Starting phenix.real_space_refine on Mon Oct 14 19:14:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odt_16816/10_2024/8odt_16816.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odt_16816/10_2024/8odt_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odt_16816/10_2024/8odt_16816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odt_16816/10_2024/8odt_16816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odt_16816/10_2024/8odt_16816.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odt_16816/10_2024/8odt_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-5477/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: 9.59, per 1000 atoms: 0.51 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: 5.29 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: 1.25 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: 7.05 Time building geometry restraints manager: 6.19 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: 2.010 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: 0.320 Extract box with map and model: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 41.760 Find NCS groups from input model: 0.460 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: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.740 ------------------------------------------------------------------------------- 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= 0.364 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 *********************** 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 fitting. rotamer outliers: 35 poor density : 406 time to evaluate : 1.401 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: 0.5714 time to fit residues: 328.6228 Evaluate side-chains 342 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 318 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 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= 0.302 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.431 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: 0.2367 (ptm) cc_final: 0.1957 (ptm) REVERT: B 41 ILE cc_start: 0.9430 (mt) cc_final: 0.9215 (tt) REVERT: B 50 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7502 (tm-30) REVERT: B 89 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6775 (tp30) REVERT: B 112 MET cc_start: 0.6795 (mtp) cc_final: 0.6355 (mtp) REVERT: B 116 MET cc_start: 0.9228 (ttt) cc_final: 0.8662 (ttm) REVERT: B 198 ARG cc_start: 0.6295 (mpt180) cc_final: 0.5695 (mmm160) REVERT: C 42 LEU cc_start: 0.9679 (mt) cc_final: 0.9466 (mt) REVERT: C 53 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8801 (tm-30) REVERT: C 150 MET cc_start: 0.9296 (mtm) cc_final: 0.9004 (mtp) REVERT: D 4 MET cc_start: 0.6102 (ttt) cc_final: 0.5563 (ptt) REVERT: D 80 GLU cc_start: 0.8837 (tt0) cc_final: 0.8263 (tt0) REVERT: D 81 GLN cc_start: 0.9330 (tt0) cc_final: 0.8637 (tt0) REVERT: D 88 LYS cc_start: 0.9347 (tttm) cc_final: 0.9070 (tppt) REVERT: D 194 ARG cc_start: 0.8811 (mmt180) cc_final: 0.8393 (ttm170) REVERT: E 116 MET cc_start: 0.9040 (ttp) cc_final: 0.8506 (tmm) REVERT: E 129 PHE cc_start: 0.9196 (t80) cc_final: 0.8881 (m-10) REVERT: E 200 ASN cc_start: 0.9288 (m-40) cc_final: 0.9057 (m-40) REVERT: E 210 MET cc_start: 0.9136 (ttp) cc_final: 0.8860 (ttp) REVERT: E 217 LEU cc_start: 0.9304 (mt) cc_final: 0.9044 (mt) REVERT: F 33 MET cc_start: 0.0423 (ttp) cc_final: 0.0145 (mtt) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.5358 time to fit residues: 267.9000 Evaluate side-chains 324 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 115 optimal weight: 0.0980 chunk 95 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** C 122 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9476 Z= 0.225 Angle : 0.587 11.642 12808 Z= 0.332 Chirality : 0.037 0.146 1478 Planarity : 0.005 0.072 1627 Dihedral : 4.191 21.564 1276 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: 1.85 (0.23), residues: 1174 helix: 1.53 (0.15), residues: 1029 sheet: None (None), residues: 0 loop : -0.71 (0.52), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 147 HIS 0.009 0.001 HIS A 126 PHE 0.024 0.002 PHE C 143 TYR 0.012 0.001 TYR A 66 ARG 0.006 0.000 ARG A 198 *********************** 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 359 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 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: A 1 MET cc_start: 0.2328 (ptm) cc_final: 0.1951 (ptm) REVERT: B 27 PHE cc_start: 0.7296 (m-10) cc_final: 0.7094 (m-80) REVERT: B 50 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7446 (tm-30) REVERT: B 112 MET cc_start: 0.6600 (mtp) cc_final: 0.6239 (mtp) REVERT: B 198 ARG cc_start: 0.6298 (mpt180) cc_final: 0.5675 (mmm160) REVERT: C 119 GLU cc_start: 0.9109 (tp30) cc_final: 0.8812 (tp30) REVERT: C 123 LEU cc_start: 0.9374 (mt) cc_final: 0.9160 (mt) REVERT: C 150 MET cc_start: 0.9270 (mtm) cc_final: 0.8941 (mtp) REVERT: C 194 ARG cc_start: 0.8820 (tpt-90) cc_final: 0.8037 (tpp80) REVERT: C 200 ASN cc_start: 0.9164 (m-40) cc_final: 0.8859 (m-40) REVERT: D 4 MET cc_start: 0.6096 (ttt) cc_final: 0.5822 (ptt) REVERT: D 8 ASP cc_start: 0.9052 (t70) cc_final: 0.8660 (p0) REVERT: D 9 LEU cc_start: 0.9434 (mt) cc_final: 0.9234 (mt) REVERT: D 88 LYS cc_start: 0.9334 (tttm) cc_final: 0.9039 (tppt) REVERT: D 106 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8961 (mt-10) REVERT: D 194 ARG cc_start: 0.8781 (mmt180) cc_final: 0.8356 (ttm170) REVERT: E 65 LEU cc_start: 0.9439 (tp) cc_final: 0.9188 (tp) REVERT: E 98 SER cc_start: 0.7899 (p) cc_final: 0.7601 (t) REVERT: E 116 MET cc_start: 0.8987 (ttp) cc_final: 0.8375 (tmm) REVERT: E 120 LEU cc_start: 0.9538 (mt) cc_final: 0.9091 (mt) REVERT: E 129 PHE cc_start: 0.9196 (t80) cc_final: 0.8871 (m-10) REVERT: E 200 ASN cc_start: 0.9238 (m-40) cc_final: 0.8979 (m-40) REVERT: E 217 LEU cc_start: 0.9296 (mt) cc_final: 0.9027 (mt) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.5021 time to fit residues: 247.4016 Evaluate side-chains 314 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 30 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** ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 GLN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9476 Z= 0.233 Angle : 0.567 11.644 12808 Z= 0.322 Chirality : 0.036 0.197 1478 Planarity : 0.004 0.055 1627 Dihedral : 4.131 21.647 1276 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: 1.99 (0.23), residues: 1174 helix: 1.63 (0.15), residues: 1031 sheet: None (None), residues: 0 loop : -0.71 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 147 HIS 0.005 0.001 HIS B 218 PHE 0.022 0.002 PHE C 143 TYR 0.020 0.002 TYR D 66 ARG 0.005 0.000 ARG A 198 *********************** 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 347 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 1.353 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 1 MET cc_start: 0.2268 (ptm) cc_final: 0.1885 (ptm) REVERT: B 1 MET cc_start: -0.3751 (mmm) cc_final: -0.4153 (mmm) REVERT: B 50 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7399 (tm-30) REVERT: B 112 MET cc_start: 0.6754 (mtp) cc_final: 0.6416 (mtp) REVERT: B 198 ARG cc_start: 0.6342 (mpt180) cc_final: 0.5680 (mmm160) REVERT: C 42 LEU cc_start: 0.9684 (mt) cc_final: 0.9469 (mt) REVERT: C 65 LEU cc_start: 0.9119 (tp) cc_final: 0.8891 (tt) REVERT: C 194 ARG cc_start: 0.8662 (tpt-90) cc_final: 0.8106 (tpp80) REVERT: C 200 ASN cc_start: 0.9159 (m-40) cc_final: 0.8850 (m-40) REVERT: C 207 ASP cc_start: 0.9217 (m-30) cc_final: 0.9016 (m-30) REVERT: D 4 MET cc_start: 0.6086 (ttt) cc_final: 0.5848 (ptp) REVERT: D 8 ASP cc_start: 0.9082 (t70) cc_final: 0.8666 (p0) REVERT: D 88 LYS cc_start: 0.9316 (tttm) cc_final: 0.9065 (tppt) REVERT: D 106 GLU cc_start: 0.9294 (mm-30) cc_final: 0.9034 (mt-10) REVERT: D 194 ARG cc_start: 0.8802 (mmt180) cc_final: 0.8378 (ttm170) REVERT: D 208 ASN cc_start: 0.9139 (t0) cc_final: 0.8912 (t0) REVERT: E 8 ASP cc_start: 0.9179 (m-30) cc_final: 0.8785 (m-30) REVERT: E 98 SER cc_start: 0.7942 (p) cc_final: 0.7633 (t) REVERT: E 116 MET cc_start: 0.9002 (ttp) cc_final: 0.8380 (tmm) REVERT: E 120 LEU cc_start: 0.9555 (mt) cc_final: 0.9100 (mt) REVERT: E 124 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8934 (mt-10) REVERT: E 129 PHE cc_start: 0.9247 (t80) cc_final: 0.8865 (m-10) REVERT: E 200 ASN cc_start: 0.9234 (m-40) cc_final: 0.8974 (m-40) REVERT: E 217 LEU cc_start: 0.9314 (mt) cc_final: 0.9043 (mt) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.5240 time to fit residues: 252.1171 Evaluate side-chains 312 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 0.0020 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 overall best weight: 2.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: