Starting phenix.real_space_refine on Wed Jun 18 13:50:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6l_29773/06_2025/8g6l_29773.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6l_29773/06_2025/8g6l_29773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g6l_29773/06_2025/8g6l_29773.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6l_29773/06_2025/8g6l_29773.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6l_29773/06_2025/8g6l_29773.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6l_29773/06_2025/8g6l_29773.cif" } resolution = 3.3 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= 0.000 sd= 0.002 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 80 5.16 5 C 6806 2.51 5 N 1875 2.21 5 O 2026 1.98 5 H 10651 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21438 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3115 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2721 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 159} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3280 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3115 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3109 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3048 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 3050 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 11.93, per 1000 atoms: 0.56 Number of scatterers: 21438 At special positions: 0 Unit cell: (126.1, 118.3, 127.4, 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 80 16.00 O 2026 8.00 N 1875 7.00 C 6806 6.00 H 10651 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.71 Conformation dependent library (CDL) restraints added in 1.7 seconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 1 sheets defined 77.9% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.732A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.528A pdb=" N GLN A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.426A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 removed outlier: 3.734A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'B' and resid 16 through 31 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 59 removed outlier: 3.848A pdb=" N VAL B 59 " --> pdb=" O MET B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.403A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 30 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 48 through 60 removed outlier: 3.887A pdb=" N THR C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 178 through 194 removed outlier: 4.301A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 3.812A pdb=" N ILE C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 31 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 84 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 116 Processing helix chain 'D' and resid 125 through 146 Processing helix chain 'D' and resid 160 through 174 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.249A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.956A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'E' and resid 16 through 31 Processing helix chain 'E' and resid 35 through 44 Processing helix chain 'E' and resid 48 through 58 Processing helix chain 'E' and resid 62 through 84 Processing helix chain 'E' and resid 110 through 120 Processing helix chain 'E' and resid 125 through 146 Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 160 through 176 removed outlier: 3.577A pdb=" N GLN E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 194 removed outlier: 4.233A pdb=" N LEU E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.512A pdb=" N ILE E 201 " --> pdb=" O ASP E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 16 through 31 Processing helix chain 'F' and resid 35 through 44 Processing helix chain 'F' and resid 48 through 58 Processing helix chain 'F' and resid 62 through 84 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 110 through 120 Processing helix chain 'F' and resid 125 through 146 Processing helix chain 'F' and resid 149 through 153 Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.288A pdb=" N TRP F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 3.507A pdb=" N ILE F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'G' and resid 16 through 29 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 146 Processing helix chain 'G' and resid 149 through 153 removed outlier: 3.651A pdb=" N ILE G 153 " --> pdb=" O ILE G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 176 removed outlier: 6.418A pdb=" N ASP G 166 " --> pdb=" O ARG G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 removed outlier: 3.851A pdb=" N TRP G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 removed outlier: 3.718A pdb=" N ILE G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 219 Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 731 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.00 Time building geometry restraints manager: 6.