=" HD2 ARG A 92 " ideal model delta sigma weight residual 109.00 78.90 30.10 3.00e+00 1.11e-01 1.01e+02 angle pdb=" NE ARG A 92 " pdb=" CD ARG A 92 " pdb=" HD3 ARG A 92 " ideal model delta sigma weight residual 108.00 79.10 28.90 3.00e+00 1.11e-01 9.28e+01 angle pdb=" HD2 ARG A 92 " pdb=" CD ARG A 92 " pdb=" HD3 ARG A 92 " ideal model delta sigma weight residual 110.00 136.32 -26.32 3.00e+00 1.11e-01 7.70e+01 angle pdb=" CG ARG A 92 " pdb=" CD ARG A 92 " pdb=" HD3 ARG A 92 " ideal model delta sigma weight residual 109.00 83.70 25.30 3.00e+00 1.11e-01 7.11e+01 ... (remaining 34297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8026 17.94 - 35.87: 519 35.87 - 53.81: 220 53.81 - 71.75: 58 71.75 - 89.69: 3 Dihedral angle restraints: 8826 sinusoidal: 4769 harmonic: 4057 Sorted by residual: dihedral pdb=" CA VAL F 24 " pdb=" C VAL F 24 " pdb=" N LEU F 25 " pdb=" CA LEU F 25 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLN B 165 " pdb=" C GLN B 165 " pdb=" N MET B 166 " pdb=" CA MET B 166 " ideal model delta harmonic sigma weight residual -180.00 -157.57 -22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA MET B 166 " pdb=" C MET B 166 " pdb=" N VAL B 167 " pdb=" CA VAL B 167 " ideal model delta harmonic sigma weight residual 180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 8823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 906 0.027 - 0.055: 338 0.055 - 0.082: 158 0.082 - 0.110: 66 0.110 - 0.137: 10 Chirality restraints: 1478 Sorted by residual: chirality pdb=" CB VAL A 146 " pdb=" CA VAL A 146 " pdb=" CG1 VAL A 146 " pdb=" CG2 VAL A 146 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE B 149 " pdb=" N ILE B 149 " pdb=" C ILE B 149 " pdb=" CB ILE B 149 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA VAL C 159 " pdb=" N VAL C 159 " pdb=" C VAL C 159 " pdb=" CB VAL C 159 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 1475 not shown) Planarity restraints: 2782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 186 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO D 187 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 187 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 187 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 186 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO E 187 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 187 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 187 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 29 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C LEU F 29 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU F 29 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU F 30 " 0.010 2.00e-02 2.50e+03 ... (remaining 2779 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.85: 68 1.85 - 2.53: 15986 2.53 - 3.22: 62646 3.22 - 3.91: 73415 3.91 - 4.60: 117169 Nonbonded interactions: 269284 Sorted by model distance: nonbonded pdb="HD22 ASN E 97 " pdb=" HE2 HIS E 99 " model vdw 1.158 2.100 nonbonded pdb=" O TRP A 147 " pdb=" HD1 HIS A 151 " model vdw 1.444 2.450 nonbonded pdb=" O ILE C 35 " pdb=" HG1 THR C 39 " model vdw 1.547 2.450 nonbonded pdb=" O GLY E 131 " pdb=" HG SER E 135 " model vdw 1.553 2.450 nonbonded pdb=" O MET D 210 " pdb=" HG1 THR D 214 " model vdw 1.555 2.450 ... (remaining 269279 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.980 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 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 0.050 9476 Z= 0.291 Angle : 0.709 10.181 12808 Z= 0.424 Chirality : 0.038 0.137 1478 Planarity : 0.005 0.064 1627 Dihedral : 12.865 89.685 3436 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.81 % Favored : 97.10 % Rotamer: Outliers : 3.61 % Allowed : 7.95 % Favored : 88.44 % 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 aren not related in a simple way. whole: 1.77 (0.23), residues: 1174 helix: 1.47 (0.15), residues: 1016 sheet: None (None), residues: 0 loop : -0.49 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 118 TYR 0.020 0.002 TYR A 66 PHE 0.019 0.002 PHE B 183 TRP 0.016 0.002 TRP A 147 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 9476) covalent geometry : angle 0.70869 (12808) hydrogen bonds : bond 0.10683 ( 860) hydrogen bonds : angle 5.80305 ( 2562) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 406 time to evaluate : 0.518 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TRP cc_start: 0.7039 (t60) cc_final: 0.6787 (t60) REVERT: A 211 GLU cc_start: 0.7288 (tt0) cc_final: 0.7015 (mt-10) REVERT: B 28 SER cc_start: 0.3026 (OUTLIER) cc_final: 0.2783 (p) REVERT: B 41 ILE cc_start: 0.9455 (mt) cc_final: 0.9194 (tt) REVERT: B 89 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6276 (tt0) REVERT: B 112 MET cc_start: 0.6692 (mtp) cc_final: 0.6215 (mtp) REVERT: B 197 GLN cc_start: 0.8471 (mt0) cc_final: 0.7665 (tm-30) REVERT: C 20 ILE cc_start: 0.9471 (mt) cc_final: 0.9226 (tp) REVERT: C 42 LEU cc_start: 0.9675 (mt) cc_final: 0.9464 (mt) REVERT: C 164 LEU cc_start: 0.1520 (OUTLIER) cc_final: 0.1155 (tp) REVERT: C 189 VAL cc_start: 0.9309 (t) cc_final: 0.9017 (p) REVERT: C 205 ASN cc_start: 0.9139 (m-40) cc_final: 0.8921 (t0) REVERT: C 210 MET cc_start: 0.9279 (mtm) cc_final: 0.8869 (mtm) REVERT: C 214 THR cc_start: 0.8652 (m) cc_final: 0.8444 (m) REVERT: D 4 MET cc_start: 0.6117 (ttt) cc_final: 0.5611 (ptt) REVERT: D 8 ASP cc_start: 0.9060 (t70) cc_final: 0.8723 (p0) REVERT: D 9 LEU cc_start: 0.9496 (mt) cc_final: 0.9253 (mt) REVERT: D 81 GLN cc_start: 0.9275 (tt0) cc_final: 0.8987 (tt0) REVERT: D 83 PHE cc_start: 0.9524 (t80) cc_final: 0.9238 (t80) REVERT: D 88 LYS cc_start: 0.9264 (tttm) cc_final: 0.9038 (tppt) REVERT: D 118 ARG cc_start: 0.9026 (mtt180) cc_final: 0.8626 (tpp80) REVERT: D 194 ARG cc_start: 0.8823 (mmt180) cc_final: 0.8288 (ttm170) REVERT: E 65 LEU cc_start: 0.9500 (tp) cc_final: 0.9258 (tp) REVERT: E 116 MET cc_start: 0.9031 (ttp) cc_final: 0.8415 (tmm) REVERT: E 120 LEU cc_start: 0.9526 (mt) cc_final: 0.9250 (mt) REVERT: E 129 PHE cc_start: 0.9203 (t80) cc_final: 0.8987 (m-10) REVERT: E 217 LEU cc_start: 0.9437 (mt) cc_final: 0.9135 (mt) REVERT: E 219 ARG cc_start: 0.8905 (ttp-170) cc_final: 0.8686 (ttm-80) REVERT: F 23 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8194 (p0) REVERT: F 33 MET cc_start: 0.0291 (ttp) cc_final: 0.0010 (mtt) outliers start: 35 outliers final: 21 residues processed: 434 average time/residue: 0.2774 time to fit residues: 159.6427 Evaluate side-chains 340 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 316 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN B 205 ASN C 81 GLN C 196 ASN ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 200 ASN E 205 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.191971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.138418 restraints weight = 69908.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.145726 restraints weight = 39860.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.150393 restraints weight = 27083.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.153450 restraints weight = 20894.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.155299 restraints weight = 17679.187| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9476 Z= 0.209 Angle : 0.617 11.184 12808 Z= 0.355 Chirality : 0.038 0.195 1478 Planarity : 0.005 0.058 1627 Dihedral : 4.275 22.363 1276 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.23), residues: 1174 helix: 1.42 (0.15), residues: 1027 sheet: None (None), residues: 0 loop : -0.89 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 219 TYR 0.017 0.002 TYR C 192 PHE 0.031 0.002 PHE C 10 TRP 0.010 0.001 TRP B 147 HIS 0.006 0.002 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9476) covalent geometry : angle 0.61727 (12808) hydrogen bonds : bond 0.05653 ( 860) hydrogen bonds : angle 4.95146 ( 2562) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.486 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2620 (ptm) cc_final: 0.2209 (ptm) REVERT: A 24 LEU cc_start: 0.6702 (mt) cc_final: 0.6465 (mt) REVERT: A 32 TRP cc_start: 0.6809 (t60) cc_final: 0.6575 (t60) REVERT: B 41 ILE cc_start: 0.9503 (mt) cc_final: 0.9245 (tt) REVERT: B 112 MET cc_start: 0.6263 (mtp) cc_final: 0.5823 (mtp) REVERT: B 116 MET cc_start: 0.9191 (ttt) cc_final: 0.8648 (ttm) REVERT: B 123 LEU cc_start: 0.9397 (mt) cc_final: 0.9163 (mt) REVERT: B 127 ILE cc_start: 0.7604 (mt) cc_final: 0.7311 (mm) REVERT: B 197 GLN cc_start: 0.8479 (mt0) cc_final: 0.7513 (tm-30) REVERT: C 20 ILE cc_start: 0.9417 (mt) cc_final: 0.9188 (tp) REVERT: C 53 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8792 (tm-30) REVERT: C 150 MET cc_start: 0.9173 (mtm) cc_final: 0.8813 (mtp) REVERT: D 8 ASP cc_start: 0.8715 (t70) cc_final: 0.8417 (p0) REVERT: D 80 GLU cc_start: 0.8686 (tt0) cc_final: 0.8257 (tt0) REVERT: D 88 LYS cc_start: 0.9191 (tttm) cc_final: 0.8990 (tppt) REVERT: D 140 ILE cc_start: 0.9528 (mm) cc_final: 0.9267 (tp) REVERT: D 207 ASP cc_start: 0.8907 (t70) cc_final: 0.8663 (t0) REVERT: E 65 LEU cc_start: 0.9208 (tp) cc_final: 0.8973 (tp) REVERT: E 98 SER cc_start: 0.7562 (p) cc_final: 0.7279 (t) REVERT: E 116 MET cc_start: 0.8795 (ttp) cc_final: 0.8157 (tmm) REVERT: E 120 LEU cc_start: 0.9296 (mt) cc_final: 0.8895 (mt) REVERT: E 210 MET cc_start: 0.8833 (ttp) cc_final: 0.8537 (ttp) REVERT: E 217 LEU cc_start: 0.9244 (mt) cc_final: 0.8978 (mt) REVERT: F 33 MET cc_start: 0.0738 (ttp) cc_final: 0.0408 (mtt) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.2574 time to fit residues: 130.8208 Evaluate side-chains 333 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 117 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN C 122 ASN C 196 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 196 ASN D 218 HIS E 200 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.196052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.142011 restraints weight = 68489.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.149017 restraints weight = 40180.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.153804 restraints weight = 27493.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.156913 restraints weight = 21214.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.158672 restraints weight = 17848.384| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 9476 Z= 0.274 Angle : 0.655 11.462 12808 Z= 0.384 Chirality : 0.037 0.147 1478 Planarity : 0.005 0.077 1627 Dihedral : 4.344 22.125 1276 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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 aren not related in a simple way. whole: 1.24 (0.23), residues: 1174 helix: 1.14 (0.15), residues: 1027 sheet: None (None), residues: 0 loop : -0.94 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.014 0.002 TYR A 66 PHE 0.024 0.002 PHE C 143 TRP 0.008 0.002 TRP C 147 HIS 0.007 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 9476) covalent geometry : angle 0.65458 (12808) hydrogen bonds : bond 0.05644 ( 860) hydrogen bonds : angle 5.11648 ( 2562) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.600 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: 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: 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: 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: A 1 MET cc_start: 0.2743 (ptm) cc_final: 0.2342 (ptm) REVERT: B 41 ILE cc_start: 0.9521 (mt) cc_final: 0.9274 (tt) REVERT: B 112 MET cc_start: 0.6598 (mtp) cc_final: 0.6208 (mtp) REVERT: B 198 ARG cc_start: 0.6728 (mpt180) cc_final: 0.5820 (mmm160) REVERT: C 150 MET cc_start: 0.9280 (mtm) cc_final: 0.8916 (mtp) REVERT: C 200 ASN cc_start: 0.9155 (m-40) cc_final: 0.8905 (m-40) REVERT: D 88 LYS cc_start: 0.9271 (tttm) cc_final: 0.9051 (tppt) REVERT: D 207 ASP cc_start: 0.9081 (t70) cc_final: 0.8820 (t0) REVERT: E 98 SER cc_start: 0.7760 (p) cc_final: 0.7460 (t) REVERT: E 116 MET cc_start: 0.8964 (ttp) cc_final: 0.8424 (tmm) REVERT: E 211 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8316 (mm-30) REVERT: E 217 LEU cc_start: 0.9294 (mt) cc_final: 0.9024 (mt) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2307 time to fit residues: 111.6072 Evaluate side-chains 308 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 9 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN C 196 ASN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 ASN ** 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 = 0.4672 r_free = 0.4672 target = 0.191154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.136540 restraints weight = 69353.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.143697 restraints weight = 39921.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.148278 restraints weight = 27441.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.151229 restraints weight = 21391.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.153182 restraints weight = 18253.517| |-----------------------------------------------------------------------------| r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9476 Z= 0.183 Angle : 0.588 11.569 12808 Z= 0.334 Chirality : 0.036 0.165 1478 Planarity : 0.005 0.058 1627 Dihedral : 4.233 22.141 1276 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.23), residues: 1174 helix: 1.36 (0.15), residues: 1031 sheet: None (None), residues: 0 loop : -0.79 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 64 TYR 0.018 0.002 TYR D 66 PHE 0.034 0.002 PHE A 143 TRP 0.010 0.001 TRP A 147 HIS 0.007 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9476) covalent geometry : angle 0.58792 (12808) hydrogen bonds : bond 0.05345 ( 860) hydrogen bonds : angle 4.71349 ( 2562) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.511 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: 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: 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: 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: A 1 MET cc_start: 0.2514 (ptm) cc_final: 0.2114 (ptm) REVERT: A 24 LEU cc_start: 0.6597 (mt) cc_final: 0.6301 (mt) REVERT: B 66 TYR cc_start: 0.7617 (t80) cc_final: 0.7368 (t80) REVERT: B 112 MET cc_start: 0.6610 (mtp) cc_final: 0.6265 (mtp) REVERT: B 123 LEU cc_start: 0.9439 (mt) cc_final: 0.9233 (mt) REVERT: B 197 GLN cc_start: 0.8913 (mp10) cc_final: 0.7869 (tm-30) REVERT: C 42 LEU cc_start: 0.9655 (mt) cc_final: 0.9449 (mt) REVERT: C 119 GLU cc_start: 0.9013 (tp30) cc_final: 0.8802 (tp30) REVERT: C 150 MET cc_start: 0.9306 (mtm) cc_final: 0.8927 (mtp) REVERT: C 200 ASN cc_start: 0.9178 (m-40) cc_final: 0.8850 (m-40) REVERT: D 8 ASP cc_start: 0.9272 (t0) cc_final: 0.8731 (p0) REVERT: D 88 LYS cc_start: 0.9327 (tttm) cc_final: 0.9084 (tppt) REVERT: D 119 GLU cc_start: 0.8983 (tp30) cc_final: 0.8713 (tp30) REVERT: E 8 ASP cc_start: 0.9139 (m-30) cc_final: 0.8719 (m-30) REVERT: E 116 MET cc_start: 0.9022 (ttp) cc_final: 0.8502 (tmm) REVERT: E 124 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8920 (mt-10) REVERT: E 211 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8457 (mm-30) REVERT: E 217 LEU cc_start: 0.9298 (mt) cc_final: 0.9031 (mt) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.2162 time to fit residues: 105.4534 Evaluate side-chains 310 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 43 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 196 ASN D 218 HIS ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.182000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.130990 restraints weight = 70637.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.137665 restraints weight = 40512.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.141968 restraints weight = 27697.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.144708 restraints weight = 21481.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.146319 restraints weight = 18269.127| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 9476 Z= 0.344 Angle : 0.725 11.483 12808 Z= 0.431 Chirality : 0.039 0.174 1478 Planarity : 0.006 0.058 1627 Dihedral : 4.661 23.981 1276 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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 aren not related in a simple way. whole: 0.33 (0.23), residues: 1174 helix: 0.52 (0.15), residues: 1033 sheet: None (None), residues: 0 loop : -1.24 (0.51), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 219 TYR 0.017 0.002 TYR A 66 PHE 0.036 0.003 PHE A 143 TRP 0.010 0.002 TRP C 32 HIS 0.007 0.002 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 9476) covalent geometry : angle 0.72523 (12808) hydrogen bonds : bond 0.05810 ( 860) hydrogen bonds : angle 5.46393 ( 2562) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.542 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2631 (ptm) cc_final: 0.2192 (ptm) REVERT: B 66 TYR cc_start: 0.7751 (t80) cc_final: 0.7485 (t80) REVERT: B 112 MET cc_start: 0.6995 (mtp) cc_final: 0.6646 (mtp) REVERT: B 198 ARG cc_start: 0.6900 (mpt180) cc_final: 0.5724 (mmm160) REVERT: C 150 MET cc_start: 0.9392 (mtm) cc_final: 0.9026 (mtp) REVERT: C 200 ASN cc_start: 0.9246 (m-40) cc_final: 0.9020 (m-40) REVERT: D 8 ASP cc_start: 0.9146 (t0) cc_final: 0.8597 (p0) REVERT: D 88 LYS cc_start: 0.9352 (tttm) cc_final: 0.9097 (tppt) REVERT: D 119 GLU cc_start: 0.9062 (tp30) cc_final: 0.8705 (tp30) REVERT: E 8 ASP cc_start: 0.9133 (m-30) cc_final: 