Starting phenix.real_space_refine on Sun Feb 18 08:04:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6l_29773/02_2024/8g6l_29773.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6l_29773/02_2024/8g6l_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6l_29773/02_2024/8g6l_29773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6l_29773/02_2024/8g6l_29773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6l_29773/02_2024/8g6l_29773.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6l_29773/02_2024/8g6l_29773.pdb" } 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 Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 163": "OD1" <-> "OD2" Residue "F TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 213": "OE1" <-> "OE2" Residue "G TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 9.47, per 1000 atoms: 0.44 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.56 Conformation dependent library (CDL) restraints added in 2.6 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: 1.38 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: 7.45 Time building geometry restraints manager: 18.13 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: 97.50 - 104.80: 314 104.80 - 112.09: 25132 112.09 - 119.39: 5487 119.39 - 126.68: 8093 126.68 - 133.98: 251 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 1.850 nonbonded pdb=" H ARG E 100 " pdb=" OD2 ASP E 103 " model vdw 1.736 1.850 nonbonded pdb=" O ILE A 115 " pdb=" HG1 THR A 119 " model vdw 1.736 1.850 nonbonded pdb=" OG SER A 16 " pdb=" H THR A 19 " model vdw 1.737 1.850 nonbonded pdb=" O GLY G 156 " pdb="HD22 ASN G 195 " model vdw 1.738 1.850 ... (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 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: 2.380 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: 0.330 Extract box with map and model: 10.230 Check model and map are aligned: 0.270 Set scattering table: 0.190 Process input model: 68.130 Find NCS groups from input model: 1.170 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.640 ------------------------------------------------------------------------------- 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= 0.256 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.860 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: 0.6643 time to fit residues: 139.7125 Evaluate side-chains 142 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.657 ------------------------------------------------------------------------------- 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: 8.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 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: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN G 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11024 Z= 0.337 Angle : 0.558 7.613 14978 Z= 0.286 Chirality : 0.039 0.140 1678 Planarity : 0.004 0.040 1941 Dihedral : 3.935 18.716 1460 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.46 % Allowed : 12.79 % Favored : 85.75 % 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: 1.82 (0.23), residues: 1351 helix: 1.64 (0.16), residues: 1001 sheet: -1.11 (0.84), residues: 9 loop : 0.14 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 184 HIS 0.002 0.001 HIS C 12 PHE 0.011 0.002 PHE B 32 TYR 0.013 0.002 TYR A 169 ARG 0.004 0.001 ARG E 173 *********************** 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 fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 GLN cc_start: 0.7450 (tm-30) cc_final: 0.7241 (tm-30) REVERT: F 39 MET cc_start: 0.7135 (tpt) cc_final: 0.6645 (tpt) REVERT: F 162 ARG cc_start: 0.5901 (ttm170) cc_final: 0.5626 (tpp80) REVERT: F 166 ASP cc_start: 0.7337 (t0) cc_final: 0.6948 (t70) outliers start: 17 outliers final: 9 residues processed: 146 average time/residue: 0.6401 time to fit residues: 124.5746 Evaluate side-chains 135 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER 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 D residue 104 ILE Chi-restraints excluded: chain D residue 197 ASP 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 67 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11024 Z= 0.183 Angle : 0.500 6.480 14978 Z= 0.249 Chirality : 0.036 0.131 1678 Planarity : 0.004 0.041 1941 Dihedral : 3.800 18.130 1460 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.77 % Allowed : 13.56 % 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: 2.08 (0.23), residues: 1351 helix: 1.84 (0.17), residues: 1001 sheet: -0.97 (0.91), residues: 9 loop : 0.18 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 184 HIS 0.003 0.000 HIS B 120 PHE 0.009 0.001 PHE B 32 TYR 0.010 0.001 TYR D 169 ARG 0.002 0.000 ARG A 82 *********************** 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 142 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 133 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 118 MET cc_start: 0.6565 (mtm) cc_final: 0.6300 (mtp) REVERT: B 176 GLN cc_start: 0.7511 (tm-30) cc_final: 0.7134 (tm-30) REVERT: E 79 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6788 (mm-30) REVERT: F 166 ASP cc_start: 0.7357 (t0) cc_final: 0.6925 (t70) outliers start: 9 outliers final: 7 residues processed: 135 average time/residue: 0.5931 time to fit residues: 109.7124 Evaluate side-chains 136 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.725 ------------------------------------------------------------------------------- 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 D residue 197 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 119 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 HIS ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11024 Z= 0.249 Angle : 0.506 6.238 14978 Z= 0.257 Chirality : 0.037 0.129 1678 Planarity : 0.004 0.039 1941 Dihedral : 3.796 18.815 1460 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.63 % Allowed : 13.30 % 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: 2.03 (0.23), residues: 1351 helix: 1.80 (0.16), residues: 1001 sheet: -0.89 (0.92), residues: 9 loop : 0.17 (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 0.010 0.001 PHE B 32 TYR 0.011 0.001 TYR D 169 ARG 0.003 0.000 ARG F 162 *********************** 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 149 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.7765 (ptt) cc_final: 0.7533 (ptt) REVERT: B 176 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7231 (tm-30) REVERT: F 39 MET cc_start: 0.7260 (tpt) cc_final: 0.6573 (tpt) REVERT: F 166 ASP cc_start: 0.7380 (t0) cc_final: 0.7151 (t70) outliers start: 19 outliers final: 11 residues processed: 142 average time/residue: 0.6045 time to fit residues: 117.3832 Evaluate side-chains 137 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER 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 C residue 102 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 146 SER 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 107 optimal weight: 0.9990 chunk 72 optimal weight: 0.0010 chunk 1 optimal weight: 0.9980 chunk 95 optimal weight: 0.3980 chunk 53 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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** ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN G 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11024 Z= 0.152 Angle : 0.483 6.708 14978 Z= 0.240 Chirality : 0.036 0.134 1678 Planarity : 0.004 0.042 1941 Dihedral : 3.690 19.016 1460 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.12 % Allowed : 13.82 % 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: 2.35 (0.23), residues: 1351 helix: 2.04 (0.17), residues: 1001 sheet: -0.76 (1.03), residues: 9 loop : 0.29 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.004 0.000 HIS B 120 PHE 0.007 0.001 PHE B 32 TYR 0.010 0.001 TYR D 169 ARG 0.002 0.000 ARG F 162 *********************** 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 fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7243 (tm-30) REVERT: F 39 MET cc_start: 0.6997 (tpt) cc_final: 0.6320 (tpt) REVERT: F 166 ASP cc_start: 0.7354 (t0) cc_final: 0.7116 (t70) REVERT: G 154 ARG cc_start: 0.6698 (tpp80) cc_final: 0.6046 (tpp80) outliers start: 13 outliers final: 11 residues processed: 140 average time/residue: 0.5937 time to fit residues: 113.3849 Evaluate side-chains 140 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER 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 83 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 103 ASP 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 43 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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** ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11024 Z= 0.278 Angle : 0.516 8.098 14978 Z= 0.263 Chirality : 0.038 0.130 1678 Planarity : 0.004 0.040 1941 Dihedral : 3.786 21.871 1460 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.63 % Allowed : 13.73 % Favored : 84.64 % 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: 2.16 (0.23), residues: 1351 helix: 1.88 (0.16), residues: 1000 sheet: -0.68 (0.98), residues: 9 loop : 0.26 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.004 0.001 HIS B 120 PHE 0.010 0.001 PHE B 32 TYR 0.012 0.002 TYR D 169 ARG 0.003 0.000 ARG E 173 *********************** 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 149 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7189 (tm-30) REVERT: C 202 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7985 (mm) REVERT: F 39 MET cc_start: 0.7011 (tpt) cc_final: 0.6518 (tpt) REVERT: F 162 ARG cc_start: 0.5987 (ttm170) cc_final: 0.5469 (tpp80) REVERT: F 166 ASP cc_start: 0.7430 (t0) cc_final: 0.7223 (t70) outliers start: 19 outliers final: 13 residues processed: 141 average time/residue: 0.6400 time to fit residues: 120.4484 Evaluate side-chains 140 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 SER 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 71 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain F residue 146 SER 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 124 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1660 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= 0.208 Angle : 0.494 8.099 14978 Z= 0.250 Chirality : 0.037 0.129 1678 Planarity : 0.004 0.041 1941 Dihedral : 3.743 22.616 1460 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.46 % Allowed : 14.25 % Favored : 84.29 % 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: 1000 sheet: -0.55 (1.00), residues: 9 loop : 0.31 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 *********************** 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 147 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 GLN cc_start: 0.7515 (tm-30) cc_final: 0.7218 (tm-30) REVERT: C 202 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8035 (mm) REVERT: F 39 MET cc_start: 0.7000 (tpt) cc_final: 0.6488 (tpt) REVERT: F 166 ASP cc_start: 0.7455 (t0) cc_final: 0.7233 (t70) outliers start: 17 outliers final: 12 residues processed: 144 average time/residue: 0.6217 time to fit residues: 119.5667 Evaluate side-chains 137 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 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 102 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain F residue 146 SER 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 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 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** ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11024 Z= 0.181 Angle : 0.486 8.103 14978 Z= 0.245 Chirality : 0.036 0.128 1678 Planarity : 0.004 0.042 1941 Dihedral : 3.687 23.052 1460 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.12 % Allowed : 14.42 % Favored : 84.46 % 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: 2.28 (0.23), residues: 1351 helix: 1.98 (0.17), residues: 1005 sheet: -0.41 (1.03), residues: 9 loop : 0.25 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.004 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 F 162 *********************** 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 140 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7257 (tm-30) REVERT: C 202 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8032 (mm) REVERT: F 39 MET cc_start: 0.7045 (tpt) cc_final: 0.6600 (tpt) REVERT: F 166 ASP cc_start: 0.7453 (t0) cc_final: 0.7229 (t70) REVERT: F 215 MET cc_start: 0.6605 (mtp) cc_final: 0.6161 (mtp) outliers start: 13 outliers final: 12 residues processed: 139 average time/residue: 0.5711 time to fit residues: 108.4759 Evaluate side-chains 137 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 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 102 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain F residue 146 SER 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 116 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 119 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11024 Z= 0.179 Angle : 0.490 8.868 14978 Z= 0.246 Chirality : 0.036 0.142 1678 Planarity : 0.004 0.042 1941 Dihedral : 3.661 23.543 1460 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.12 % Allowed : 14.59 % Favored : 84.29 % 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: 2.32 (0.23), residues: 1351 helix: 2.01 (0.17), residues: 1005 sheet: -0.28 (1.07), residues: 9 loop : 0.26 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.005 0.000 HIS B 120 PHE 0.007 0.001 PHE E 161 TYR 0.010 0.001 TYR D 169 ARG 0.002 0.000 ARG F 162 *********************** 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 139 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.6880 (pmm) cc_final: 0.6542 (pmm) REVERT: B 176 GLN cc_start: 0.7486 (tm-30) cc_final: 0.7255 (tm-30) REVERT: C 202 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8017 (mm) REVERT: F 39 MET cc_start: 0.7132 (tpt) cc_final: 0.6572 (tpt) REVERT: F 166 ASP cc_start: 0.7466 (t0) cc_final: 0.7239 (t70) REVERT: F 215 MET cc_start: 0.6574 (mtp) cc_final: 0.6087 (mtp) REVERT: G 154 ARG cc_start: 0.6827 (tpp80) cc_final: 0.6172 (tpp80) outliers start: 13 outliers final: 12 residues processed: 138 average time/residue: 0.6053 time to fit residues: 113.1104 Evaluate side-chains 136 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 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 102 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain F residue 146 SER 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 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 81 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1787 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= 0.171 Angle : 0.491 11.165 14978 Z= 0.247 Chirality : 0.036 0.139 1678 Planarity : 0.004 0.042 1941 Dihedral : 3.636 24.604 1460 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.12 % Allowed : 14.51 % 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: 2.45 (0.23), residues: 1351 helix: 2.09 (0.17), residues: 1001 sheet: -0.26 (1.09), residues: 9 loop : 0.36 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 0.004 0.000 ARG D 162 ********************** 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 140 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.6893 (pmm) cc_final: 0.6549 (pmm) REVERT: C 202 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8022 (mm) REVERT: F 39 MET cc_start: 0.7129 (tpt) cc_final: 0.6569 (tpt) REVERT: F 166 ASP cc_start: 0.7465 (t0) cc_final: 0.7240 (t70) REVERT: F 215 MET cc_start: 0.6577 (mtp) cc_final: 0.6065 (mtp) REVERT: G 154 ARG cc_start: 0.6826 (tpp80) cc_final: 0.6179 (tpp80) outliers start: 13 outliers final: 12 residues processed: 139 average time/residue: 0.5765 time to fit residues: 111.3501 Evaluate side-chains 139 residues out of total 1188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 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 102 SER Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain F residue 146 SER 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 32 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.129528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.105482 restraints weight = 58437.850| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.48 r_work: 0.3312 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11024 Z= 0.262 Angle : 0.519 10.645 14978 Z= 0.265 Chirality : 0.037 0.143 1678 Planarity : 0.004 0.041 1941 Dihedral : 3.736 26.391 1460 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.12 % Allowed : 14.33 % 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: 2.26 (0.23), residues: 1351 helix: 1.96 (0.16), residues: 1000 sheet: -0.33 (1.04), residues: 9 loop : 0.29 (0.34), 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 0.012 0.001 TYR A 169 ARG 0.003 0.000 ARG F 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4661.29 seconds wall clock time: 83 minutes 13.95 seconds (4993.95 seconds total)