Starting phenix.real_space_refine on Mon Jul 22 14:10:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odt_16816/07_2024/8odt_16816.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odt_16816/07_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_16816/07_2024/8odt_16816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odt_16816/07_2024/8odt_16816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odt_16816/07_2024/8odt_16816.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odt_16816/07_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 Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 8.83, per 1000 atoms: 0.47 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 - 3.50 Amino acid : False - 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: 17.45 Conformation dependent library (CDL) restraints added in 1.8 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: 1.19 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: 6.51 Time building geometry restraints manager: 17.81 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: 77.06 - 88.91: 4 88.91 - 100.76: 17 100.76 - 112.62: 22332 112.62 - 124.47: 10583 124.47 - 136.32: 1366 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 1.850 nonbonded pdb=" O ILE C 35 " pdb=" HG1 THR C 39 " model vdw 1.547 1.850 nonbonded pdb=" O GLY E 131 " pdb=" HG SER E 135 " model vdw 1.553 1.850 nonbonded pdb=" O MET D 210 " pdb=" HG1 THR D 214 " model vdw 1.555 1.850 ... (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 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: 3.570 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: 0.260 Extract box with map and model: 1.080 Check model and map are aligned: 0.000 Set scattering table: 0.080 Process input model: 62.870 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.110 ------------------------------------------------------------------------------- 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 : 1.449 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: 0.5667 time to fit residues: 328.9838 Evaluate side-chains 342 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 318 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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: 4.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 0.0870 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN ** B 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3673 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= 0.268 Angle : 0.610 10.849 12808 Z= 0.352 Chirality : 0.037 0.228 1478 Planarity : 0.005 0.058 1627 Dihedral : 4.314 22.755 1276 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: 1.62 (0.23), residues: 1174 helix: 1.40 (0.15), residues: 1027 sheet: None (None), residues: 0 loop : -0.94 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 147 HIS 0.006 0.002 HIS C 218 PHE 0.031 0.002 PHE C 143 TYR 0.017 0.002 TYR C 192 ARG 0.005 0.000 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 379 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.787 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: 0.2370 (ptm) cc_final: 0.1953 (ptm) REVERT: A 32 TRP cc_start: 0.7001 (t60) cc_final: 0.6797 (t60) REVERT: B 41 ILE cc_start: 0.9434 (mt) cc_final: 0.9212 (tt) REVERT: B 89 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6752 (tp30) REVERT: B 112 MET cc_start: 0.6764 (mtp) cc_final: 0.6327 (mtp) REVERT: B 116 MET cc_start: 