0.8865 (m-30) REVERT: E 53 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8377 (mt-10) REVERT: E 98 SER cc_start: 0.7735 (p) cc_final: 0.7419 (t) REVERT: E 116 MET cc_start: 0.9059 (ttp) cc_final: 0.8518 (tmm) REVERT: E 208 ASN cc_start: 0.9325 (t0) cc_final: 0.9066 (t0) REVERT: E 211 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8577 (mm-30) REVERT: E 217 LEU cc_start: 0.9294 (mt) cc_final: 0.8987 (mt) REVERT: F 33 MET cc_start: 0.0927 (ttp) cc_final: 0.0655 (mpp) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.2249 time to fit residues: 104.4946 Evaluate side-chains 294 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 HIS B 43 ASN C 196 ASN D 218 HIS E 208 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.188613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.134406 restraints weight = 69896.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.141576 restraints weight = 40053.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.146166 restraints weight = 27474.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.149083 restraints weight = 21489.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.150878 restraints weight = 18381.835| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9476 Z= 0.165 Angle : 0.574 11.284 12808 Z= 0.320 Chirality : 0.036 0.122 1478 Planarity : 0.005 0.052 1627 Dihedral : 4.281 25.284 1276 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % 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 : 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 aren not related in a simple way. whole: 1.33 (0.23), residues: 1174 helix: 1.19 (0.15), residues: 1037 sheet: None (None), residues: 0 loop : -1.06 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 219 TYR 0.014 0.001 TYR A 66 PHE 0.029 0.002 PHE C 27 TRP 0.023 0.001 TRP A 147 HIS 0.011 0.002 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9476) covalent geometry : angle 0.57418 (12808) hydrogen bonds : bond 0.05239 ( 860) hydrogen bonds : angle 4.65222 ( 2562) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.501 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2516 (ptm) cc_final: 0.2067 (ptm) REVERT: B 66 TYR cc_start: 0.7737 (t80) cc_final: 0.7505 (t80) REVERT: B 112 MET cc_start: 0.6786 (mtp) cc_final: 0.6498 (mtp) REVERT: B 198 ARG cc_start: 0.6896 (mpt180) cc_final: 0.5780 (mmm160) REVERT: C 119 GLU cc_start: 0.8827 (tp30) cc_final: 0.8385 (tm-30) REVERT: C 123 LEU cc_start: 0.9395 (mt) cc_final: 0.8977 (mt) REVERT: C 150 MET cc_start: 0.9289 (mtm) cc_final: 0.8956 (mtp) REVERT: D 8 ASP cc_start: 0.9181 (t0) cc_final: 0.8514 (p0) REVERT: D 9 LEU cc_start: 0.9388 (mt) cc_final: 0.9134 (mt) REVERT: D 12 LYS cc_start: 0.9424 (pttt) cc_final: 0.9144 (pttp) REVERT: D 88 LYS cc_start: 0.9344 (tttm) cc_final: 0.9070 (tppt) REVERT: D 207 ASP cc_start: 0.9145 (t70) cc_final: 0.8839 (t0) REVERT: E 8 ASP cc_start: 0.9054 (m-30) cc_final: 0.8783 (m-30) REVERT: E 98 SER cc_start: 0.7738 (p) cc_final: 0.7377 (t) REVERT: E 116 MET cc_start: 0.8949 (ttp) cc_final: 0.8225 (tmm) REVERT: E 120 LEU cc_start: 0.9534 (mt) cc_final: 0.9175 (mt) REVERT: E 205 ASN cc_start: 0.8546 (t0) cc_final: 0.8123 (t0) REVERT: E 208 ASN cc_start: 0.9227 (t160) cc_final: 0.8995 (t0) REVERT: E 210 MET cc_start: 0.9396 (ttm) cc_final: 0.9158 (ttt) REVERT: E 211 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8337 (mm-30) REVERT: E 217 LEU cc_start: 0.9317 (mt) cc_final: 0.9028 (mt) REVERT: F 33 MET cc_start: 0.0793 (ttp) cc_final: 0.0538 (mtp) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2177 time to fit residues: 107.1998 Evaluate side-chains 316 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 89 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN C 196 ASN E 117 ASN E 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.190319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.138122 restraints weight = 67961.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.145292 restraints weight = 39290.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.149962 restraints weight = 26655.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.153011 restraints weight = 20564.