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10639 1.03 - 1.23: 201 1.23 - 1.43: 4226 1.43 - 1.63: 6461 1.63 - 1.82: 148 Bond restraints: 21675 Sorted by residual: bond pdb=" N HIS G 12 " pdb=" CA HIS G 12 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N HIS F 12 " pdb=" CA HIS F 12 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" CG PRO D 207 " pdb=" CD PRO D 207 " ideal model delta sigma weight residual 1.503 1.446 0.057 3.40e-02 8.65e+02 2.79e+00 bond pdb=" N HIS F 12 " pdb=" H HIS F 12 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" N HIS G 12 " pdb=" H HIS G 12 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.22e+00 ... (remaining 21670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 38831 2.48 - 4.97: 408 4.97 - 7.45: 34 7.45 - 9.93: 2 9.93 - 12.42: 2 Bond angle restraints: 39277 Sorted by residual: angle pdb=" C ARG G 162 " pdb=" N ASP G 163 " pdb=" CA ASP G 163 " ideal model delta sigma weight residual 121.54 133.96 -12.42 1.91e+00 2.74e-01 4.23e+01 angle pdb=" CA PRO D 207 " pdb=" N PRO D 207 " pdb=" CD PRO D 207 " ideal model delta sigma weight residual 112.00 104.76 7.24 1.40e+00 5.10e-01 2.67e+01 angle pdb=" N PRO D 207 " pdb=" CD PRO D 207 " pdb=" CG PRO D 207 " ideal model delta sigma weight residual 103.20 97.50 5.70 1.50e+00 4.44e-01 1.44e+01 angle pdb=" CB MET D 68 " pdb=" CG MET D 68 " pdb=" SD MET D 68 " ideal model delta sigma weight residual 112.70 101.72 10.98 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA MET G 215 " pdb=" CB MET G 215 " pdb=" CG MET G 215 " ideal model delta sigma weight residual 114.10 120.07 -5.97 2.00e+00 2.50e-01 8.91e+00 ... (remaining 39272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8852 17.91 - 35.82: 953 35.82 - 53.73: 341 53.73 - 71.63: 80 71.63 - 89.54: 17 Dihedral angle restraints: 10243 sinusoidal: 5704 harmonic: 4539 Sorted by residual: dihedral pdb=" CA ILE D 115 " pdb=" C ILE D 115 " pdb=" N GLY D 116 " pdb=" CA GLY D 116 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ASP E 163 " pdb=" CB ASP E 163 " pdb=" CG ASP E 163 " pdb=" OD1 ASP E 163 " ideal model delta sinusoidal sigma weight residual -30.00 -88.14 58.14 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CB GLU A 98 " pdb=" CG GLU A 98 " pdb=" CD GLU A 98 " pdb=" OE1 GLU A 98 " ideal model delta sinusoidal sigma weight residual 0.00 89.54 -89.54 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 10240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1086 0.030 - 0.060: 395 0.060 - 0.091: 123 0.091 - 0.121: 61 0.121 - 0.151: 13 Chirality restraints: 1678 Sorted by residual: chirality pdb=" CA MET F 215 " pdb=" N MET F 215 " pdb=" C MET F 215 " pdb=" CB MET F 215 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA ILE B 124 " pdb=" N ILE B 124 " pdb=" C ILE B 124 " pdb=" CB ILE B 124 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 1675 not shown) Planarity restraints: 3205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG G 162 " 0.017 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ARG G 162 " -0.061 2.00e-02 2.50e+03 pdb=" O ARG G 162 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP G 163 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 206 " -0.060 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO D 207 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO D 207 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 207 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 163 " -0.015 2.00e-02 2.50e+03 3.00e-02 8.97e+00 pdb=" C ASP G 163 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP G 163 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR G 164 " -0.018 2.00e-02 2.50e+03 ... (remaining 3202 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.28: 3366 2.28 - 2.86: 47774 2.86 - 3.44: 57994 3.44 - 4.02: 74769 4.02 - 4.60: 116079 Nonbonded interactions: 299982 Sorted by model distance: nonbonded pdb=" O ASN A 57 " pdb="HH22 ARG D 173 " model vdw 1.695 2.450 nonbonded pdb=" H ARG E 100 " pdb=" OD2 ASP E 103 " model vdw 1.736 2.450 nonbonded pdb=" O ILE A 115 " pdb=" HG1 THR A 119 " model vdw 1.736 2.450 nonbonded pdb=" OG SER A 16 " pdb=" H THR A 19 " model vdw 1.737 2.450 nonbonded pdb=" O GLY G 156 " pdb="HD22 ASN G 195 " model vdw 1.738 2.450 ... (remaining 299977 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 12 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid \ 80 through 85 or (resid 96 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 97 through 99 or (resid 100 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 101 through \ 119 or (resid 120 and (name N or name CA or name C or name O or name CB or name \ CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name \ HB2 or name HB3 or name HD2 or name HE1)) or resid 121 through 157 or (resid 15 \ 8 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 