Starting phenix.real_space_refine on Fri Dec 8 09:17:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/12_2023/8dzr_27806_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/12_2023/8dzr_27806.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/12_2023/8dzr_27806_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/12_2023/8dzr_27806_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/12_2023/8dzr_27806_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/12_2023/8dzr_27806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/12_2023/8dzr_27806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/12_2023/8dzr_27806_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/12_2023/8dzr_27806_updated.pdb" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 58 5.16 5 Cl 2 4.86 5 C 5092 2.51 5 N 1322 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7944 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1934 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 4 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1494 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 2, 'TRANS': 202} Chain breaks: 4 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 91 Chain: "C" Number of atoms: 2455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2455 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 112 Chain: "D" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 251 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'U9I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.77, per 1000 atoms: 0.60 Number of scatterers: 7944 At special positions: 0 Unit cell: (86.24, 121.44, 124.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 58 16.00 O 1470 8.00 N 1322 7.00 C 5092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 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: 3.17 Conformation dependent library (CDL) restraints added in 1.5 seconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 12 sheets defined 31.9% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 58 through 79 removed outlier: 3.647A pdb=" N THR A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TYR A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 113 through 120 removed outlier: 4.540A pdb=" N VAL A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 161 removed outlier: 5.024A pdb=" N LEU A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 removed outlier: 3.876A pdb=" N LEU A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.960A pdb=" N VAL A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 236 through 255 removed outlier: 3.674A pdb=" N SER A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 297 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 310 through 331 removed outlier: 3.875A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.695A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 212 through 215 Processing helix chain 'B' and resid 243 through 254 Processing helix chain 'B' and resid 271 through 280 removed outlier: 4.048A pdb=" N THR B 279 " --> pdb=" O GLN B 275 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 331 through 351 Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 30 through 34 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 30 through 44 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.774A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N HIS B 195 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU B 36 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG B 197 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU B 38 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N PHE B 199 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N GLY B 40 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.812A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 7.073A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.706A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 187 through 192 removed outlier: 7.113A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.776A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.561A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.760A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.875A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 143 through 148 Processing sheet with id= L, first strand: chain 'E' and resid 213 through 219 removed outlier: 3.812A pdb=" N ILE E 177 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1086 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: 2.51 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2055 1.33 - 1.45: 1638 1.45 - 1.58: 4322 1.58 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 8100 Sorted by residual: bond pdb=" C17 U9I A 401 " pdb=" C18 U9I A 401 " ideal model delta sigma weight residual 1.351 1.518 -0.167 2.00e-02 2.50e+03 6.95e+01 bond pdb=" C18 U9I A 401 " pdb=" N3 U9I A 401 " ideal model delta sigma weight residual 1.622 1.467 0.155 2.00e-02 2.50e+03 6.02e+01 bond pdb=" C5 U9I A 401 " pdb=" N2 U9I A 401 " ideal model delta sigma weight residual 1.497 1.359 0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C15 U9I A 401 " pdb=" N3 U9I A 401 " ideal model delta sigma weight residual 1.334 1.464 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C2 U9I A 401 " pdb=" N1 U9I A 401 " ideal model delta sigma weight residual 1.432 1.350 0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 8095 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.10: 136 106.10 - 113.10: 4462 113.10 - 120.09: 2712 120.09 - 127.08: 3635 127.08 - 134.08: 84 Bond angle restraints: 11029 Sorted by residual: angle pdb=" N PRO A 56 " pdb=" CA PRO A 56 " pdb=" CB PRO A 56 " ideal model delta sigma weight residual 103.00 110.47 -7.47 1.10e+00 8.26e-01 4.61e+01 angle pdb=" N ASP C 170 " pdb=" CA ASP C 170 " pdb=" C ASP C 170 " ideal model delta sigma weight residual 108.96 101.81 7.15 1.59e+00 3.96e-01 2.02e+01 angle pdb=" N SER C 161 " pdb=" CA SER C 161 " pdb=" C SER C 161 " ideal model delta sigma weight residual 108.74 113.37 -4.63 1.38e+00 5.25e-01 1.13e+01 angle pdb=" N ASP C 170 " pdb=" CA ASP C 170 " pdb=" CB ASP C 170 " ideal model delta sigma weight residual 110.17 115.01 -4.84 1.68e+00 3.54e-01 8.31e+00 angle pdb=" C VAL A 80 " pdb=" N MET A 81 " pdb=" CA MET A 81 " ideal model delta sigma weight residual 121.54 126.99 -5.45 1.91e+00 2.74e-01 8.15e+00 ... (remaining 11024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.86: 4611 29.86 - 59.72: 103 59.72 - 89.58: 13 89.58 - 119.44: 2 119.44 - 149.30: 1 Dihedral angle restraints: 4730 sinusoidal: 1621 harmonic: 3109 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 172.73 -79.73 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" C19 U9I A 401 " pdb=" C13 U9I A 401 " pdb=" C14 U9I A 401 " pdb=" N3 U9I A 401 " ideal model delta sinusoidal sigma weight residual -59.26 90.04 -149.30 1 3.00e+01 1.11e-03 1.98e+01 dihedral pdb=" CA TYR E 178 " pdb=" C TYR E 178 " pdb=" N ARG E 179 " pdb=" CA ARG E 179 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1008 0.052 - 0.104: 249 0.104 - 0.156: 57 0.156 - 0.208: 2 0.208 - 0.260: 4 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CB THR E 160 " pdb=" CA THR E 160 " pdb=" OG1 THR E 160 " pdb=" CG2 THR E 160 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ASP C 170 " pdb=" N ASP C 170 " pdb=" C ASP C 170 " pdb=" CB ASP C 170 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO A 56 " pdb=" N PRO A 56 " pdb=" C PRO A 56 " pdb=" CB PRO A 56 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1317 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 199 " 0.010 2.00e-02 2.50e+03 1.59e-02 4.43e+00 pdb=" CG PHE B 199 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 199 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 199 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 199 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 199 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 199 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 171 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 172 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 172 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 172 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO C 236 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.024 5.00e-02 4.00e+02 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1189 2.76 - 3.29: 7473 3.29 - 3.83: 13344 3.83 - 4.36: 15344 4.36 - 4.90: 27308 Nonbonded interactions: 64658 Sorted by model distance: nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.224 2.440 nonbonded pdb=" O GLN C 75 " pdb=" OG SER C 98 " model vdw 2.268 2.440 nonbonded pdb=" O VAL A 284 " pdb=" OG1 THR A 288 " model vdw 2.286 2.440 nonbonded pdb=" O THR A 111 " pdb=" OH TYR A 320 " model vdw 2.292 2.440 nonbonded pdb=" NE2 HIS C 225 " pdb=" OG1 THR C 243 " model vdw 2.293 2.520 ... (remaining 64653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.650 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: 0.000 Extract box with map and model: 5.220 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.060 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 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 : 0.005 0.167 8100 Z= 0.343 Angle : 0.704 8.223 11029 Z= 0.370 Chirality : 0.048 0.260 1320 Planarity : 0.004 0.044 1374 Dihedral : 13.752 149.298 2712 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.09 (0.25), residues: 1045 helix: 1.15 (0.27), residues: 345 sheet: 0.49 (0.30), residues: 294 loop : -1.56 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.003 0.001 HIS C 142 PHE 0.034 0.002 PHE B 199 TYR 0.023 0.002 TYR C 59 ARG 0.004 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.841 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.8917 time to fit residues: 164.5346 Evaluate side-chains 159 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 0.0000 chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 50 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 95 optimal weight: 0.0980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 230 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8100 Z= 0.161 Angle : 0.509 8.135 11029 Z= 0.264 Chirality : 0.041 0.140 1320 Planarity : 0.003 0.038 1374 Dihedral : 7.863 168.160 1148 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.50 % Allowed : 11.97 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.32 (0.26), residues: 1045 helix: 1.80 (0.28), residues: 346 sheet: 0.65 (0.30), residues: 285 loop : -1.53 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 169 HIS 0.003 0.001 HIS C 142 PHE 0.018 0.001 PHE A 126 TYR 0.018 0.002 TYR E 102 ARG 0.003 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 165 time to evaluate : 0.934 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 169 average time/residue: 0.9072 time to fit residues: 165.5069 Evaluate side-chains 167 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 161 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 3 average time/residue: 0.4634 time to fit residues: 2.8983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8100 Z= 0.262 Angle : 0.556 8.354 11029 Z= 0.290 Chirality : 0.043 0.144 1320 Planarity : 0.003 0.039 1374 Dihedral : 8.069 172.760 1148 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.37 % Allowed : 13.72 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.42 (0.26), residues: 1045 helix: 1.97 (0.28), residues: 347 sheet: 0.69 (0.30), residues: 286 loop : -1.56 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 211 HIS 0.003 0.001 HIS D 44 PHE 0.016 0.002 PHE B 196 TYR 0.028 0.002 TYR E 178 ARG 0.007 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 0.886 Fit side-chains outliers start: 27 outliers final: 13 residues processed: 183 average time/residue: 0.8550 time to fit residues: 169.5970 Evaluate side-chains 181 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 168 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 6 residues processed: 7 average time/residue: 0.2442 time to fit residues: 3.4500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8100 Z= 0.224 Angle : 0.538 8.392 11029 Z= 0.280 Chirality : 0.042 0.140 1320 Planarity : 0.003 0.036 1374 Dihedral : 7.946 170.325 1148 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.74 % Allowed : 16.33 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.48 (0.26), residues: 1045 helix: 2.08 (0.28), residues: 347 sheet: 0.69 (0.31), residues: 281 loop : -1.53 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.003 0.001 HIS D 44 PHE 0.017 0.001 PHE B 199 TYR 0.023 0.002 TYR E 178 ARG 0.006 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 0.889 Fit side-chains outliers start: 30 outliers final: 17 residues processed: 184 average time/residue: 0.8217 time to fit residues: 164.2098 Evaluate side-chains 184 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 10 residues processed: 7 average time/residue: 0.2379 time to fit residues: 3.3329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 75 optimal weight: 0.0270 chunk 41 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8100 Z= 0.227 Angle : 0.557 9.222 11029 Z= 0.286 Chirality : 0.042 0.139 1320 Planarity : 0.003 0.035 1374 Dihedral : 7.974 170.389 1148 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.24 % Allowed : 17.96 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.48 (0.26), residues: 1045 helix: 2.07 (0.28), residues: 347 sheet: 0.68 (0.31), residues: 281 loop : -1.52 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.003 0.001 HIS D 44 PHE 0.019 0.001 PHE B 199 TYR 0.023 0.002 TYR E 178 ARG 0.005 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 162 time to evaluate : 0.881 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 176 average time/residue: 0.8738 time to fit residues: 166.3433 Evaluate side-chains 177 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 7 average time/residue: 0.2695 time to fit residues: 3.6174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8100 Z= 0.249 Angle : 0.568 9.215 11029 Z= 0.291 Chirality : 0.042 0.165 1320 Planarity : 0.003 0.036 1374 Dihedral : 8.001 170.792 1148 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.87 % Allowed : 17.71 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.44 (0.26), residues: 1045 helix: 1.98 (0.28), residues: 351 sheet: 0.67 (0.30), residues: 281 loop : -1.54 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.003 0.001 HIS D 44 PHE 0.019 0.002 PHE B 199 TYR 0.025 0.002 TYR E 178 ARG 0.004 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 0.833 Fit side-chains outliers start: 31 outliers final: 19 residues processed: 178 average time/residue: 0.8841 time to fit residues: 170.0992 Evaluate side-chains 175 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 6 average time/residue: 0.1017 time to fit residues: 2.2005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8100 Z= 0.260 Angle : 0.581 9.457 11029 Z= 0.297 Chirality : 0.043 0.215 1320 Planarity : 0.003 0.036 1374 Dihedral : 8.041 171.587 1148 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.62 % Allowed : 18.58 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.45 (0.26), residues: 1045 helix: 1.97 (0.28), residues: 351 sheet: 0.68 (0.30), residues: 281 loop : -1.50 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 211 HIS 0.003 0.001 HIS D 44 PHE 0.020 0.002 PHE B 199 TYR 0.027 0.002 TYR E 178 ARG 0.003 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 0.924 Fit side-chains outliers start: 29 outliers final: 19 residues processed: 177 average time/residue: 0.9300 time to fit residues: 178.5456 Evaluate side-chains 176 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 0.804 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 13 residues processed: 6 average time/residue: 0.2847 time to fit residues: 3.3354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 30 optimal weight: 0.0470 chunk 19 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 92 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8100 Z= 0.228 Angle : 0.579 10.670 11029 Z= 0.293 Chirality : 0.042 0.186 1320 Planarity : 0.003 0.036 1374 Dihedral : 7.964 169.163 1148 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.24 % Allowed : 19.45 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.50 (0.26), residues: 1045 helix: 2.03 (0.28), residues: 351 sheet: 0.70 (0.30), residues: 281 loop : -1.50 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.021 0.001 PHE B 199 TYR 0.025 0.002 TYR E 102 ARG 0.004 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 0.917 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 177 average time/residue: 0.9066 time to fit residues: 173.3600 Evaluate side-chains 168 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 2 average time/residue: 0.1580 time to fit residues: 1.6849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8100 Z= 0.305 Angle : 0.628 9.913 11029 Z= 0.319 Chirality : 0.046 0.337 1320 Planarity : 0.003 0.036 1374 Dihedral : 8.140 174.618 1148 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.12 % Allowed : 20.20 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.45 (0.26), residues: 1045 helix: 1.97 (0.28), residues: 350 sheet: 0.69 (0.30), residues: 286 loop : -1.53 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 211 HIS 0.003 0.001 HIS D 44 PHE 0.022 0.002 PHE B 199 TYR 0.032 0.002 TYR E 102 ARG 0.007 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 0.959 Fit side-chains outliers start: 25 outliers final: 20 residues processed: 165 average time/residue: 0.9326 time to fit residues: 165.8487 Evaluate side-chains 166 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 5 average time/residue: 0.1562 time to fit residues: 2.3626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 64 optimal weight: 0.0010 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8100 Z= 0.203 Angle : 0.581 9.298 11029 Z= 0.293 Chirality : 0.043 0.293 1320 Planarity : 0.003 0.036 1374 Dihedral : 7.903 167.301 1148 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.12 % Allowed : 21.45 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.53 (0.26), residues: 1045 helix: 2.10 (0.28), residues: 350 sheet: 0.72 (0.30), residues: 281 loop : -1.52 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.002 0.001 HIS E 35 PHE 0.021 0.001 PHE B 199 TYR 0.025 0.002 TYR E 102 ARG 0.004 0.000 ARG C 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 0.770 Fit side-chains outliers start: 17 outliers final: 15 residues processed: 181 average time/residue: 0.8777 time to fit residues: 171.4962 Evaluate side-chains 177 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 1.031 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 3 average time/residue: 0.1255 time to fit residues: 1.8921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 10 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 255 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 = 0.4045 r_free = 0.4045 target = 0.151717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.132112 restraints weight = 11075.660| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.84 r_work: 0.3700 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8100 Z= 0.221 Angle : 0.604 15.808 11029 Z= 0.302 Chirality : 0.043 0.315 1320 Planarity : 0.003 0.037 1374 Dihedral : 7.927 167.605 1148 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.49 % Allowed : 21.45 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 0.49 (0.26), residues: 1045 helix: 2.01 (0.28), residues: 351 sheet: 0.69 (0.30), residues: 287 loop : -1.51 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.002 0.001 HIS E 35 PHE 0.021 0.001 PHE B 199 TYR 0.027 0.002 TYR E 102 ARG 0.004 0.000 ARG C 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3508.21 seconds wall clock time: 63 minutes 2.64 seconds (3782.64 seconds total)