Starting phenix.real_space_refine on Sat Apr 6 10:15:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/04_2024/8dzr_27806_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/04_2024/8dzr_27806.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/04_2024/8dzr_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_27806/04_2024/8dzr_27806_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/04_2024/8dzr_27806_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/04_2024/8dzr_27806.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/04_2024/8dzr_27806.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/04_2024/8dzr_27806_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzr_27806/04_2024/8dzr_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 4.57, per 1000 atoms: 0.58 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: 2.87 Conformation dependent library (CDL) restraints added in 1.4 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: 1.53 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: 2.24 Time building geometry restraints manager: 3.14 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: 2.140 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: 0.010 Extract box with map and model: 5.250 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.490 Find NCS groups from input model: 0.240 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.760 ------------------------------------------------------------------------------- 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 : 0.839 Fit side-chains REVERT: A 288 THR cc_start: 0.7351 (m) cc_final: 0.7091 (m) REVERT: B 18 MET cc_start: 0.7284 (mmm) cc_final: 0.6942 (mmm) REVERT: B 323 MET cc_start: 0.6589 (mpp) cc_final: 0.5984 (mpp) REVERT: E 95 TYR cc_start: 0.8540 (m-80) cc_final: 0.8287 (m-80) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.8856 time to fit residues: 163.6083 Evaluate side-chains 157 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.7097 moved from start: 0.0748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8100 Z= 0.160 Angle : 0.508 8.082 11029 Z= 0.263 Chirality : 0.041 0.140 1320 Planarity : 0.003 0.038 1374 Dihedral : 7.873 167.527 1148 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.37 % Allowed : 11.72 % Favored : 86.91 % 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: 1.79 (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 0.018 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 176 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 0.882 Fit side-chains REVERT: A 288 THR cc_start: 0.7387 (m) cc_final: 0.7165 (m) REVERT: A 318 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7122 (mp) REVERT: B 323 MET cc_start: 0.6575 (mpp) cc_final: 0.5945 (mpp) REVERT: C 132 ASN cc_start: 0.8023 (p0) cc_final: 0.7676 (p0) REVERT: E 95 TYR cc_start: 0.8555 (m-80) cc_final: 0.8259 (m-80) outliers start: 11 outliers final: 6 residues processed: 169 average time/residue: 0.9262 time to fit residues: 168.9811 Evaluate side-chains 168 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain E residue 23 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7166 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8100 Z= 0.279 Angle : 0.563 8.344 11029 Z= 0.294 Chirality : 0.043 0.146 1320 Planarity : 0.003 0.038 1374 Dihedral : 8.118 173.981 1148 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.24 % Allowed : 13.59 % Favored : 83.17 % 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: 0.38 (0.26), residues: 1045 helix: 1.92 (0.28), residues: 346 sheet: 0.68 (0.30), residues: 286 loop : -1.58 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 211 HIS 0.004 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 193 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 0.895 Fit side-chains REVERT: A 226 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.6101 (tpp) REVERT: A 318 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7092 (mp) REVERT: A 328 ILE cc_start: 0.7198 (OUTLIER) cc_final: 0.6825 (mp) REVERT: B 18 MET cc_start: 0.7264 (mmm) cc_final: 0.7016 (mmm) REVERT: B 323 MET cc_start: 0.6643 (mpp) cc_final: 0.5997 (mpp) REVERT: C 132 ASN cc_start: 0.8074 (p0) cc_final: 0.7728 (p0) outliers start: 26 outliers final: 12 residues processed: 175 average time/residue: 0.8709 time to fit residues: 164.8483 Evaluate side-chains 179 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 164 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 212 VAL 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: 1.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 101 optimal weight: 0.3980 chunk 50 optimal weight: 0.2980 chunk 90 optimal weight: 0.0270 chunk 27 optimal weight: 2.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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: 0.7138 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8100 Z= 0.186 Angle : 0.522 8.378 11029 Z= 0.271 Chirality : 0.041 0.137 1320 Planarity : 0.003 0.036 1374 Dihedral : 7.882 168.565 1148 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.99 % Allowed : 17.08 % 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: 0.50 (0.26), residues: 1045 helix: 2.14 (0.28), residues: 345 sheet: 0.69 (0.31), residues: 281 loop : -1.55 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.003 0.001 HIS C 142 PHE 0.016 0.001 PHE B 199 TYR 0.021 0.002 TYR E 102 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 197 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 0.792 Fit side-chains REVERT: A 107 LEU cc_start: 0.8224 (mp) cc_final: 0.7995 (mp) REVERT: A 226 MET