Starting phenix.real_space_refine on Mon Jun 16 12:55:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8odt_16816/06_2025/8odt_16816.cif Found real_map, /net/cci-nas-00/data/ceres_data/8odt_16816/06_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_16816/06_2025/8odt_16816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8odt_16816/06_2025/8odt_16816.map" model { file = "/net/cci-nas-00/data/ceres_data/8odt_16816/06_2025/8odt_16816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8odt_16816/06_2025/8odt_16816.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.40, per 1000 atoms: 0.50 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: 5.77 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.17 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: 6.88 Time building geometry restraints manager: 6.55 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.280 Extract box with map and model: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 41.820 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.630 ------------------------------------------------------------------------------- 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 : 17.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP A 147 HIS 0.004 0.001 HIS D 94 PHE 0.019 0.002 PHE B 183 TYR 0.020 0.002 TYR A 66 ARG 0.008 0.001 ARG C 118 Details of bonding type rmsd hydrogen bonds : bond 0.10683 ( 860) hydrogen bonds : angle 5.80305 ( 2562) covalent geometry : bond 0.00552 ( 9476) covalent geometry : angle 0.70869 (12808) *********************** 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 : 1.500 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: A 32 TRP cc_start: 0.7039 (t60) cc_final: 0.6785 (t60) REVERT: A 211 GLU cc_start: 0.7288 (tt0) cc_final: 0.7020 (mt-10) REVERT: B 28 SER cc_start: 0.3026 (OUTLIER) cc_final: 0.2779 (p) REVERT: B 41 ILE cc_start: 0.9455 (mt) cc_final: 0.9193 (tt) REVERT: B 89 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6277 (tt0) REVERT: B 112 MET cc_start: 0.6692 (mtp) cc_final: 0.6217 (mtp) REVERT: B 197 GLN cc_start: 0.8471 (mt0) cc_final: 0.7666 (tm-30) REVERT: C 20 ILE cc_start: 0.9471 (mt) cc_final: 0.9227 (tp) REVERT: C 42 LEU cc_start: 0.9675 (mt) cc_final: 0.9465 (mt) REVERT: C 164 LEU cc_start: 0.1520 (OUTLIER) cc_final: 0.1152 (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: 0.9037 (mtm) REVERT: C 214 THR cc_start: 0.8652 (m) cc_final: 0.8448 (m) REVERT: D 4 MET cc_start: 0.6117 (ttt) cc_final: 0.5601 (ptt) REVERT: D 8 ASP cc_start: 0.9060 (t70) cc_final: 0.8802 (p0) REVERT: D 9 LEU cc_start: 0.9496 (mt) cc_final: 0.9258 (mt) REVERT: D 81 GLN cc_start: 0.9275 (tt0) cc_final: 0.8990 (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: 0.9132 (mt) REVERT: F 23 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8200 (p0) REVERT: F 33 MET cc_start: 0.0291 (ttp) cc_final: 0.0012 (mtt) outliers start: 35 outliers final: 21 residues processed: 434 average time/residue: 0.5855 time to fit residues: 342.4502 Evaluate side-chains 342 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 318 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 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 D 208 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.191072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.137946 restraints weight = 69823.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.145190 restraints weight = 39975.