0.9230 (ttt) cc_final: 0.8700 (ttm) REVERT: B 197 GLN cc_start: 0.8669 (mt0) cc_final: 0.7710 (tm-30) REVERT: C 20 ILE cc_start: 0.9446 (mt) cc_final: 0.9244 (tp) REVERT: C 42 LEU cc_start: 0.9674 (mt) cc_final: 0.9472 (mt) REVERT: C 53 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8977 (tm-30) REVERT: C 150 MET cc_start: 0.9306 (mtm) cc_final: 0.8978 (mtp) REVERT: D 4 MET cc_start: 0.6126 (ttt) cc_final: 0.5832 (ptt) REVERT: D 8 ASP cc_start: 0.9032 (t70) cc_final: 0.8715 (p0) REVERT: D 80 GLU cc_start: 0.8859 (tt0) cc_final: 0.8282 (tt0) REVERT: D 81 GLN cc_start: 0.9334 (tt0) cc_final: 0.9104 (tt0) REVERT: D 88 LYS cc_start: 0.9346 (tttm) cc_final: 0.9065 (tppt) REVERT: D 194 ARG cc_start: 0.8791 (mmt180) cc_final: 0.8370 (ttm170) REVERT: E 116 MET cc_start: 0.9022 (ttp) cc_final: 0.8364 (tmm) REVERT: E 120 LEU cc_start: 0.9531 (mt) cc_final: 0.9189 (mt) REVERT: E 129 PHE cc_start: 0.9184 (t80) cc_final: 0.8870 (m-10) REVERT: E 200 ASN cc_start: 0.9270 (m-40) cc_final: 0.9017 (m-40) REVERT: E 208 ASN cc_start: 0.9068 (t0) cc_final: 0.8810 (t0) REVERT: E 210 MET cc_start: 0.9082 (ttp) cc_final: 0.8785 (ttp) REVERT: E 217 LEU cc_start: 0.9278 (mt) cc_final: 0.9013 (mt) REVERT: F 33 MET cc_start: 0.0289 (ttp) cc_final: 0.0031 (mtt) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.5022 time to fit residues: 257.5244 Evaluate side-chains 332 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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: 3.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 115 optimal weight: 0.0040 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN C 122 ASN C 196 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9476 Z= 0.277 Angle : 0.607 11.113 12808 Z= 0.350 Chirality : 0.036 0.141 1478 Planarity : 0.005 0.073 1627 Dihedral : 4.234 22.088 1276 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: 1.68 (0.23), residues: 1174 helix: 1.42 (0.15), residues: 1027 sheet: None (None), residues: 0 loop : -0.76 (0.50), residues: 147 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 0.024 0.002 PHE C 143 TYR 0.013 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 : 1.417 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: 0.2344 (ptm) cc_final: 0.1958 (ptm) REVERT: B 50 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7535 (tm-30) REVERT: B 112 MET cc_start: 0.6827 (mtp) cc_final: 0.6493 (mtp) REVERT: B 198 ARG cc_start: 0.6287 (mpt180) cc_final: 0.5655 (mmm160) REVERT: C 42 LEU cc_start: 0.9685 (mt) cc_final: 0.9482 (mt) REVERT: C 150 MET cc_start: 0.9332 (mtm) cc_final: 0.8988 (mtp) REVERT: C 200 ASN cc_start: 0.9206 (m-40) cc_final: 0.8925 (m-40) REVERT: D 4 MET cc_start: 0.6151 (ttt) cc_final: 0.5808 (ptt) REVERT: D 8 ASP cc_start: 0.9033 (t70) cc_final: 0.8710 (p0) REVERT: D 88 LYS cc_start: 0.9368 (tttm) cc_final: 0.9071 (tppt) REVERT: D 194 ARG cc_start: 0.8819 (mmt180) cc_final: 0.8398 (ttm170) REVERT: E 98 SER cc_start: 0.7897 (p) cc_final: 0.7611 (t) REVERT: E 116 MET cc_start: 0.9019 (ttp) cc_final: 0.8374 (tmm) REVERT: E 120 LEU cc_start: 0.9530 (mt) cc_final: 0.9098 (mt) REVERT: E 129 PHE cc_start: 0.9223 (t80) cc_final: 0.8869 (m-10) REVERT: E 200 ASN cc_start: 0.9254 (m-40) cc_final: 0.8998 (m-40) REVERT: E 217 LEU cc_start: 0.9315 (mt) cc_final: 0.9043 (mt) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.4847 time to fit residues: 241.1024 Evaluate side-chains 315 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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: 0.8980 chunk 55 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6800 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9476 Z= 0.213 Angle : 0.562 11.130 12808 Z= 0.318 Chirality : 0.035 0.123 1478 Planarity : 0.004 0.056 1627 Dihedral : 4.137 22.391 1276 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 1.98 (0.23), residues: 1174 helix: 1.62 (0.15), residues: 1030 sheet: None (None), residues: 0 loop : -0.72 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 147 HIS 0.008 0.001 HIS C 218 PHE 0.023 0.002 PHE C 143 TYR 0.027 0.001 TYR D 66 ARG 0.009 0.000 ARG D 113 *********************** 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 359 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2365 (ptm) cc_final: 0.1977 (ptm) REVERT: B 1 MET cc_start: -0.3920 (mmm) cc_final: -0.4344 (mmm) REVERT: B 50 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7463 (tm-30) REVERT: B 66 TYR cc_start: 0.7517 (t80) cc_final: 0.7260 (t80) REVERT: B 112 MET cc_start: 0.6722 (mtp) cc_final: 0.6513 (mtp) REVERT: B 197 GLN cc_start: 0.8889 (mp10) cc_final: 0.7976 (tm-30) REVERT: C 42 LEU cc_start: 0.9687 (mt) cc_final: 0.9476 (mt) REVERT: C 65 LEU cc_start: 0.9138 (tp) cc_final: 0.8911 (tp) REVERT: C 119 GLU cc_start: 0.9132 (tp30) cc_final: 0.8924 (tp30) REVERT: C 200 ASN cc_start: 0.9152 (m-40) cc_final: 0.8816 (m-40) REVERT: D 4 MET cc_start: 0.6037 (ttt) cc_final: 0.5833 (ptt) REVERT: D 8 ASP cc_start: 0.9005 (t70) cc_final: 0.8710 (p0) REVERT: D 81 GLN cc_start: 0.9373 (tt0) cc_final: 0.8295 (tt0) REVERT: D 88 LYS cc_start: 0.9331 (tttm) cc_final: 0.9071 (tppt) REVERT: D 194 ARG cc_start: 0.8797 (mmt180) cc_final: 0.8379 (ttm170) REVERT: E 8 ASP cc_start: 0.9194 (m-30) cc_final: 0.8814 (m-30) REVERT: E 98 SER cc_start: 0.7981 (p) cc_final: 0.7554 (t) REVERT: E 116 MET cc_start: 0.9016 (ttp) cc_final: 0.8395 (tmm) REVERT: E 120 LEU cc_start: 0.9546 (mt) cc_final: 0.9102 (mt) REVERT: E 124 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8979 (mt-10) REVERT: E 129 PHE cc_start: 0.9221 (t80) cc_final: 0.8843 (m-10) REVERT: E 200 ASN cc_start: 0.9208 (m-40) cc_final: 0.8941 (m-40) REVERT: E 210 MET cc_start: 0.9456 (ttm) cc_final: 0.9198 (ttm) REVERT: E 217 LEU cc_start: 0.9302 (mt) cc_final: 0.9041 (mt) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.4709 time to fit residues: 235.7053 Evaluate side-chains 317 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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: 2.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 205 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9476 Z= 0.205 Angle : 0.543 10.947 12808 Z= 0.308 Chirality : 0.035 0.172 1478 Planarity : 0.004 0.054 1627 Dihedral : 4.050 21.596 1276 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.10 % Allowed : 1.86 % Favored : 98.04 % 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: 2.23 (0.24), residues: 1174 helix: 1.79 (0.15), residues: 1033 sheet: None (None), residues: 0 loop : -0.67 (0.54), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.004 0.001 HIS B 218 PHE 0.020 0.002 PHE C 143 TYR 0.011 0.001 TYR A 66 ARG 0.004 0.000 ARG A 92 *********************** 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 357 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 356 time to evaluate : 1.397 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: A 1 MET cc_start: 0.2327 (ptm) cc_final: 0.1976 (ptm) REVERT: B 1 MET cc_start: -0.3901 (mmm) cc_final: -0.4337 (mmm) REVERT: B 50 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7435 (tm-30) REVERT: B 66 TYR cc_start: 0.7575 (t80) cc_final: 0.7308 (t80) REVERT: B 127 ILE cc_start: 0.7872 (mt) cc_final: 0.7509 (mm) REVERT: B 197 GLN cc_start: 0.8885 (mp10) cc_final: 0.7966 (tm-30) REVERT: C 65 LEU cc_start: 0.9122 (tp) cc_final: 0.8816 (tt) REVERT: C 119 GLU cc_start: 0.9099 (tp30) cc_final: 0.8860 (tp30) REVERT: C 200 ASN cc_start: 0.9150 (m-40) cc_final: 0.8823 (m-40) REVERT: D 4 MET cc_start: 0.6110 (ttt) cc_final: 0.5867 (ptp) REVERT: D 8 ASP cc_start: 0.8979 (t70) cc_final: 0.8704 (p0) REVERT: D 88 LYS cc_start: 0.9342 (tttm) cc_final: 0.9058 (tppt) REVERT: D 129 PHE cc_start: 0.9429 (t80) cc_final: 0.9228 (t80) REVERT: D 194 ARG cc_start: 0.8762 (mmt180) cc_final: 0.8363 (ttm170) REVERT: D 208 ASN cc_start: 0.9108 (t0) cc_final: 0.8860 (t0) REVERT: E 8 ASP cc_start: 0.9219 (m-30) cc_final: 0.8852 (m-30) REVERT: E 98 SER cc_start: 0.7851 (p) cc_final: 0.7464 (t) REVERT: E 116 MET cc_start: 0.9014 (ttp) cc_final: 0.8390 (tmm) REVERT: E 120 LEU cc_start: 0.9540 (mt) cc_final: 0.9100 (mt) REVERT: E 129 PHE cc_start: 0.9240 (t80) cc_final: 0.8789 (m-10) REVERT: E 204 LEU cc_start: 0.9420 (mt) cc_final: 0.9212 (mt) REVERT: E 205 ASN cc_start: 0.8689 (t0) cc_final: 0.8240 (t0) REVERT: E 208 ASN cc_start: 0.9297 (t0) cc_final: 0.9031 (t0) REVERT: E 210 MET cc_start: 0.9452 (ttm) cc_final: 0.9141 (ttm) REVERT: E 211 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8442 (mm-30) REVERT: E 217 LEU cc_start: 0.9311 (mt) cc_final: 0.9044 (mt) outliers start: 1 outliers final: 0 residues processed: 357 average time/residue: 0.4552 time to fit residues: 226.6752 Evaluate side-chains 324 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN C 161 GLN C 196 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 ASN ** 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: 0.6884 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9476 Z= 0.258 Angle : 0.582 10.981 12808 Z= 0.335 Chirality : 0.036 0.164 1478 Planarity : 0.004 0.053 1627 Dihedral : 4.116 20.197 1276 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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: 1.89 (0.24), residues: 1174 helix: 1.57 (0.15), residues: 1031 sheet: None (None), residues: 0 loop : -0.84 (0.53), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 147 HIS 0.007 0.001 HIS A 126 PHE 0.019 0.002 PHE D 87 TYR 0.020 0.002 TYR C 192 ARG 0.004 0.000 ARG A 92 *********************** 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 347 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 1.292 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: A 1 MET cc_start: 0.2324 (ptm) cc_final: 0.1948 (ptm) REVERT: A 24 LEU cc_start: 0.6811 (mt) cc_final: 0.6356 (mt) REVERT: B 1 MET cc_start: -0.3888 (mmm) cc_final: -0.4320 (mmm) REVERT: B 66 TYR cc_start: 0.7590 (t80) cc_final: 0.7318 (t80) REVERT: B 112 MET cc_start: 0.6758 (mtp) cc_final: 0.6378 (mtp) REVERT: B 127 ILE cc_start: 0.7906 (mt) cc_final: 0.7563 (mm) REVERT: B 197 GLN cc_start: 0.8920 (mp10) cc_final: 0.8091 (tm-30) REVERT: C 119 GLU cc_start: 0.9070 (tp30) cc_final: 0.8711 (tm-30) REVERT: C 200 ASN cc_start: 0.9207 (m-40) cc_final: 0.8915 (m-40) REVERT: D 8 ASP cc_start: 0.8986 (t70) cc_final: 0.8555 (p0) REVERT: D 88 LYS cc_start: 0.9351 (tttm) cc_final: 0.9083 (tppt) REVERT: D 106 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8989 (mt-10) REVERT: D 129 PHE cc_start: 0.9507 (t80) cc_final: 0.9287 (t80) REVERT: D 194 ARG cc_start: 0.8808 (mmt180) cc_final: 0.8443 (ttm170) REVERT: D 207 ASP cc_start: 0.9322 (t70) cc_final: 0.9104 (t0) REVERT: D 208 ASN cc_start: 0.9128 (t0) cc_final: 0.8899 (t0) REVERT: E 8 ASP cc_start: 0.9256 (m-30) cc_final: 0.8937 (m-30) REVERT: E 15 LEU cc_start: 0.7852 (mm) cc_final: 0.7589 (pt) REVERT: E 70 GLN cc_start: 0.8837 (tt0) cc_final: 0.8592 (tp-100) REVERT: E 98 SER cc_start: 0.7981 (p) cc_final: 0.7641 (t) REVERT: E 116 MET cc_start: 0.8940 (ttp) cc_final: 0.8524 (tmm) REVERT: E 129 PHE cc_start: 0.9255 (t80) cc_final: 0.8823 (m-10) REVERT: E 200 ASN cc_start: 0.9182 (m110) cc_final: 0.8845 (m110) REVERT: E 205 ASN cc_start: 0.8796 (t0) cc_final: 0.8321 (t0) REVERT: E 208 ASN cc_start: 0.9347 (t0) cc_final: 0.9098 (t0) REVERT: E 211 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8491 (mm-30) REVERT: E 217 LEU cc_start: 0.9311 (mt) cc_final: 0.9020 (mt) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.4607 time to fit residues: 224.5267 Evaluate side-chains 314 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9476 Z= 0.187 Angle : 0.533 10.919 12808 Z= 0.299 Chirality : 0.034 0.120 1478 Planarity : 0.004 0.049 1627 Dihedral : 4.003 20.045 1276 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 2.30 (0.24), residues: 1174 helix: 1.84 (0.15), residues: 1032 sheet: None (None), residues: 0 loop : -0.66 (0.54), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 147 HIS 0.005 0.001 HIS C 126 PHE 0.050 0.002 PHE C 143 TYR 0.010 0.001 TYR A 66 ARG 0.004 0.000 ARG A 92 *********************** 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 358 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2233 (ptm) cc_final: 0.1831 (ptm) REVERT: B 1 MET cc_start: -0.3876 (mmm) cc_final: -0.4295 (mmm) REVERT: B 27 PHE cc_start: 0.7174 (m-80) cc_final: 0.6805 (m-80) REVERT: B 66 TYR cc_start: 0.7612 (t80) cc_final: 0.7354 (t80) REVERT: B 112 MET cc_start: 0.6527 (mtp) cc_final: 0.6159 (mtp) REVERT: B 127 ILE cc_start: 0.7888 (mt) cc_final: 0.7495 (mm) REVERT: B 197 GLN cc_start: 0.8884 (mp10) cc_final: 0.8090 (tm-30) REVERT: C 83 PHE cc_start: 0.9037 (t80) cc_final: 0.8735 (t80) REVERT: C 112 MET cc_start: 0.7806 (mtm) cc_final: 0.7544 (mtm) REVERT: C 119 GLU cc_start: 0.9051 (tp30) cc_final: 0.8687 (tm-30) REVERT: C 200 ASN cc_start: 0.9143 (m-40) cc_final: 0.8799 (m-40) REVERT: D 8 ASP cc_start: 0.9019 (t70) cc_final: 0.8558 (p0) REVERT: D 88 LYS cc_start: 0.9353 (tttm) cc_final: 0.9067 (tppt) REVERT: D 106 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8989 (mt-10) REVERT: D 115 SER cc_start: 0.9181 (m) cc_final: 0.8910 (t) REVERT: D 129 PHE cc_start: 0.9465 (t80) cc_final: 0.9238 (t80) REVERT: D 151 HIS cc_start: 0.8196 (m-70) cc_final: 0.7667 (m170) REVERT: D 194 ARG cc_start: 0.8747 (mmt180) cc_final: 0.8410 (ttm170) REVERT: D 207 ASP cc_start: 0.9285 (t70) cc_final: 0.9060 (t0) REVERT: D 208 ASN cc_start: 0.9067 (t0) cc_final: 0.8864 (t0) REVERT: E 8 ASP cc_start: 0.9273 (m-30) cc_final: 0.8957 (m-30) REVERT: E 15 LEU cc_start: 0.7809 (mm) cc_final: 0.7532 (pt) REVERT: E 98 SER cc_start: 0.7939 (p) cc_final: 0.7607 (t) REVERT: E 116 MET cc_start: 0.8892 (ttp) cc_final: 0.8358 (tmm) REVERT: E 120 LEU cc_start: 0.9578 (mt) cc_final: 0.9231 (mt) REVERT: E 129 PHE cc_start: 0.9219 (t80) cc_final: 0.8755 (m-10) REVERT: E 200 ASN cc_start: 0.9159 (m110) cc_final: 0.8795 (m110) REVERT: E 205 ASN cc_start: 0.8727 (t0) cc_final: 0.8318 (t0) REVERT: E 207 ASP cc_start: 0.8811 (t0) cc_final: 0.8609 (t0) REVERT: E 208 ASN cc_start: 0.9324 (t0) cc_final: 0.9057 (t0) REVERT: E 217 LEU cc_start: 0.9307 (mt) cc_final: 0.9019 (mt) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.4547 time to fit residues: 228.9647 Evaluate side-chains 317 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** B 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN C 228 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.5965 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= 0.256 Angle : 0.580 11.155 12808 Z= 0.337 Chirality : 0.036 0.147 1478 Planarity : 0.004 0.052 1627 Dihedral : 4.101 19.985 1276 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: 1.95 (0.24), residues: 1174 helix: 1.64 (0.15), residues: 1030 sheet: None (None), residues: 0 loop : -1.00 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 147 HIS 0.004 0.001 HIS E 151 PHE 0.039 0.002 PHE C 143 TYR 0.016 0.001 TYR D 66 ARG 0.005 0.000 ARG A 92 *********************** 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 338 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.470 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: 0.2226 (ptm) cc_final: 0.1763 (ptm) REVERT: B 1 MET cc_start: -0.3913 (mmm) cc_final: -0.4380 (mmm) REVERT: B 66 TYR cc_start: 0.7664 (t80) cc_final: 0.7416 (t80) REVERT: B 112 MET cc_start: 0.6860 (mtp) cc_final: 0.6536 (mtp) REVERT: B 127 ILE cc_start: 0.7925 (mt) cc_final: 0.7598 (mm) REVERT: C 119 GLU cc_start: 0.9047 (tp30) cc_final: 0.8727 (tm-30) REVERT: C 200 ASN cc_start: 0.9188 (m-40) cc_final: 0.8856 (m-40) REVERT: D 8 ASP cc_start: 0.9039 (t70) cc_final: 0.8537 (p0) REVERT: D 9 LEU cc_start: 0.9617 (mt) cc_final: 0.9379 (mt) REVERT: D 88 LYS cc_start: 0.9365 (tttm) cc_final: 0.9112 (tppt) REVERT: D 106 GLU cc_start: 0.9330 (mm-30) cc_final: 0.8983 (mt-10) REVERT: D 115 SER cc_start: 0.9252 (m) cc_final: 0.8974 (t) REVERT: D 194 ARG cc_start: 0.8825 (mmt180) cc_final: 0.8449 (ttm170) REVERT: D 207 ASP cc_start: 0.9312 (t70) cc_final: 0.9091 (t0) REVERT: D 208 ASN cc_start: 0.9090 (t0) cc_final: 0.8885 (t0) REVERT: E 8 ASP cc_start: 0.9275 (m-30) cc_final: 0.8993 (m-30) REVERT: E 15 LEU cc_start: 0.7831 (mm) cc_final: 0.7557 (pt) REVERT: E 94 HIS cc_start: 0.6626 (t70) cc_final: 0.6236 (t70) REVERT: E 98 SER cc_start: 0.7917 (p) cc_final: 0.7573 (t) REVERT: E 116 MET cc_start: 0.8946 (ttp) cc_final: 0.8519 (tmm) REVERT: E 129 PHE cc_start: 0.9245 (t80) cc_final: 0.8774 (m-10) REVERT: E 200 ASN cc_start: 0.9166 (m110) cc_final: 0.8825 (m110) REVERT: E 205 ASN cc_start: 0.8795 (t0) cc_final: 0.8381 (t0) REVERT: E 208 ASN cc_start: 0.9367 (t0) cc_final: 0.9085 (t0) REVERT: E 211 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8560 (mm-30) REVERT: E 217 LEU cc_start: 0.9328 (mt) cc_final: 0.9025 (mt) REVERT: G 32 PHE cc_start: 0.7365 (t80) cc_final: 0.7109 (t80) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.4452 time to fit residues: 212.4275 Evaluate side-chains 308 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN C 196 ASN C 205 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: 0.6860 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9476 Z= 0.186 Angle : 0.534 