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.154664 restraints weight = 17308.893| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.6234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9476 Z= 0.163 Angle : 0.561 12.038 12808 Z= 0.312 Chirality : 0.035 0.127 1478 Planarity : 0.004 0.049 1627 Dihedral : 4.165 23.249 1276 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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 aren not related in a simple way. whole: 1.65 (0.23), residues: 1174 helix: 1.42 (0.15), residues: 1037 sheet: None (None), residues: 0 loop : -1.09 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 219 TYR 0.026 0.001 TYR C 192 PHE 0.029 0.002 PHE C 83 TRP 0.006 0.001 TRP A 32 HIS 0.007 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9476) covalent geometry : angle 0.56067 (12808) hydrogen bonds : bond 0.05092 ( 860) hydrogen bonds : angle 4.60232 ( 2562) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.518 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2409 (ptm) cc_final: 0.1821 (ptm) REVERT: B 1 MET cc_start: -0.3814 (mmm) cc_final: -0.4271 (mmm) REVERT: B 66 TYR cc_start: 0.7808 (t80) cc_final: 0.7567 (t80) REVERT: B 112 MET cc_start: 0.6636 (mtp) cc_final: 0.6369 (mtp) REVERT: B 198 ARG cc_start: 0.6849 (mpt180) cc_final: 0.5727 (mmm160) REVERT: C 80 GLU cc_start: 0.9312 (tt0) cc_final: 0.8497 (tp30) REVERT: C 150 MET cc_start: 0.9188 (mtm) cc_final: 0.8857 (mtp) REVERT: D 8 ASP cc_start: 0.9169 (t0) cc_final: 0.8521 (p0) REVERT: D 88 LYS cc_start: 0.9335 (tttm) cc_final: 0.9056 (tppt) REVERT: D 133 VAL cc_start: 0.9592 (t) cc_final: 0.9375 (t) REVERT: D 207 ASP cc_start: 0.9160 (t70) cc_final: 0.8874 (t0) REVERT: E 8 ASP cc_start: 0.9042 (m-30) cc_final: 0.8826 (m-30) REVERT: E 98 SER cc_start: 0.7670 (p) cc_final: 0.7317 (t) REVERT: E 205 ASN cc_start: 0.8582 (t0) cc_final: 0.8194 (t0) REVERT: E 208 ASN cc_start: 0.9215 (t160) cc_final: 0.8971 (t0) REVERT: E 211 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8376 (mm-30) REVERT: E 217 LEU cc_start: 0.9326 (mt) cc_final: 0.9031 (mt) REVERT: F 33 MET cc_start: 0.0864 (ttp) cc_final: 0.0563 (mtp) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2167 time to fit residues: 106.1926 Evaluate side-chains 309 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 100 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 ASN C 196 ASN D 218 HIS E 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.188742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.135615 restraints weight = 68686.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.142624 restraints weight = 39987.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.147223 restraints weight = 27527.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.149758 restraints weight = 21468.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.151786 restraints weight = 18568.012| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.6434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9476 Z= 0.158 Angle : 0.569 11.509 12808 Z= 0.318 Chirality : 0.035 0.163 1478 Planarity : 0.005 0.087 1627 Dihedral : 4.129 23.801 1276 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 aren not related in a simple way. whole: 1.91 (0.23), residues: 1174 helix: 1.56 (0.15), residues: 1040 sheet: None (None), residues: 0 loop : -0.77 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 219 TYR 0.011 0.001 TYR A 66 PHE 0.024 0.002 PHE C 143 TRP 0.006 0.001 TRP A 147 HIS 0.007 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9476) covalent geometry : angle 0.56943 (12808) hydrogen bonds : bond 0.04998 ( 860) hydrogen bonds : angle 4.51960 ( 2562) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.510 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2147 (ptm) cc_final: 0.1654 (ptm) REVERT: B 1 MET cc_start: -0.3811 (mmm) cc_final: -0.4269 (mmm) REVERT: B 27 PHE cc_start: 0.7054 (m-80) cc_final: 0.6672 (m-80) REVERT: B 66 TYR cc_start: 0.7789 (t80) cc_final: 0.7551 (t80) REVERT: B 112 MET cc_start: 0.6737 (mtp) cc_final: 0.6490 (mtp) REVERT: B 198 ARG cc_start: 0.6819 (mpt180) cc_final: 0.5748 (mmm160) REVERT: C 80 GLU cc_start: 0.9362 (tt0) cc_final: 0.8505 (tp30) REVERT: C 116 MET cc_start: 0.8363 (tmm) cc_final: 0.8008 (tmm) REVERT: C 120 LEU cc_start: 0.9307 (mt) cc_final: 0.8942 (mt) REVERT: C 150 MET cc_start: 0.9232 (mtm) cc_final: 0.8913 (mtp) REVERT: D 8 ASP cc_start: 0.9219 (t0) cc_final: 0.8570 (p0) REVERT: D 88 LYS cc_start: 0.9385 (tttm) cc_final: 0.9078 (tppt) REVERT: D 207 ASP cc_start: 0.9204 (t70) cc_final: 0.8918 (t0) REVERT: E 8 ASP cc_start: 0.9105 (m-30) cc_final: 0.8873 (m-30) REVERT: E 80 GLU cc_start: 0.9122 (tt0) cc_final: 0.8729 (tt0) REVERT: E 98 SER cc_start: 0.7744 (p) cc_final: 0.7377 (t) REVERT: E 116 MET cc_start: 0.9018 (ttp) cc_final: 0.8496 (tmm) REVERT: E 119 GLU cc_start: 0.9411 (tp30) cc_final: 0.9191 (tp30) REVERT: E 205 ASN cc_start: 0.8715 (t0) cc_final: 0.8287 (t0) REVERT: E 208 ASN cc_start: 0.9265 (t160) cc_final: 0.9018 (t0) REVERT: E 211 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8409 (mm-30) REVERT: E 217 LEU cc_start: 0.9336 (mt) cc_final: 0.9047 (mt) REVERT: F 33 MET cc_start: 0.0945 (ttp) cc_final: 0.0661 (mtp) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.2268 time to fit residues: 111.5125 Evaluate side-chains 318 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS C 196 ASN E 208 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.189283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.134836 restraints weight = 70588.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.141941 restraints weight = 40978.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.146441 restraints weight = 28325.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.149413 restraints weight = 22295.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.151215 restraints weight = 19098.503| |-----------------------------------------------------------------------------| r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.6635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9476 Z= 0.155 Angle : 0.558 11.597 12808 Z= 0.311 Chirality : 0.036 0.243 1478 Planarity : 0.004 0.048 1627 Dihedral : 4.093 22.113 1276 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 aren not related in a simple way. whole: 2.07 (0.24), residues: 1174 helix: 1.67 (0.15), residues: 1043 sheet: None (None), residues: 0 loop : -0.79 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 219 TYR 0.023 0.001 TYR C 192 PHE 0.023 0.002 PHE C 143 TRP 0.007 0.001 TRP A 147 HIS 0.006 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 9476) covalent geometry : angle 0.55818 (12808) hydrogen bonds : bond 0.04915 ( 860) hydrogen bonds : angle 4.49384 ( 2562) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.537 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: 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: 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: A 1 MET cc_start: 0.2161 (ptm) cc_final: 0.1674 (ptm) REVERT: A 4 MET cc_start: 0.4895 (tpp) cc_final: 0.4252 (mmm) REVERT: B 1 MET cc_start: -0.3668 (mmm) cc_final: -0.4085 (mmm) REVERT: B 27 PHE cc_start: 0.7034 (m-80) cc_final: 0.6644 (m-80) REVERT: B 66 TYR cc_start: 0.7829 (t80) cc_final: 0.7585 (t80) REVERT: B 112 MET cc_start: 0.6793 (mtp) cc_final: 0.6554 (mtp) REVERT: B 198 ARG cc_start: 0.6779 (mpt180) cc_final: 0.5679 (mmm160) REVERT: C 61 GLU cc_start: 0.7454 (tt0) cc_final: 0.6955 (tp30) REVERT: C 65 LEU cc_start: 0.8840 (tt) cc_final: 0.8558 (tt) REVERT: C 80 GLU cc_start: 0.9347 (tt0) cc_final: 0.8514 (tp30) REVERT: C 116 MET cc_start: 0.8317 (tmm) cc_final: 0.8116 (tmm) REVERT: C 150 MET cc_start: 0.9205 (mtm) cc_final: 0.8919 (mtp) REVERT: C 200 ASN cc_start: 0.8978 (m-40) cc_final: 0.8699 (m-40) REVERT: D 8 ASP cc_start: 0.9160 (t0) cc_final: 0.8520 (p0) REVERT: D 133 VAL cc_start: 0.9589 (t) cc_final: 0.9358 (t) REVERT: D 207 ASP cc_start: 0.9097 (t70) cc_final: 0.8787 (t0) REVERT: E 80 GLU cc_start: 0.9059 (tt0) cc_final: 0.8706 (tt0) REVERT: E 98 SER cc_start: 0.7744 (p) cc_final: 0.7379 (t) REVERT: E 116 MET cc_start: 0.8953 (ttp) cc_final: 0.8300 (tmm) REVERT: E 120 LEU cc_start: 0.9496 (mt) cc_final: 0.9187 (mt) REVERT: E 205 ASN cc_start: 0.8469 (t0) cc_final: 0.8084 (t0) REVERT: E 207 ASP cc_start: 0.8778 (t0) cc_final: 0.8571 (t0) REVERT: E 208 ASN cc_start: 0.9151 (t160) cc_final: 0.8907 (t0) REVERT: E 217 LEU cc_start: 0.9334 (mt) cc_final: 0.9062 (mt) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.2198 time to fit residues: 107.0593 Evaluate side-chains 313 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 7 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 126 HIS B 43 ASN C 228 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 HIS ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.186121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.134005 restraints weight = 70138.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.140775 restraints weight = 41038.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.145160 restraints weight = 28382.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.148027 restraints weight = 22250.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.149450 restraints weight = 19061.132| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9476 Z= 0.210 Angle : 0.592 11.894 12808 Z= 0.342 Chirality : 0.036 0.227 1478 Planarity : 0.004 0.049 1627 Dihedral : 4.160 21.871 1276 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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 aren not related in a simple way. whole: 1.77 (0.23), residues: 1174 helix: 1.48 (0.15), residues: 1039 sheet: None (None), residues: 0 loop : -0.95 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 219 TYR 0.010 0.002 TYR A 66 PHE 0.026 0.002 PHE C 83 TRP 0.007 0.001 TRP C 57 HIS 0.008 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9476) covalent geometry : angle 0.59244 (12808) hydrogen bonds : bond 0.05000 ( 860) hydrogen bonds : angle 4.74600 ( 2562) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.514 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: 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: 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: A 1 MET cc_start: 0.2221 (ptm) cc_final: 0.1696 (ptm) REVERT: A 4 MET cc_start: 0.5051 (tpp) cc_final: 0.4435 (mmm) REVERT: B 1 MET cc_start: -0.3654 (mmm) cc_final: -0.4066 (mmm) REVERT: B 66 TYR cc_start: 0.7865 (t80) cc_final: 0.7637 (t80) REVERT: B 112 MET cc_start: 0.7090 (mtp) cc_final: 0.6865 (mtp) REVERT: B 196 ASN cc_start: 0.5134 (m-40) cc_final: 0.4865 (m110) REVERT: B 197 GLN cc_start: 0.8904 (mp10) cc_final: 0.8060 (tm-30) REVERT: C 116 MET cc_start: 0.8417 (tmm) cc_final: 0.8210 (tmm) REVERT: C 150 MET cc_start: 0.9276 (mtm) cc_final: 0.8976 (mtp) REVERT: C 200 ASN cc_start: 0.9122 (m-40) cc_final: 0.8834 (m-40) REVERT: D 8 ASP cc_start: 0.9204 (t0) cc_final: 0.8545 (p0) REVERT: D 133 VAL cc_start: 0.9591 (t) cc_final: 0.9363 (t) REVERT: D 207 ASP cc_start: 0.9209 (t70) cc_final: 0.8935 (t0) REVERT: E 8 ASP cc_start: 0.9314 (m-30) cc_final: 0.9067 (m-30) REVERT: E 98 SER cc_start: 0.7876 (p) cc_final: 0.7513 (t) REVERT: E 205 ASN cc_start: 0.8774 (t0) cc_final: 0.8364 (t0) REVERT: E 208 ASN cc_start: 0.9243 (t0) cc_final: 0.8996 (t0) REVERT: E 211 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8521 (mm-30) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.2112 time to fit residues: 101.2961 Evaluate side-chains 302 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 69 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN C 97 ASN C 196 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.189656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.136950 restraints weight = 66864.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.144089 restraints weight = 38168.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.148609 restraints weight = 25885.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.151539 restraints weight = 20085.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.153349 restraints weight = 16987.249| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.7077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9476 Z= 0.193 Angle : 0.583 11.789 12808 Z= 0.332 Chirality : 0.036 0.299 1478 Planarity : 0.004 0.050 1627 Dihedral : 4.175 21.980 1276 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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 aren not related in a simple way. whole: 1.69 (0.24), residues: 1174 helix: 1.42 (0.15), residues: 1041 sheet: None (None), residues: 0 loop : -0.96 (0.54), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 219 TYR 0.015 0.002 TYR A 66 PHE 0.028 0.002 PHE C 27 TRP 0.009 0.001 TRP A 32 HIS 0.008 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9476) covalent geometry : angle 0.58312 (12808) hydrogen bonds : bond 0.04992 ( 860) hydrogen bonds : angle 4.69490 ( 2562) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4542.96 seconds wall clock time: 78 minutes 6.06 seconds (4686.06 seconds total)