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.149884 restraints weight = 27230.468| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9476 Z= 0.239 Angle : 0.637 11.143 12808 Z= 0.370 Chirality : 0.038 0.223 1478 Planarity : 0.005 0.060 1627 Dihedral : 4.349 22.644 1276 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.23), residues: 1174 helix: 1.23 (0.15), residues: 1027 sheet: None (None), residues: 0 loop : -0.93 (0.51), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 147 HIS 0.005 0.002 HIS A 94 PHE 0.034 0.003 PHE C 10 TYR 0.016 0.002 TYR C 66 ARG 0.006 0.001 ARG D 219 Details of bonding type rmsd hydrogen bonds : bond 0.05728 ( 860) hydrogen bonds : angle 5.09230 ( 2562) covalent geometry : bond 0.00456 ( 9476) covalent geometry : angle 0.63721 (12808) *********************** 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 372 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.309 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: A 1 MET cc_start: 0.2589 (ptm) cc_final: 0.2163 (ptm) REVERT: B 41 ILE cc_start: 0.9506 (mt) cc_final: 0.9259 (tt) REVERT: B 112 MET cc_start: 0.6328 (mtp) cc_final: 0.5900 (mtp) REVERT: B 116 MET cc_start: 0.9226 (ttt) cc_final: 0.8690 (ttm) REVERT: B 123 LEU cc_start: 0.9399 (mt) cc_final: 0.9178 (mt) REVERT: B 198 ARG cc_start: 0.6378 (mpt180) cc_final: 0.5658 (mmm160) REVERT: C 20 ILE cc_start: 0.9412 (mt) cc_final: 0.9186 (tp) REVERT: C 53 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8775 (tm-30) REVERT: C 150 MET cc_start: 0.9172 (mtm) cc_final: 0.8830 (mtp) REVERT: D 4 MET cc_start: 0.5963 (ttt) cc_final: 0.5512 (ptt) REVERT: D 80 GLU cc_start: 0.8734 (tt0) cc_final: 0.8298 (tt0) REVERT: D 81 GLN cc_start: 0.9197 (tt0) cc_final: 0.8544 (tt0) REVERT: D 88 LYS cc_start: 0.9213 (tttm) cc_final: 0.9005 (tppt) REVERT: D 207 ASP cc_start: 0.8927 (t70) cc_final: 0.8707 (t0) REVERT: E 116 MET cc_start: 0.8812 (ttp) cc_final: 0.8281 (tmm) REVERT: E 210 MET cc_start: 0.8826 (ttp) cc_final: 0.8552 (ttp) REVERT: E 217 LEU cc_start: 0.9284 (mt) cc_final: 0.9034 (mt) REVERT: F 33 MET cc_start: 0.0768 (ttp) cc_final: 0.0422 (mtt) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.5276 time to fit residues: 265.9508 Evaluate side-chains 322 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 0 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 218 HIS E 200 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.193260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.140126 restraints weight = 68250.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.147376 restraints weight = 38980.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.151925 restraints weight = 26732.136| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9476 Z= 0.202 Angle : 0.600 11.560 12808 Z= 0.343 Chirality : 0.037 0.149 1478 Planarity : 0.005 0.071 1627 Dihedral : 4.237 21.508 1276 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.23), residues: 1174 helix: 1.40 (0.15), residues: 1029 sheet: None (None), residues: 0 loop : -0.80 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 147 HIS 0.008 0.001 HIS A 126 PHE 0.024 0.002 PHE C 143 TYR 0.013 0.001 TYR A 66 ARG 0.006 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.05469 ( 860) hydrogen bonds : angle 4.83689 ( 2562) covalent geometry : bond 0.00393 ( 9476) covalent geometry : angle 0.59997 (12808) *********************** 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 354 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 1.250 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: 0.2505 (ptm) cc_final: 0.2099 (ptm) REVERT: B 112 MET cc_start: 0.6576 (mtp) cc_final: 0.6205 (mtp) REVERT: B 123 LEU