11.090 12808 Z= 0.302 Chirality : 0.035 0.163 1478 Planarity : 0.004 0.049 1627 Dihedral : 4.031 22.860 1276 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.10 % Allowed : 0.62 % Favored : 99.28 % 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: 2.32 (0.24), residues: 1174 helix: 1.88 (0.15), residues: 1035 sheet: None (None), residues: 0 loop : -0.96 (0.52), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 147 HIS 0.004 0.001 HIS A 126 PHE 0.041 0.002 PHE C 143 TYR 0.010 0.001 TYR A 66 ARG 0.005 0.000 ARG A 92 *********************** 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 349 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 348 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2260 (ptm) cc_final: 0.1779 (ptm) REVERT: B 1 MET cc_start: -0.3914 (mmm) cc_final: -0.4391 (mmm) REVERT: B 66 TYR cc_start: 0.7729 (t80) cc_final: 0.7472 (t80) REVERT: B 112 MET cc_start: 0.6620 (mtp) cc_final: 0.6281 (mtp) REVERT: C 119 GLU cc_start: 0.9021 (tp30) cc_final: 0.8683 (tm-30) REVERT: D 8 ASP cc_start: 0.9047 (t70) cc_final: 0.8530 (p0) REVERT: D 88 LYS cc_start: 0.9370 (tttm) cc_final: 0.9085 (tppt) REVERT: D 106 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8980 (mt-10) REVERT: D 115 SER cc_start: 0.9171 (m) cc_final: 0.8907 (t) REVERT: D 194 ARG cc_start: 0.8789 (mmt180) cc_final: 0.8428 (ttm170) REVERT: D 207 ASP cc_start: 0.9262 (t70) cc_final: 0.9036 (t0) REVERT: D 208 ASN cc_start: 0.9053 (t0) cc_final: 0.8836 (t0) REVERT: E 8 ASP cc_start: 0.9279 (m-30) cc_final: 0.9042 (m-30) REVERT: E 15 LEU cc_start: 0.7760 (mm) cc_final: 0.7467 (pt) REVERT: E 80 GLU cc_start: 0.9141 (tt0) cc_final: 0.8774 (tt0) REVERT: E 94 HIS cc_start: 0.6600 (t70) cc_final: 0.6250 (t70) REVERT: E 98 SER cc_start: 0.7966 (p) cc_final: 0.7674 (t) REVERT: E 116 MET cc_start: 0.8888 (ttp) cc_final: 0.8358 (tmm) REVERT: E 120 LEU cc_start: 0.9571 (mt) cc_final: 0.9231 (mt) REVERT: E 129 PHE cc_start: 0.9212 (t80) cc_final: 0.8748 (m-10) REVERT: E 200 ASN cc_start: 0.9117 (m110) cc_final: 0.8748 (m110) REVERT: E 205 ASN cc_start: 0.8719 (t0) cc_final: 0.8328 (t0) REVERT: E 207 ASP cc_start: 0.8828 (t0) cc_final: 0.8602 (t0) REVERT: E 208 ASN cc_start: 0.9334 (t0) cc_final: 0.9040 (t0) REVERT: E 217 LEU cc_start: 0.9313 (mt) cc_final: 0.9018 (mt) REVERT: G 32 PHE cc_start: 0.7301 (t80) cc_final: 0.7053 (t80) outliers start: 1 outliers final: 0 residues processed: 349 average time/residue: 0.4483 time to fit residues: 219.3338 Evaluate side-chains 306 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 117 optimal weight: 0.4980 chunk 108 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN C 196 ASN C 205 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.6308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9476 Z= 0.194 Angle : 0.541 11.241 12808 Z= 0.303 Chirality : 0.036 0.239 1478 Planarity : 0.004 0.047 1627 Dihedral : 4.001 22.198 1276 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.10 % Allowed : 0.62 % Favored : 99.28 % 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: 2.50 (0.24), residues: 1174 helix: 1.99 (0.15), residues: 1036 sheet: None (None), residues: 0 loop : -0.87 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 147 HIS 0.004 0.001 HIS B 126 PHE 0.049 0.002 PHE A 143 TYR 0.030 0.001 TYR C 192 ARG 0.005 0.000 ARG A 92 ********************** 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 344 