159 through 161 or (resid 162 and (name N or name CA or name C or name \ O or name CB )) or (resid 163 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name OD2)) or resid 164 through 181 or (resid 182 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 183 through 193)) selection = (chain 'B' and ((resid 12 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 13 throug \ h 78 or (resid 79 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name OE1 or name OE2)) or resid 80 through 85 or (resid 96 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 97 through 99 or (resid 100 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 101 through 119 or (resid 120 and (name N \ or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or \ name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or \ name HE1)) or resid 121 through 157 or (resid 158 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 159 through 161 or (re \ sid 162 and (name N or name CA or name C or name O or name CB )) or (resid 163 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame OD2)) or resid 164 through 193)) selection = (chain 'C' and (resid 12 through 61 or (resid 62 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name H \ E2)) or resid 63 through 78 or (resid 79 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 80 throu \ gh 85 or (resid 96 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 97 through 99 or (resid 100 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 101 through 119 or \ (resid 120 and (name N or name CA or name C or name O or name CB or name CG or n \ ame ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or \ name HB3 or name HD2 or name HE1)) or resid 121 through 157 or (resid 158 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 159 through 161 or (resid 162 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 163 and (name N or name CA or name C or name O or name CB or n \ ame CG or name OD1 or name OD2)) or resid 164 through 181 or (resid 182 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 1 \ 83 through 186 or (resid 187 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 188 through 193)) selection = (chain 'D' and ((resid 12 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 13 throug \ h 78 or (resid 79 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name OE1 or name OE2)) or resid 80 through 83 or (resid 84 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD1 or name HD2 or name HE1)) or resid 85 through 99 or (resid 100 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 101 \ through 119 or (resid 120 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD2 or name HE1)) or resid 121 through 157 or (r \ esid 158 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 159 through 161 or (resid 162 and (name N or name CA or name C o \ r name O or name CB )) or (resid 163 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2)) or resid 164 through 181 or (res \ id 182 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 183 through 186 or (resid 187 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 188 through 193)) selection = (chain 'E' and ((resid 12 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or resid 13 throug \ h 85 or (resid 96 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 97 through 99 or (resid 100 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 101 through 119 or ( \ resid 120 and (name N or name CA or name C or name O or name CB or name CG or na \ me ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or n \ ame HB3 or name HD2 or name HE1)) or resid 121 through 157 or (resid 158 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 159 through 161 or (resid 162 and (name N or name CA or name C or name O or name \ CB )) or (resid 163 and (name N or name CA or name C or name O or name CB or na \ me CG or name OD1 or name OD2)) or resid 164 through 181 or (resid 182 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 18 \ 3 through 193)) selection = (chain 'F' and (resid 12 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid \ 80 through 85 or (resid 96 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 97 through 119 or (resid 120 and (name N or na \ me CA or name C or name O or name CB or name CG or name ND1 or name CD2 or name \ CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name \ HE1)) or resid 121 through 161 or (resid 162 and (name N or name CA or name C o \ r name O or name CB )) or (resid 163 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2)) or resid 164 through 193)) selection = (chain 'G' and (resid 12 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid \ 80 through 85 or (resid 96 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 97 through 119 or (resid 120 and (name N or na \ me CA or name C or name O or name CB or name CG or name ND1 or name CD2 or name \ CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name \ HE1)) or resid 121 through 161 or (resid 162 and (name N or name CA or name C o \ r name O or name CB )) or resid 163 through 193)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.560 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: 0.390 Extract box with map and model: 0.910 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 47.490 Find NCS groups from input model: 0.810 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 : 0.004 0.062 11024 Z= 0.164 Angle : 0.725 12.416 14978 Z= 0.358 Chirality : 0.039 0.151 1678 Planarity : 0.005 0.087 1941 Dihedral : 16.553 89.543 4141 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.09 % Allowed : 13.30 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 1.80 (0.23), residues: 1351 helix: 1.60 (0.17), residues: 1002 sheet: -1.04 (0.92), residues: 9 loop : 0.20 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 117 HIS 0.010 0.001 HIS B 120 PHE 0.010 0.001 PHE F 161 TYR 0.029 0.002 TYR F 145 ARG 0.005 0.000 ARG G 82 Details of bonding type rmsd hydrogen bonds : bond 0.09446 ( 731) hydrogen bonds : angle 4.42553 ( 2160) covalent geometry : bond 0.00391 (11024) covalent geometry : angle 0.72502 (14978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 2.040 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: B 118 MET cc_start: 0.6543 (mtm) cc_final: 0.6316 (mtp) REVERT: C 120 HIS cc_start: 0.4907 (t-90) cc_final: 0.4626 (t-90) REVERT: F 121 ASN cc_start: 0.5222 (t0) cc_final: 0.4846 (t0) REVERT: F 166 ASP cc_start: 0.7158 (t0) cc_final: 0.6690 (t70) REVERT: G 80 TRP cc_start: 0.6868 (t-100) cc_final: 0.6599 (t-100) REVERT: G 154 ARG cc_start: 0.6459 (tpp80) cc_final: 0.5979 (mpt180) outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.7326 time to fit residues: 156.8920 Evaluate side-chains 142 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 183 ASN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN G 63 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.128921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.103596 restraints weight = 58516.796| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.97 r_work: 0.3225 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11024 Z= 0.176 Angle : 0.540 7.335 14978 Z= 0.275 Chirality : 0.038 0.139 1678 Planarity : 0.004 0.040 1941 Dihedral : 3.880 18.440 1460 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.03 % Allowed : 13.30 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.23), residues: 1351 helix: 1.77 (0.16), residues: 1001 sheet: -1.29 (0.70), residues: 9 loop : 0.19 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.004 0.001 HIS A 120 PHE 0.009 0.001 PHE B 32 TYR 0.011 0.001 TYR D 169 ARG 0.004 0.000 ARG D 143 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 731) hydrogen bonds : angle 4.07043 ( 2160) covalent geometry : bond 0.00409 (11024) covalent geometry : angle 0.54039 (14978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 MET cc_start: 0.6629 (mtm) cc_final: 0.6174 (mtp) REVERT: B 176 GLN cc_start: 0.7470 (tm-30) cc_final: 0.7184 (tm-30) REVERT: F 39 MET cc_start: 0.8382 (tpt) cc_final: 0.7847 (tpt) REVERT: F 140 LYS cc_start: 0.8159 (mptt) cc_final: 0.7835 (mmtm) REVERT: F 162 ARG cc_start: 0.6427 (ttm170) cc_final: 0.5944 (tpp80) REVERT: F 166 ASP cc_start: 0.8154 (t0) cc_final: 0.7707 (t70) REVERT: G 80 TRP cc_start: 0.7435 (t-100) cc_final: 0.7190 (t-100) outliers start: 12 outliers final: 6 residues processed: 146 average time/residue: 0.7597 time to fit residues: 150.9365 Evaluate side-chains 139 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain F residue 26 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 59 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 GLN F 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.129421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.104084 restraints weight = 58172.226| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.86 r_work: 0.3242 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11024 Z= 0.123 Angle : 0.494 6.139 14978 Z= 0.248 Chirality : 0.037 0.143 1678 Planarity : 0.004 0.042 1941 Dihedral : 3.764 17.200 1460 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.12 % Allowed : 12.96 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.19 (0.23), residues: 1351 helix: 1.93 (0.17), residues: 1001 sheet: -1.45 (0.66), residues: 9 loop : 0.24 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.003 0.001 HIS B 120 PHE 0.008 0.001 PHE B 32 TYR 0.010 0.001 TYR D 169 ARG 0.003 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 731) hydrogen bonds : angle 3.90594 ( 2160) covalent geometry : bond 0.00281 (11024) covalent geometry : angle 0.49416 (14978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 1.775 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: B 80 TRP cc_start: 0.8007 (t-100) cc_final: 0.7466 (t-100) REVERT: B 118 MET cc_start: 0.6700 (mtm) cc_final: 0.6361 (mtp) REVERT: B 176 GLN cc_start: 0.7624 (tm-30) cc_final: 0.7146 (tm-30) REVERT: E 118 MET cc_start: 0.6863 (mmt) cc_final: 0.6658 (mtt) REVERT: F 140 LYS cc_start: 0.8182 (mptt) cc_final: 0.7834 (mmtm) REVERT: F 166 ASP cc_start: 0.8106 (t0) cc_final: 0.7655 (t70) REVERT: G 80 TRP cc_start: 0.7446 (t-100) cc_final: 0.7236 (t-100) outliers start: 13 outliers final: 8 residues processed: 146 average time/residue: 0.6080 time to fit residues: 117.9994 Evaluate side-chains 141 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain F residue 26 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 HIS F 67 GLN G 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.127498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102778 restraints weight = 58907.369| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.87 r_work: 0.3204 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11024 Z= 0.197 Angle : 0.538 8.266 14978 Z= 0.274 Chirality : 0.038 0.141 1678 Planarity : 0.005 0.041 1941 Dihedral : 3.894 19.008 1460 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.55 % Allowed : 12.88 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.23), residues: 1351 helix: 1.76 (0.16), residues: 1001 sheet: -1.67 (0.73), residues: 9 loop : 0.25 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.003 0.001 HIS B 120 PHE 0.012 0.002 PHE B 32 TYR 0.013 0.002 TYR A 169 ARG 0.004 0.000 ARG F 162 Details of bonding type rmsd hydrogen bonds : bond 0.04047 ( 731) hydrogen bonds : angle 4.02451 ( 2160) covalent geometry : bond 0.00463 (11024) covalent geometry : angle 0.53756 (14978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 GLN cc_start: 0.7689 (tm-30) cc_final: 0.7250 (tm-30) REVERT: F 39 MET cc_start: 0.8380 (tpt) cc_final: 0.7801 (tpt) REVERT: F 140 LYS cc_start: 0.8167 (mptt) cc_final: 0.7821 (mmtm) REVERT: F 166 ASP cc_start: 0.8164 (t0) cc_final: 0.7667 (t70) REVERT: G 145 TYR cc_start: 0.7874 (m-80) cc_final: 0.7524 (m-80) outliers start: 18 outliers final: 11 residues processed: 142 average time/residue: 0.5867 time to fit residues: 112.2692 Evaluate side-chains 137 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 181 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 123 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.129900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.105581 restraints weight = 58703.677| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.59 r_work: 0.3283 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11024 Z= 0.125 Angle : 0.494 6.788 14978 Z= 0.248 Chirality : 0.037 0.142 1678 Planarity : 0.004 0.041 1941 Dihedral : 3.800 19.380 1460 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.37 % Allowed : 13.05 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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 (0.23), residues: 1351 helix: 1.93 (0.16), residues: 1001 sheet: -1.79 (0.81), residues: 9 loop : 0.33 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.003 0.001 HIS B 120 PHE 0.009 0.001 PHE B 32 TYR 0.010 0.001 TYR D 169 ARG 0.003 0.000 ARG F 162 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 731) hydrogen bonds : angle 3.86869 ( 2160) covalent geometry : bond 0.00287 (11024) covalent geometry : angle 0.49389 (14978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 2.186 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: B 80 TRP cc_start: 0.8157 (t-100) cc_final: 0.7704 (t-100) REVERT: B 176 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7266 (tm-30) REVERT: F 140 LYS cc_start: 0.8147 (mptt) cc_final: 0.7842 (mmtm) REVERT: F 166 ASP cc_start: 0.8076 (t0) cc_final: 0.7847 (t70) REVERT: F 199 LYS cc_start: 0.7592 (mttt) cc_final: 0.7295 (mtpt) REVERT: G 145 TYR cc_start: 0.7758 (m-80) cc_final: 0.7447 (m-80) outliers start: 16 outliers final: 13 residues processed: 141 average time/residue: 0.5990 time to fit residues: 114.9190 Evaluate side-chains 138 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 181 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 64 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.129247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.105181 restraints weight = 58279.512| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.60 r_work: 0.3278 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11024 Z= 0.149 Angle : 0.501 8.329 14978 Z= 0.254 Chirality : 0.037 0.138 1678 Planarity : 0.004 0.041 1941 Dihedral : 3.790 19.845 1460 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.46 % Allowed : 13.48 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.22 (0.23), residues: 1351 helix: 1.92 (0.16), residues: 1000 sheet: -1.82 (0.87), residues: 9 loop : 0.34 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 184 HIS 0.004 0.001 HIS B 120 PHE 0.009 0.001 PHE B 32 TYR 0.011 0.001 TYR D 169 