cc_start: 0.9379 (mt) cc_final: 0.9176 (mt) REVERT: B 198 ARG cc_start: 0.6379 (mpt180) cc_final: 0.5621 (mmm160) REVERT: C 119 GLU cc_start: 0.8989 (tp30) cc_final: 0.8691 (tp30) REVERT: C 123 LEU cc_start: 0.9414 (mt) cc_final: 0.9191 (mt) REVERT: C 150 MET cc_start: 0.9276 (mtm) cc_final: 0.8896 (mtp) REVERT: C 194 ARG cc_start: 0.8840 (tpt-90) cc_final: 0.8103 (tpp80) REVERT: C 200 ASN cc_start: 0.9173 (m-40) cc_final: 0.8876 (m-40) REVERT: D 4 MET cc_start: 0.6022 (ttt) cc_final: 0.5770 (ptt) REVERT: D 8 ASP cc_start: 0.8942 (t70) cc_final: 0.8593 (p0) REVERT: D 9 LEU cc_start: 0.9401 (mt) cc_final: 0.9191 (mt) REVERT: D 81 GLN cc_start: 0.9319 (tt0) cc_final: 0.8314 (tt0) REVERT: D 88 LYS cc_start: 0.9300 (tttm) cc_final: 0.9040 (tppt) REVERT: D 106 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8844 (mt-10) REVERT: D 140 ILE cc_start: 0.9571 (mm) cc_final: 0.9355 (tp) REVERT: E 65 LEU cc_start: 0.9391 (tp) cc_final: 0.9154 (tp) REVERT: E 98 SER cc_start: 0.7810 (p) cc_final: 0.7509 (t) REVERT: E 116 MET cc_start: 0.8943 (ttp) cc_final: 0.8434 (tmm) REVERT: E 217 LEU cc_start: 0.9291 (mt) cc_final: 0.9025 (mt) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.4721 time to fit residues: 230.7548 Evaluate side-chains 319 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 74 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 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 = 0.4669 r_free = 0.4669 target = 0.194601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.140478 restraints weight = 67354.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.147637 restraints weight = 38917.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.152398 restraints weight = 26728.719| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 0.5139 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= 0.203 Angle : 0.590 11.556 12808 Z= 0.339 Chirality : 0.036 0.163 1478 Planarity : 0.005 0.056 1627 Dihedral : 4.222 22.020 1276 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.23), residues: 1174 helix: 1.43 (0.15), residues: 1031 sheet: None (None), residues: 0 loop : -0.76 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.005 0.001 HIS B 218 PHE 0.033 0.002 PHE A 143 TYR 0.025 0.002 TYR D 66 ARG 0.005 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.05385 ( 860) hydrogen bonds : angle 4.76766 ( 2562) covalent geometry : bond 0.00390 ( 9476) covalent geometry : angle 0.58960 (12808) *********************** 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 352 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.363 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: A 1 MET cc_start: 0.2491 (ptm) cc_final: 0.2115 (ptm) REVERT: B 1 MET cc_start: -0.3745 (mmm) cc_final: -0.4194 (mmm) REVERT: B 112 MET cc_start: 0.6553 (mtp) cc_final: 0.6178 (mtp) REVERT: B 198 ARG cc_start: 0.6502 (mpt180) cc_final: 0.5689 (mmm160) REVERT: C 65 LEU cc_start: 0.9044 (tp) cc_final: 0.8831 (tt) REVERT: C 119 GLU cc_start: 0.8911 (tp30) cc_final: 0.8711 (tp30) REVERT: C 150 MET cc_start: 0.9226 (mtm) cc_final: 0.8869 (mtp) REVERT: C 194 ARG cc_start: 0.8674 (tpt-90) cc_final: 0.8165 (tpp80) REVERT: C 200 ASN cc_start: 0.9096 (m-40) cc_final: 0.8784 (m-40) REVERT: D 4 MET cc_start: 0.5965 (ttt) cc_final: 0.5761 (ptp) REVERT: D 8 ASP cc_start: 0.8883 (t70) cc_final: 0.8575 (p0) REVERT: D 88 LYS cc_start: 0.9260 (tttm) cc_final: 0.9042 (tppt) REVERT: D 140 ILE cc_start: 0.9583 (mm) cc_final: 0.9362 (tp) REVERT: D 208 ASN cc_start: 0.9007 (t0) cc_final: 0.8795 (t0) REVERT: E 8 ASP cc_start: 0.9082 (m-30) cc_final: 0.8656 (m-30) REVERT: E 116 MET cc_start: 0.8940 (ttp) cc_final: 0.8397 (tmm) REVERT: E 211 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8383 (mm-30) REVERT: E 217 LEU cc_start: 0.9283 (mt) cc_final: 0.9021 (mt) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.5620 time to fit residues: 276.2491 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 : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN D 218 HIS ** 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 = 0.4634 r_free = 0.4634 target = 0.188314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.133906 restraints weight = 70459.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.141022 restraints weight = 39726.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.145625 restraints weight = 27188.606| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9476 Z= 0.253 Angle : 0.623 11.425 12808 Z= 0.364 Chirality : 0.037 0.204 1478 Planarity : 0.005 0.058 1627 Dihedral : 4.322 22.094 1276 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.23), residues: 1174 helix: 1.23 (0.15), residues: 1031 sheet: None (None), residues: 0 loop : -0.83 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 147 HIS 0.004 0.001 HIS C 94 PHE 0.035 0.002 PHE A 143 TYR 0.022 0.002 TYR D 66 ARG 0.008 0.001 ARG E 64 Details of bonding type rmsd hydrogen bonds : bond 0.05359 ( 860) hydrogen bonds : angle 4.96430 ( 2562) covalent geometry : bond 0.00466 ( 9476) covalent geometry : angle 0.62280 (12808) *********************** 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 335 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.517 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: A 1 MET cc_start: 0.2503 (ptm) cc_final: 0.2111 (ptm) REVERT: A 24 LEU cc_start: 0.6965 (mt) cc_final: 0.6586 (mt) REVERT: B 112 MET cc_start: 0.6820 (mtp) cc_final: 0.6514 (mtp) REVERT: B 127 ILE cc_start: 0.7744 (mt) cc_final: 0.7479 (mm) REVERT: B 197 GLN cc_start: 0.8900 (mp10) cc_final: 0.7816 (tm-30) REVERT: C 112 MET cc_start: 0.7895 (mtm) cc_final: 0.7677 (mtm) REVERT: C 150 MET cc_start: 0.9267 (mtm) cc_final: 0.8937 (mtp) REVERT: C 200 ASN cc_start: 0.9045 (m-40) cc_final: 0.8783 (m-40) REVERT: D 4 MET cc_start: 0.6086 (ttt) cc_final: 0.5857 (ptt) REVERT: D 8 ASP cc_start: 0.8873 (t70) cc_final: 0.8462 (p0) REVERT: D 9 LEU cc_start: 0.9476 (mt) cc_final: 0.9267 (mt) REVERT: D 88 LYS cc_start: 0.9284 (tttm) cc_final: 0.9043 (tppt) REVERT: D 106 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8567 (mt-10) REVERT: D 207 ASP cc_start: 0.9143 (t0) cc_final: 0.8931 (t0) REVERT: D 208 ASN cc_start: 0.8939 (t0) cc_final: 0.8728 (t0) REVERT: E 8 ASP cc_start: 0.9080 (m-30) cc_final: 0.8678 (m-30) REVERT: E 98 SER cc_start: 0.7841 (p) cc_final: 0.7534 (t) REVERT: E 116 MET cc_start: 0.8971 (ttp) cc_final: 0.8401 (tmm) REVERT: E 211 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8489 (mm-30) REVERT: E 217 LEU cc_start: 0.9303 (mt) cc_final: 0.9056 (mt) REVERT: F 33 MET cc_start: 0.0915 (ttp) cc_final: 0.0542 (mpp) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.4343 time to fit residues: 203.5251 Evaluate side-chains 298 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 11 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 109 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 ** 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 = 0.4638 r_free = 0.4638 target = 0.189461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.136175 restraints weight = 69780.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.143200 restraints weight = 39757.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.147677 restraints weight = 27256.522| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.5889 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= 0.198 Angle : 0.580 11.359 12808 Z= 0.331 Chirality : 0.035 0.142 1478 Planarity : 0.005 0.052 1627 Dihedral : 4.256 21.245 1276 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.23), residues: 1174 helix: 1.38 (0.15), residues: 1033 sheet: None (None), residues: 0 loop : -0.82 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 147 HIS 0.004 0.001 HIS E 151 PHE 0.033 0.002 PHE A 27 TYR 0.013 0.001 TYR A 66 ARG 0.009 0.001 ARG E 219 Details of bonding type rmsd hydrogen bonds : bond 0.05175 ( 860) hydrogen bonds : angle 4.78061 ( 2562) covalent geometry : bond 0.00380 ( 9476) covalent geometry : angle 0.57982 (12808) *********************** 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 339 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.2436 (ptm) cc_final: 0.1968 (ptm) REVERT: A 24 LEU cc_start: 0.6770 (mt) cc_final: 0.6396 (mt) REVERT: B 112 MET cc_start: 0.6754 (mtp) cc_final: 0.6499 (mtp) REVERT: B 127 ILE cc_start: 0.7746 (mt) cc_final: 0.7480 (mm) REVERT: B 197 GLN cc_start: 0.8884 (mp10) cc_final: 0.7823 (tm-30) REVERT: C 200 ASN cc_start: 0.9041 (m-40) cc_final: 0.8716 (m-40) REVERT: D 8 ASP cc_start: 0.8914 (t70) cc_final: 0.8414 (p0) REVERT: D 88 LYS cc_start: 0.9291 (tttm) cc_final: 0.9039 (tppt) REVERT: D 106 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8589 (mt-10) REVERT: D 115 SER cc_start: 0.9235 (m) cc_final: 0.8987 (t) REVERT: D 208 ASN cc_start: 0.8962 (t0) cc_final: 0.8720 (t0) REVERT: E 8 ASP cc_start: 0.9104 (m-30) cc_final: 0.8788 (m-30) REVERT: E 15 LEU cc_start: 0.7817 (mm) cc_final: 0.7473 (pt) REVERT: E 98 SER cc_start: 0.7785 (p) cc_final: 0.7427 (t) REVERT: E 116 MET cc_start: 0.8956 (ttp) cc_final: 0.8372 (tmm) REVERT: E 205 ASN cc_start: 0.8343 (t0) cc_final: 0.7948 (t0) REVERT: E 208 ASN cc_start: 0.9138 (t0) cc_final: 0.8904 (t0) REVERT: E 211 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8435 (mm-30) REVERT: E 217 LEU cc_start: 0.9308 (mt) cc_final: 0.9055 (mt) REVERT: F 33 MET cc_start: 0.0814 (ttp) cc_final: 0.0548 (mtp) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.4530 time to fit residues: 216.9873 Evaluate side-chains 303 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.188035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.134266 restraints weight = 69444.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.141224 restraints weight = 39982.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.145668 restraints weight = 27595.044| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9476 Z= 0.207 Angle : 0.582 11.463 12808 Z= 0.336 Chirality : 0.035 0.147 1478 Planarity : 0.005 0.050 1627 Dihedral : 4.254 21.205 1276 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.23), residues: 1174 helix: 1.35 (0.15), residues: 1036 sheet: None (None), residues: 0 loop : -0.99 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 57 HIS 0.007 0.001 HIS B 218 PHE 0.032 0.002 PHE C 83 TYR 0.022 0.002 TYR C 192 ARG 0.005 0.001 ARG E 219 Details of bonding type rmsd hydrogen bonds : bond 0.05164 ( 860) hydrogen bonds : angle 4.81587 ( 2562) covalent geometry : bond 0.00390 ( 9476) covalent geometry : angle 0.58200 (12808) *********************** 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 339 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 1.445 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: A 1 MET cc_start: 0.2376 (ptm) cc_final: 0.1920 (ptm) REVERT: B 1 MET cc_start: -0.3588 (mmm) cc_final: -0.4017 (mmm) REVERT: B 127 ILE cc_start: 0.7766 (mt) cc_final: 0.7523 (mm) REVERT: C 150 MET cc_start: 0.9172 (mtm) cc_final: 0.8907 (mtp) REVERT: D 8 ASP cc_start: 0.8900 (t70) cc_final: 0.8410 (p0) REVERT: D 88 LYS cc_start: 0.9322 (tttm) cc_final: 0.9071 (tppt) REVERT: D 115 SER cc_start: 0.9243 (m) cc_final: 0.9037 (t) REVERT: D 208 ASN cc_start: 0.8942 (t0) cc_final: 0.8727 (t0) REVERT: E 8 ASP cc_start: 0.9041 (m-30) cc_final: 0.8783 (m-30) REVERT: E 15 LEU cc_start: 0.7789 (mm) cc_final: 0.7461 (pt) REVERT: E 98 SER cc_start: 0.7764 (p) cc_final: 0.7404 (t) REVERT: E 116 MET cc_start: 0.8976 (ttp) cc_final: 0.8384 (tmm) REVERT: E 119 GLU cc_start: 0.9364 (tp30) cc_final: 0.9119 (tp30) REVERT: E 205 ASN cc_start: 0.8308 (t0) cc_final: 0.7937 (t0) REVERT: E 208 ASN cc_start: 0.9116 (t0) cc_final: 0.8901 (t0) REVERT: E 211 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8416 (mm-30) REVERT: E 217 LEU cc_start: 0.9326 (mt) cc_final: 0.9044 (mt) REVERT: F 33 MET cc_start: 0.0805 (ttp) cc_final: 0.0531 (mtp) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.4580 time to fit residues: 218.9636 Evaluate side-chains 306 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 81 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.188563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.134322 restraints weight = 68954.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.141391 restraints weight = 40155.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.146038 restraints weight = 27724.940| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9476 Z= 0.185 Angle : 0.577 11.503 12808 Z= 0.329 Chirality : 0.036 0.168 1478 Planarity : 0.004 0.049 1627 Dihedral : 4.245 24.108 1276 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.23), residues: 1174 helix: 1.41 (0.15), residues: 1036 sheet: None (None), residues: 0 loop : -1.12 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.011 0.001 HIS A 151 PHE 0.030 0.002 PHE C 27 TYR 0.011 0.001 TYR A 66 ARG 0.005 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.05135 ( 860) hydrogen bonds : angle 4.76451 ( 2562) covalent geometry : bond 0.00358 ( 9476) covalent geometry : angle 0.57728 (12808) *********************** 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 337 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 1.953 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: A 1 MET cc_start: 0.2390 (ptm) cc_final: 0.1919 (ptm) REVERT: B 1 MET cc_start: -0.3630 (mmm) cc_final: -0.4084 (mmm) REVERT: B 127 ILE cc_start: 0.7767 (mt) cc_final: 0.7501 (mm) REVERT: C 119 GLU cc_start: 0.8799 (tp30) cc_final: 0.8486 (tm-30) REVERT: C 200 ASN cc_start: 0.9056 (m-40) cc_final: 0.8738 (m-40) REVERT: D 8 ASP cc_start: 0.8944 (t70) cc_final: 0.8398 (p0) REVERT: D 88 LYS cc_start: 0.9335 (tttm) cc_final: 0.9060 (tppt) REVERT: D 115 SER cc_start: 0.9236 (m) cc_final: 0.9015 (t) REVERT: E 8 ASP cc_start: 0.9075 (m-30) cc_final: 0.8856 (m-30) REVERT: E 15 LEU cc_start: 0.7846 (mm) cc_final: 0.7489 (pt) REVERT: E 53 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8194 (mt-10) REVERT: E 80 GLU cc_start: 0.9048 (tt0) cc_final: 0.8764 (tt0) REVERT: E 98 SER cc_start: 0.7713 (p) cc_final: 0.7356 (t) REVERT: E 119 GLU cc_start: 0.9425 (tp30) cc_final: 0.9126 (tp30) REVERT: E 208 ASN cc_start: 0.9150 (t0) cc_final: 0.8934 (t0) REVERT: E 211 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8446 (mm-30) REVERT: E 217 LEU cc_start: 0.9323 (mt) cc_final: 0.9049 (mt) REVERT: F 33 MET cc_start: 0.0789 (ttp) cc_final: 0.0461 (mtp) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.4287 time to fit residues: 204.1250 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 : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 51 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.186980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.132698 restraints weight = 70869.