cc_start: 0.7538 (OUTLIER) cc_final: 0.6101 (tpp) REVERT: A 318 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7037 (mp) REVERT: B 18 MET cc_start: 0.7254 (mmm) cc_final: 0.7004 (mmm) REVERT: B 323 MET cc_start: 0.6558 (mpp) cc_final: 0.5920 (mpp) REVERT: C 132 ASN cc_start: 0.8008 (p0) cc_final: 0.7660 (p0) outliers start: 24 outliers final: 11 residues processed: 184 average time/residue: 0.8597 time to fit residues: 171.0577 Evaluate side-chains 180 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 167 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain E residue 23 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 75 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8100 Z= 0.237 Angle : 0.556 9.009 11029 Z= 0.287 Chirality : 0.042 0.154 1320 Planarity : 0.003 0.036 1374 Dihedral : 7.976 169.955 1148 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.24 % Allowed : 17.21 % Favored : 79.55 % 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: 2.11 (0.28), residues: 346 sheet: 0.68 (0.31), residues: 281 loop : -1.52 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 82 HIS 0.003 0.001 HIS D 44 PHE 0.018 0.002 PHE B 199 TYR 0.024 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 191 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 0.825 Fit side-chains REVERT: A 107 LEU cc_start: 0.8252 (mp) cc_final: 0.8026 (mp) REVERT: A 318 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7005 (mp) REVERT: A 328 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7082 (mp) REVERT: B 18 MET cc_start: 0.7255 (mmm) cc_final: 0.7034 (mmm) REVERT: B 323 MET cc_start: 0.6605 (mpp) cc_final: 0.5942 (mpp) REVERT: C 132 ASN cc_start: 0.8071 (p0) cc_final: 0.7731 (p0) outliers start: 26 outliers final: 19 residues processed: 179 average time/residue: 0.8778 time to fit residues: 169.8442 Evaluate side-chains 184 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 163 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 23 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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: 0.7156 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 : 0.003 0.035 8100 Z= 0.221 Angle : 0.548 8.980 11029 Z= 0.282 Chirality : 0.042 0.163 1320 Planarity : 0.003 0.035 1374 Dihedral : 7.908 168.207 1148 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.87 % Allowed : 17.21 % Favored : 78.93 % 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: 0.53 (0.26), residues: 1045 helix: 2.18 (0.28), residues: 346 sheet: 0.69 (0.30), residues: 281 loop : -1.53 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 82 HIS 0.002 0.001 HIS E 35 PHE 0.021 0.001 PHE B 199 TYR 0.023 0.002 TYR E 102 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 195 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 0.872 Fit side-chains REVERT: A 107 LEU cc_start: 0.8236 (mp) cc_final: 0.8019 (mp) REVERT: A 250 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7627 (mp) REVERT: A 318 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7006 (mp) REVERT: B 323 MET cc_start: 0.6586 (mpp) cc_final: 0.5922 (mpp) REVERT: C 132 ASN cc_start: 0.8069 (p0) cc_final: 0.7732 (p0) REVERT: C 315 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7667 (t) outliers start: 31 outliers final: 17 residues processed: 179 average time/residue: 0.8644 time to fit residues: 167.2887 Evaluate side-chains 180 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 23 SER 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: 0.5980 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7179 moved from start: 0.1538 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= 0.278 Angle : 0.585 9.586 11029 Z= 0.301 Chirality : 0.043 0.185 1320 Planarity : 0.003 0.036 1374 Dihedral : 8.052 171.701 1148 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.99 % Allowed : 17.96 % Favored : 78.05 % 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: 1.96 (0.28), residues: 350 sheet: 0.60 (0.30), residues: 290 loop : -1.48 (0.29), residues: 405 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 0.021 0.002 PHE B 199 TYR 0.028 0.002 TYR E 178 ARG 0.004 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 193 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 0.794 Fit side-chains REVERT: A 250 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7673 (mp) REVERT: A 318 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7021 (mp) REVERT: B 323 MET cc_start: 0.6652 (mpp) cc_final: 0.5988 (mpp) REVERT: C 132 ASN cc_start: 0.8079 (p0) cc_final: 0.7737 (p0) REVERT: C 315 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7704 (t) outliers start: 32 outliers final: 20 residues processed: 177 average time/residue: 0.9141 time to fit residues: 174.4524 Evaluate side-chains 173 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 150 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 337 LYS Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.0970 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 79 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8100 Z= 0.238 Angle : 0.582 9.408 11029 Z= 0.296 Chirality : 0.043 0.198 1320 Planarity : 0.003 0.036 1374 Dihedral : 7.981 169.511 1148 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.24 % Allowed : 18.45 % 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: 0.48 (0.26), residues: 1045 helix: 1.97 (0.28), residues: 352 sheet: 0.72 (0.30), residues: 281 loop : -1.49 (0.29), residues: 412 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 0.021 0.002 PHE B 199 TYR 0.026 0.002 TYR E 102 ARG 0.004 0.000 ARG C 314 *********************** 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 193 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 159 time to evaluate : 0.871 Fit side-chains REVERT: A 107 LEU cc_start: 0.8244 (mp) cc_final: 0.8010 (mp) REVERT: A 250 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7639 (mp) REVERT: A 318 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7003 (mp) REVERT: B 323 MET cc_start: 0.6615 (mpp) cc_final: 0.5951 (mpp) REVERT: B 327 THR cc_start: 0.7538 (p) cc_final: 0.7274 (p) REVERT: C 132 ASN cc_start: 0.8078 (p0) cc_final: 0.7738 (p0) REVERT: C 314 ARG cc_start: 0.7753 (ptp-170) cc_final: 0.7531 (ptm160) REVERT: C 315 VAL cc_start: 0.7952 (OUTLIER) cc_final: 0.7688 (t) outliers start: 34 outliers final: 21 residues processed: 176 average time/residue: 0.8993 time to fit residues: 170.8692 Evaluate side-chains 178 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 337 LYS Chi-restraints excluded: chain E residue 23 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.0070 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.6800 ------------------------------------------------------------------------------- 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: 0.7172 moved from start: 0.1620 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= 0.249 Angle : 0.585 9.620 11029 Z= 0.299 Chirality : 0.044 0.286 1320 Planarity : 0.003 0.036 1374 Dihedral : 7.984 170.042 1148 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.62 % Allowed : 19.83 % Favored : 76.56 % 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: 1.99 (0.28), residues: 351 sheet: 0.73 (0.30), residues: 281 loop : -1.50 (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 0.021 0.001 PHE B 199 TYR 0.027 0.002 TYR E 102 ARG 0.004 0.000 ARG C 96 *********************** 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 184 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 0.901 Fit side-chains REVERT: A 250 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7649 (mp) REVERT: A 318 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6981 (mp) REVERT: B 323 MET cc_start: 0.6610 (mpp) cc_final: 0.5936 (mpp) REVERT: B 327 THR cc_start: 0.7544 (p) cc_final: 0.7280 (p) REVERT: C 132 ASN cc_start: 0.8072 (p0) cc_final: 0.7737 (p0) REVERT: C 146 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8376 (mp) REVERT: C 314 ARG cc_start: 0.7755 (ptp-170) cc_final: 0.7554 (ptm160) REVERT: C 315 VAL cc_start: 0.7950 (OUTLIER) cc_final: 0.7714 (t) REVERT: D 37 LEU cc_start: 0.5905 (OUTLIER) cc_final: 0.5650 (mm) outliers start: 29 outliers final: 22 residues processed: 173 average time/residue: 0.9272 time to fit residues: 173.2814 Evaluate side-chains 180 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 337 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 178 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 0.0970 chunk 104 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 64 optimal weight: 0.0970 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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: 0.7143 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8100 Z= 0.185 Angle : 0.561 9.238 11029 Z= 0.285 Chirality : 0.042 0.221 1320 Planarity : 0.003 0.036 1374 Dihedral : 7.807 164.919 1148 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.49 % Allowed : 20.95 % Favored : 76.56 % 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: 0.52 (0.26), residues: 1045 helix: 2.05 (0.28), residues: 349 sheet: 0.76 (0.31), residues: 282 loop : -1.52 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.002 0.001 HIS E 35 PHE 0.021 0.001 PHE B 199 TYR 0.023 0.001 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 187 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 0.741 Fit side-chains REVERT: A 111 THR cc_start: 0.7306 (m) cc_final: 0.7060 (m) REVERT: A 318 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6956 (mp) REVERT: B 323 MET cc_start: 0.6598 (mpp) cc_final: 0.5925 (mpp) REVERT: B 327 THR cc_start: 0.7542 (p) cc_final: 0.7279 (p) REVERT: C 132 ASN cc_start: 0.8016 (p0) cc_final: 0.7673 (p0) REVERT: C 146 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8394 (mp) REVERT: C 315 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7692 (t) REVERT: D 37 LEU cc_start: 0.5886 (OUTLIER) cc_final: 0.5653 (mm) outliers start: 20 outliers final: 14 residues processed: 178 average time/residue: 0.8959 time to fit residues: 172.1128 Evaluate side-chains 179 residues out of total 926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 161 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 337 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 178 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.152084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.132524 restraints weight = 11018.609| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.83 r_work: 0.3704 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8100 Z= 0.228 Angle : 0.586 9.602 11029 Z= 0.297 Chirality : 0.044 0.321 1320 Planarity : 0.003 0.036 1374 Dihedral : 7.845 166.678 1148 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.74 % Allowed : 21.32 % Favored : 75.94 % 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: 0.52 (0.26), residues: 1045 helix: 2.07 (0.28), residues: 350 sheet: 0.65 (0.30), residues: 291 loop : -1.49 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.003 0.001 HIS E 35 PHE 0.021 0.001 PHE B 199 TYR 0.026 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: 3529.19 seconds wall clock time: 63 minutes 46.33 seconds (3826.33 seconds total)