ARG 0.002 0.000 ARG F 162 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 731) hydrogen bonds : angle 3.87316 ( 2160) covalent geometry : bond 0.00349 (11024) covalent geometry : angle 0.50063 (14978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 2.102 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: B 176 GLN cc_start: 0.7593 (tm-30) cc_final: 0.7266 (tm-30) REVERT: F 39 MET cc_start: 0.8326 (tpt) cc_final: 0.7832 (tpt) REVERT: F 140 LYS cc_start: 0.8163 (mptt) cc_final: 0.7842 (mmtm) REVERT: F 166 ASP cc_start: 0.8157 (t0) cc_final: 0.7924 (t70) REVERT: G 145 TYR cc_start: 0.7796 (m-80) cc_final: 0.7510 (m-80) outliers start: 17 outliers final: 15 residues processed: 142 average time/residue: 0.6432 time to fit residues: 122.6488 Evaluate side-chains 140 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 181 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 103 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.130251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.106026 restraints weight = 58485.907| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.42 r_work: 0.3308 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11024 Z= 0.108 Angle : 0.479 8.333 14978 Z= 0.240 Chirality : 0.036 0.141 1678 Planarity : 0.004 0.042 1941 Dihedral : 3.701 19.540 1460 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.20 % Allowed : 14.08 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.35 (0.23), residues: 1351 helix: 2.03 (0.17), residues: 1005 sheet: -1.68 (0.92), residues: 9 loop : 0.31 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.003 0.000 HIS B 120 PHE 0.007 0.001 PHE B 32 TYR 0.010 0.001 TYR F 169 ARG 0.003 0.000 ARG F 162 Details of bonding type rmsd hydrogen bonds : bond 0.03605 ( 731) hydrogen bonds : angle 3.77844 ( 2160) covalent geometry : bond 0.00244 (11024) covalent geometry : angle 0.47866 (14978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.812 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: B 80 TRP cc_start: 0.8136 (t-100) cc_final: 0.7717 (t-100) REVERT: B 176 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7307 (tm-30) REVERT: C 68 MET cc_start: 0.7342 (ptp) cc_final: 0.7135 (ptm) REVERT: F 13 GLN cc_start: 0.4556 (pm20) cc_final: 0.3913 (pp30) REVERT: F 39 MET cc_start: 0.8278 (tpt) cc_final: 0.7734 (tpt) REVERT: F 140 LYS cc_start: 0.8186 (mptt) cc_final: 0.7862 (mmtm) REVERT: F 166 ASP cc_start: 0.8158 (t0) cc_final: 0.7924 (t70) REVERT: G 145 TYR cc_start: 0.7814 (m-80) cc_final: 0.7539 (m-80) outliers start: 14 outliers final: 14 residues processed: 146 average time/residue: 0.6148 time to fit residues: 122.1630 Evaluate side-chains 143 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 181 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.130058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.105791 restraints weight = 58588.836| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.55 r_work: 0.3291 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11024 Z= 0.118 Angle : 0.484 8.449 14978 Z= 0.245 Chirality : 0.036 0.138 1678 Planarity : 0.004 0.042 1941 Dihedral : 3.668 19.566 1460 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.29 % Allowed : 14.33 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.35 (0.23), residues: 1351 helix: 2.03 (0.17), residues: 1005 sheet: -1.60 (0.97), residues: 9 loop : 0.33 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.003 0.000 HIS B 120 PHE 0.007 0.001 PHE B 32 TYR 0.010 0.001 TYR D 169 ARG 0.003 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 731) hydrogen bonds : angle 3.79075 ( 2160) covalent geometry : bond 0.00272 (11024) covalent geometry : angle 0.48432 (14978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 2.084 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: B 80 TRP cc_start: 0.8159 (t-100) cc_final: 0.7752 (t-100) REVERT: B 176 GLN cc_start: 0.7572 (tm-30) cc_final: 0.7264 (tm-30) REVERT: C 68 MET cc_start: 0.7374 (ptp) cc_final: 0.7169 (ptm) REVERT: F 13 GLN cc_start: 0.4617 (pm20) cc_final: 0.3972 (pp30) REVERT: F 39 MET cc_start: 0.8312 (tpt) cc_final: 0.7757 (tpt) REVERT: F 140 LYS cc_start: 0.8158 (mptt) cc_final: 0.7850 (mmtm) REVERT: F 166 ASP cc_start: 0.8162 (t0) cc_final: 0.7920 (t70) REVERT: F 199 LYS cc_start: 0.7668 (mttt) cc_final: 0.7333 (mtpt) REVERT: G 145 TYR cc_start: 0.7871 (m-80) cc_final: 0.7587 (m-80) outliers start: 15 outliers final: 14 residues processed: 149 average time/residue: 0.6294 time to fit residues: 125.4393 Evaluate side-chains 144 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 181 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 50 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.130009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.105787 restraints weight = 58576.302| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.47 r_work: 0.3295 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11024 Z= 0.127 Angle : 0.491 8.955 14978 Z= 0.248 Chirality : 0.037 0.137 1678 Planarity : 0.004 0.041 1941 Dihedral : 3.685 21.322 1460 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.20 % Allowed : 14.42 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.33 (0.23), residues: 1351 helix: 2.01 (0.17), residues: 1005 sheet: -1.50 (1.03), residues: 9 loop : 0.31 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 184 HIS 0.003 0.000 HIS B 120 PHE 0.008 0.001 PHE B 32 TYR 0.011 0.001 TYR D 169 ARG 0.003 0.000 ARG D 162 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 731) hydrogen bonds : angle 3.79718 ( 2160) covalent geometry : bond 0.00295 (11024) covalent geometry : angle 0.49075 (14978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 TRP cc_start: 0.8163 (t-100) cc_final: 0.7767 (t-100) REVERT: B 176 GLN cc_start: 0.7577 (tm-30) cc_final: 0.7287 (tm-30) REVERT: C 68 MET cc_start: 0.7390 (ptp) cc_final: 0.7178 (ptm) REVERT: F 39 MET cc_start: 0.8300 (tpt) cc_final: 0.7743 (tpt) REVERT: F 140 LYS cc_start: 0.8161 (mptt) cc_final: 0.7850 (mmtm) REVERT: F 166 ASP cc_start: 0.8178 (t0) cc_final: 0.7944 (t70) REVERT: F 199 LYS cc_start: 0.7665 (mttt) cc_final: 0.7337 (mtpt) REVERT: G 145 TYR cc_start: 0.7853 (m-80) cc_final: 0.7544 (m-80) outliers start: 14 outliers final: 14 residues processed: 140 average time/residue: 0.7048 time to fit residues: 134.6989 Evaluate side-chains 144 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 118 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 181 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 41 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 106 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.130451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.106257 restraints weight = 58856.293| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.47 r_work: 0.3308 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11024 Z= 0.106 Angle : 0.484 9.719 14978 Z= 0.244 Chirality : 0.036 0.137 1678 Planarity : 0.004 0.042 1941 Dihedral : 3.636 21.522 1460 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.20 % Allowed : 14.25 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.46 (0.23), residues: 1351 helix: 2.11 (0.17), residues: 1005 sheet: -1.65 (0.92), residues: 9 loop : 0.35 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 184 HIS 0.005 0.000 HIS B 120 PHE 0.007 0.001 PHE B 32 TYR 0.010 0.001 TYR D 169 ARG 0.003 0.000 ARG D 162 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 731) hydrogen bonds : angle 3.75276 ( 2160) covalent geometry : bond 0.00240 (11024) covalent geometry : angle 0.48401 (14978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 182 is missing expected H atoms. Skipping. Residue LEU 6 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue LYS 182 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.830 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: B 80 TRP cc_start: 0.8151 (t-100) cc_final: 0.7759 (t-100) REVERT: B 176 GLN cc_start: 0.7570 (tm-30) cc_final: 0.7289 (tm-30) REVERT: F 39 MET cc_start: 0.8292 (tpt) cc_final: 0.7736 (tpt) REVERT: F 140 LYS cc_start: 0.8163 (mptt) cc_final: 0.7851 (mmtm) REVERT: F 199 LYS cc_start: 0.7659 (mttt) cc_final: 0.7324 (mtpt) REVERT: G 145 TYR cc_start: 0.7848 (m-80) cc_final: 0.7542 (m-80) REVERT: G 154 ARG cc_start: 0.6713 (tpp80) cc_final: 0.6011 (tpp80) outliers start: 14 outliers final: 14 residues processed: 144 average time/residue: 0.6275 time to fit residues: 124.3388 Evaluate side-chains 143 residues out of total 1188 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 118 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 181 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.129278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.105100 restraints weight = 58753.523| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.49 r_work: 0.3285 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11024 Z= 0.174 Angle : 0.534 10.341 14978 Z= 0.272 Chirality : 0.038 0.177 1678 Planarity : 0.004 0.041 1941 Dihedral : 3.757 23.841 1460 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.29 % Allowed : 13.99 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.29 % 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: 2.27 (0.23), residues: 1351 helix: 1.96 (0.16), residues: 1001 sheet: -1.62 (0.98), residues: 9 loop : 0.36 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 184 HIS 0.004 0.001 HIS B 120 PHE 0.009 0.001 PHE B 32 TYR 0.012 0.002 TYR A 169 ARG 0.004 0.000 ARG E 173 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 731) hydrogen bonds : angle 3.87120 ( 2160) covalent geometry : bond 0.00411 (11024) covalent geometry : angle 0.53376 (14978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9983.36 seconds wall clock time: 172 minutes 56.58 seconds (10376.58 seconds total)