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.139981 restraints weight = 40540.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.144127 restraints weight = 27627.951| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.6626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9476 Z= 0.206 Angle : 0.592 11.699 12808 Z= 0.338 Chirality : 0.036 0.150 1478 Planarity : 0.005 0.050 1627 Dihedral : 4.249 22.873 1276 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.23), residues: 1174 helix: 1.34 (0.15), residues: 1039 sheet: None (None), residues: 0 loop : -1.06 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 147 HIS 0.009 0.001 HIS A 151 PHE 0.024 0.002 PHE C 143 TYR 0.032 0.002 TYR C 192 ARG 0.006 0.000 ARG E 219 Details of bonding type rmsd hydrogen bonds : bond 0.05137 ( 860) hydrogen bonds : angle 4.82381 ( 2562) covalent geometry : bond 0.00394 ( 9476) covalent geometry : angle 0.59174 (12808) *********************** 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 335 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.406 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: 0.2308 (ptm) cc_final: 0.1824 (ptm) REVERT: B 1 MET cc_start: -0.3543 (mmm) cc_final: -0.3983 (mmm) REVERT: B 112 MET cc_start: 0.6835 (mtp) cc_final: 0.6392 (mtp) REVERT: B 127 ILE cc_start: 0.7759 (mt) cc_final: 0.7485 (mm) REVERT: B 150 MET cc_start: -0.0145 (ttp) cc_final: -0.0401 (ttm) REVERT: C 4 MET cc_start: 0.1900 (ppp) cc_final: 0.1636 (ppp) REVERT: C 150 MET cc_start: 0.9179 (mtm) cc_final: 0.8947 (mtp) REVERT: C 200 ASN cc_start: 0.9066 (m-40) cc_final: 0.8799 (m-40) REVERT: D 8 ASP cc_start: 0.8945 (t70) cc_final: 0.8365 (p0) REVERT: D 88 LYS cc_start: 0.9357 (tttm) cc_final: 0.9091 (tppt) REVERT: D 207 ASP cc_start: 0.9105 (t70) cc_final: 0.8806 (t0) REVERT: E 8 ASP cc_start: 0.9094 (m-30) cc_final: 0.8877 (m-30) REVERT: E 15 LEU cc_start: 0.7836 (mm) cc_final: 0.7473 (pt) REVERT: E 29 ILE cc_start: 0.9509 (mt) cc_final: 0.9243 (tp) REVERT: E 98 SER cc_start: 0.7775 (p) cc_final: 0.7414 (t) REVERT: E 119 GLU cc_start: 0.9405 (tp30) cc_final: 0.9133 (tp30) REVERT: E 208 ASN cc_start: 0.9098 (t0) cc_final: 0.8873 (t0) REVERT: E 211 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8415 (mm-30) REVERT: E 217 LEU cc_start: 0.9315 (mt) cc_final: 0.9056 (mt) REVERT: F 33 MET cc_start: 0.0935 (ttp) cc_final: 0.0650 (mtp) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.4559 time to fit residues: 217.1761 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 : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.188311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.134444 restraints weight = 68855.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.141838 restraints weight = 39086.