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 343 time to evaluate : 1.426 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: 0.2270 (ptm) cc_final: 0.1776 (ptm) REVERT: B 1 MET cc_start: -0.3928 (mmm) cc_final: -0.4390 (mmm) REVERT: B 66 TYR cc_start: 0.7818 (t80) cc_final: 0.7571 (t80) REVERT: B 112 MET cc_start: 0.6699 (mtp) cc_final: 0.6374 (mtp) REVERT: C 200 ASN cc_start: 0.9100 (m-40) cc_final: 0.8765 (m-40) REVERT: D 1 MET cc_start: -0.1313 (ttt) cc_final: -0.1664 (ttt) REVERT: D 8 ASP cc_start: 0.9032 (t70) cc_final: 0.8537 (p0) REVERT: D 9 LEU cc_start: 0.9625 (mt) cc_final: 0.9375 (mt) REVERT: D 106 GLU cc_start: 0.9312 (mm-30) cc_final: 0.8970 (mt-10) REVERT: D 115 SER cc_start: 0.9174 (m) cc_final: 0.8974 (t) REVERT: D 129 PHE cc_start: 0.9396 (t80) cc_final: 0.9195 (t80) REVERT: D 194 ARG cc_start: 0.8766 (mmt180) cc_final: 0.8462 (ttm170) REVERT: D 207 ASP cc_start: 0.9267 (t70) cc_final: 0.9034 (t0) REVERT: E 8 ASP cc_start: 0.9301 (m-30) cc_final: 0.9064 (m-30) REVERT: E 15 LEU cc_start: 0.7735 (mm) cc_final: 0.7448 (pt) REVERT: E 80 GLU cc_start: 0.9107 (tt0) cc_final: 0.8732 (tt0) REVERT: E 94 HIS cc_start: 0.6662 (t70) cc_final: 0.6283 (t-90) REVERT: E 98 SER cc_start: 0.8019 (p) cc_final: 0.7731 (t) REVERT: E 116 MET cc_start: 0.8896 (ttp) cc_final: 0.8373 (tmm) REVERT: E 120 LEU cc_start: 0.9570 (mt) cc_final: 0.9234 (mt) REVERT: E 129 PHE cc_start: 0.9217 (t80) cc_final: 0.8723 (m-10) REVERT: E 200 ASN cc_start: 0.9118 (m110) cc_final: 0.8728 (m110) REVERT: E 205 ASN cc_start: 0.8716 (t0) cc_final: 0.8317 (t0) REVERT: E 207 ASP cc_start: 0.8839 (t0) cc_final: 0.8600 (t0) REVERT: E 208 ASN cc_start: 0.9347 (t160) cc_final: 0.9047 (t0) REVERT: E 217 LEU cc_start: 0.9318 (mt) cc_final: 0.9030 (mt) REVERT: G 32 PHE cc_start: 0.7222 (t80) cc_final: 0.6957 (t80) outliers start: 1 outliers final: 0 residues processed: 344 average time/residue: 0.4278 time to fit residues: 207.1665 Evaluate side-chains 312 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 1.416 ------------------------------------------------------------------------------- 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: 4.9990 chunk 86 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 93 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 126 HIS ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 ASN C 196 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 218 HIS E 117 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.185841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.134557 restraints weight = 69159.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.141259 restraints weight = 40039.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.145753 restraints weight = 27361.755| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.6523 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= 0.292 Angle : 0.605 11.509 12808 Z= 0.352 Chirality : 0.037 0.211 1478 Planarity : 0.004 0.052 1627 Dihedral : 4.164 22.227 1276 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: 1.87 (0.24), residues: 1174 helix: 1.57 (0.15), residues: 1034 sheet: None (None), residues: 0 loop : -1.00 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 32 HIS 0.005 0.001 HIS B 218 PHE 0.042 0.002 PHE A 143 TYR 0.011 0.002 TYR A 84 ARG 0.005 0.001 ARG A 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5288.67 seconds wall clock time: 92 minutes 55.03 seconds (5575.03 seconds total)