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.146413 restraints weight = 26525.199| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.6839 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= 0.170 Angle : 0.567 11.695 12808 Z= 0.319 Chirality : 0.036 0.202 1478 Planarity : 0.004 0.049 1627 Dihedral : 4.172 22.817 1276 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.35 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.24), residues: 1174 helix: 1.54 (0.15), residues: 1043 sheet: None (None), residues: 0 loop : -1.11 (0.53), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 147 HIS 0.008 0.001 HIS A 126 PHE 0.025 0.002 PHE C 143 TYR 0.034 0.002 TYR C 192 ARG 0.006 0.000 ARG E 219 Details of bonding type rmsd hydrogen bonds : bond 0.04983 ( 860) hydrogen bonds : angle 4.66429 ( 2562) covalent geometry : bond 0.00329 ( 9476) covalent geometry : angle 0.56707 (12808) ********************** 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 342 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.702 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: 0.2365 (ptm) cc_final: 0.1825 (ptm) REVERT: B 1 MET cc_start: -0.3608 (mmm) cc_final: -0.4053 (mmm) REVERT: B 112 MET cc_start: 0.6729 (mtp) cc_final: 0.6255 (mtp) REVERT: B 127 ILE cc_start: 0.7754 (mt) cc_final: 0.7482 (mm) REVERT: B 150 MET cc_start: -0.0024 (ttp) cc_final: -0.0260 (ttm) REVERT: C 4 MET cc_start: 0.1834 (ppp) cc_final: 0.1595 (ppp) REVERT: C 119 GLU cc_start: 0.8719 (tp30) cc_final: 0.8256 (tm-30) REVERT: C 123 LEU cc_start: 0.9388 (mt) cc_final: 0.8848 (mt) REVERT: D 1 MET cc_start: -0.1624 (ttt) cc_final: -0.2043 (ttt) REVERT: D 8 ASP cc_start: 0.8895 (t70) cc_final: 0.8355 (p0) REVERT: D 88 LYS cc_start: 0.9370 (tttm) cc_final: 0.9093 (tppt) REVERT: D 207 ASP cc_start: 0.9096 (t70) cc_final: 0.8788 (t0) REVERT: E 8 ASP cc_start: 0.9128 (m-30) cc_final: 0.8915 (m-30) REVERT: E 15 LEU cc_start: 0.7803 (mm) cc_final: 0.7440 (pt) REVERT: E 29 ILE cc_start: 0.9510 (mt) cc_final: 0.9230 (tp) REVERT: E 98 SER cc_start: 0.7732 (p) cc_final: 0.7367 (t) REVERT: E 119 GLU cc_start: 0.9339 (tp30) cc_final: 0.9047 (tp30) REVERT: E 208 ASN cc_start: 0.9120 (t0) cc_final: 0.8883 (t0) REVERT: E 217 LEU cc_start: 0.9320 (mt) cc_final: 0.9044 (mt) REVERT: E 219 ARG cc_start: 0.8597 (ttm-80) cc_final: 0.8337 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.4532 time to fit residues: 216.0076 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 : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 96 optimal weight: 4.9990 chunk 69 optimal weight: 0.0770 chunk 63 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- 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** ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.188577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.134453 restraints weight = 69084.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.141850 restraints weight = 38967.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.146563 restraints weight = 26500.986| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.7025 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= 0.149 Angle : 0.563 11.790 12808 Z= 0.313 Chirality : 0.035 0.209 1478 Planarity : 0.004 0.048 1627 Dihedral : 4.106 22.035 1276 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.24), residues: 1174 helix: 1.70 (0.15), residues: 1041 sheet: None (None), residues: 0 loop : -0.94 (0.52), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.007 0.001 HIS A 218 PHE 0.024 0.002 PHE C 143 TYR 0.033 0.002 TYR C 192 ARG 0.006 0.000 ARG E 219 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 860) hydrogen bonds : angle 4.60430 ( 2562) covalent geometry : bond 0.00299 ( 9476) covalent geometry : angle 0.56256 (12808) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7631.65 seconds wall clock time: 133 minutes 37.44 seconds (8017.44 seconds total)