Starting phenix.real_space_refine on Mon Dec 30 12:41:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hps_34942/12_2024/8hps_34942.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hps_34942/12_2024/8hps_34942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hps_34942/12_2024/8hps_34942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hps_34942/12_2024/8hps_34942.map" model { file = "/net/cci-nas-00/data/ceres_data/8hps_34942/12_2024/8hps_34942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hps_34942/12_2024/8hps_34942.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 8310 2.51 5 N 2194 2.21 5 O 2438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12984 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2153 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 14, 'TRANS': 270} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1994 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 247} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2684 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Chain breaks: 2 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2725 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "E" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3341 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 405} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.49, per 1000 atoms: 0.65 Number of scatterers: 12984 At special positions: 0 Unit cell: (86.1, 86.1, 168.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 34 16.00 P 6 15.00 Mg 2 11.99 O 2438 8.00 N 2194 7.00 C 8310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-1 " GLC H 1 " - " GLC H 2 " Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3198 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 13 sheets defined 56.2% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 15 through 50 removed outlier: 3.640A pdb=" N SER A 19 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Proline residue: A 30 - end of helix removed outlier: 3.699A pdb=" N VAL A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix removed outlier: 3.785A pdb=" N SER A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 75 removed outlier: 3.515A pdb=" N VAL A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 111 removed outlier: 3.569A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.523A pdb=" N THR A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 161 through 190 removed outlier: 4.010A pdb=" N LYS A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 193 through 202 removed outlier: 3.514A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.518A pdb=" N LYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 235 Proline residue: A 221 - end of helix removed outlier: 4.052A pdb=" N VAL A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 272 through 294 removed outlier: 3.977A pdb=" N ILE A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 37 Proline residue: B 27 - end of helix Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 64 through 98 removed outlier: 3.629A pdb=" N ALA B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 removed outlier: 3.818A pdb=" N ILE B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 133 removed outlier: 3.845A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix removed outlier: 3.646A pdb=" N GLY B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 162 Proline residue: B 144 - end of helix Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 165 through 175 removed outlier: 3.995A pdb=" N GLU B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 186 Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.756A pdb=" N LEU B 190 " --> pdb=" O VAL B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 208 removed outlier: 3.611A pdb=" N ASN B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 216 removed outlier: 3.607A pdb=" N SER B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 253 through 264 removed outlier: 4.007A pdb=" N VAL B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'C' and resid 46 through 55 Processing helix chain 'C' and resid 76 through 81 Processing helix chain 'C' and resid 96 through 108 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 111 through 127 Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 140 through 155 removed outlier: 3.757A pdb=" N GLY C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG C 151 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 188 removed outlier: 4.335A pdb=" N GLN C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA C 179 " --> pdb=" O VAL C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 206 removed outlier: 3.734A pdb=" N ALA C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 266 through 276 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 298 through 304 removed outlier: 3.983A pdb=" N ILE C 303 " --> pdb=" O GLY C 299 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 Processing helix chain 'D' and resid 76 through 81 Processing helix chain 'D' and resid 96 through 108 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.934A pdb=" N LYS D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 140 through 155 removed outlier: 4.287A pdb=" N ARG D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 188 Processing helix chain 'D' and resid 198 through 206 removed outlier: 3.982A pdb=" N THR D 204 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 229 Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 266 through 276 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 374 through 377 removed outlier: 3.584A pdb=" N LEU D 377 " --> pdb=" O THR D 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 374 through 377' Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 55 removed outlier: 4.474A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 83 removed outlier: 3.997A pdb=" N LEU E 75 " --> pdb=" O ASP E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 104 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 127 through 134 Processing helix chain 'E' and resid 165 through 180 Processing helix chain 'E' and resid 192 through 206 removed outlier: 4.112A pdb=" N VAL E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 243 Processing helix chain 'E' and resid 249 through 253 removed outlier: 3.537A pdb=" N THR E 253 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 275 through 286 removed outlier: 3.600A pdb=" N SER E 279 " --> pdb=" O TYR E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 297 Processing helix chain 'E' and resid 313 through 326 removed outlier: 3.538A pdb=" N LYS E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 371 Processing helix chain 'E' and resid 372 through 382 Processing helix chain 'E' and resid 389 through 394 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 404 through 414 removed outlier: 3.582A pdb=" N ASN E 414 " --> pdb=" O GLN E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 436 Processing helix chain 'E' and resid 437 through 441 Processing helix chain 'E' and resid 442 through 460 Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 31 removed outlier: 6.632A pdb=" N ALA C 23 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N SER C 12 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LYS C 25 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR C 10 " --> pdb=" O LYS C 25 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE C 27 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL C 9 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER C 62 " --> pdb=" O VAL C 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.121A pdb=" N ALA C 83 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ASP C 163 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL C 85 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE C 160 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL C 195 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N MET C 162 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N PHE C 36 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL C 210 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE C 38 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N MET C 212 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL C 40 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL C 209 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE C 220 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL C 211 " --> pdb=" O GLN C 218 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 261 through 264 Processing sheet with id=AA4, first strand: chain 'C' and resid 291 through 293 Processing sheet with id=AA5, first strand: chain 'D' and resid 21 through 31 removed outlier: 6.239A pdb=" N ALA D 23 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N SER D 12 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS D 25 " --> pdb=" O THR D 10 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR D 10 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N PHE D 27 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N VAL D 9 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER D 62 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 85 removed outlier: 6.296A pdb=" N ALA D 83 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP D 163 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL D 85 " --> pdb=" O ASP D 163 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE D 160 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL D 195 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N MET D 162 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE D 36 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL D 210 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE D 38 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N MET D 212 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL D 40 " --> pdb=" O MET D 212 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL D 209 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE D 220 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 262 through 264 Processing sheet with id=AA8, first strand: chain 'D' and resid 291 through 293 removed outlier: 3.701A pdb=" N LEU D 306 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 321 through 325 Processing sheet with id=AB1, first strand: chain 'E' and resid 59 through 65 removed outlier: 7.045A pdb=" N ILE E 30 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA E 62 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE E 32 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG E 64 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR E 34 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL E 353 " --> pdb=" O VAL E 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 59 through 65 removed outlier: 7.045A pdb=" N ILE E 30 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA E 62 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE E 32 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG E 64 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR E 34 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY E 347 " --> pdb=" O THR E 147 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR E 147 " --> pdb=" O GLY E 347 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU E 349 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 135 through 136 Processing sheet with id=AB4, first strand: chain 'E' and resid 184 through 186 removed outlier: 6.136A pdb=" N TRP E 184 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU E 269 " --> pdb=" O TRP E 184 " (cutoff:3.500A) 699 hydrogen bonds defined for protein. 1974 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: 4.22 Time building geometry restraints manager: 3.63 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: 3007 1.33 - 1.45: 2612 1.45 - 1.58: 7553 1.58 - 1.70: 10 1.70 - 1.82: 64 Bond restraints: 13246 Sorted by residual: bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.01e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.87e+01 bond pdb=" C5 ATP D 501 " pdb=" C6 ATP D 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.40e+01 bond pdb=" C5 ATP C 501 " pdb=" C6 ATP C 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.30e+01 bond pdb=" C5 GLC H 1 " pdb=" O5 GLC H 1 " ideal model delta sigma weight residual 1.415 1.548 -0.133 2.00e-02 2.50e+03 4.43e+01 ... (remaining 13241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 17608 3.92 - 7.84: 464 7.84 - 11.76: 11 11.76 - 15.68: 0 15.68 - 19.59: 4 Bond angle restraints: 18087 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 120.28 19.59 1.00e+00 1.00e+00 3.84e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.36 19.51 1.00e+00 1.00e+00 3.81e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 120.33 16.50 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PA ATP D 501 " pdb=" O3A ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 136.83 120.51 16.32 1.00e+00 1.00e+00 2.66e+02 angle pdb=" C5 ATP C 501 " pdb=" C4 ATP C 501 " pdb=" N3 ATP C 501 " ideal model delta sigma weight residual 126.80 118.65 8.15 1.00e+00 1.00e+00 6.65e+01 ... (remaining 18082 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 7424 17.82 - 35.63: 434 35.63 - 53.45: 83 53.45 - 71.27: 31 71.27 - 89.08: 8 Dihedral angle restraints: 7980 sinusoidal: 3024 harmonic: 4956 Sorted by residual: dihedral pdb=" CA SER C 129 " pdb=" C SER C 129 " pdb=" N GLU C 130 " pdb=" CA GLU C 130 " ideal model delta harmonic sigma weight residual 180.00 151.19 28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ASP A 161 " pdb=" C ASP A 161 " pdb=" N GLN A 162 " pdb=" CA GLN A 162 " ideal model delta harmonic sigma weight residual 180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA THR C 328 " pdb=" C THR C 328 " pdb=" N GLU C 329 " pdb=" CA GLU C 329 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 7977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1461 0.094 - 0.187: 584 0.187 - 0.281: 82 0.281 - 0.374: 19 0.374 - 0.468: 4 Chirality restraints: 2150 Sorted by residual: chirality pdb=" C1 GLC H 1 " pdb=" C2 GLC H 1 " pdb=" O5 GLC H 1 " pdb=" O1 GLC H 2 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.31e+01 chirality pdb=" CA THR A 130 " pdb=" N THR A 130 " pdb=" C THR A 130 " pdb=" CB THR A 130 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" CA LEU A 148 " pdb=" N LEU A 148 " pdb=" C LEU A 148 " pdb=" CB LEU A 148 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.95e+00 ... (remaining 2147 not shown) Planarity restraints: 2313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 153 " 0.130 2.00e-02 2.50e+03 6.54e-02 1.07e+02 pdb=" CG TRP E 153 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP E 153 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP E 153 " -0.054 2.00e-02 2.50e+03 pdb=" NE1 TRP E 153 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP E 153 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 153 " -0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 153 " 0.086 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 153 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP E 153 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 333 " -0.116 2.00e-02 2.50e+03 6.15e-02 7.56e+01 pdb=" CG TYR E 333 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR E 333 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR E 333 " 0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR E 333 " 0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR E 333 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR E 333 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 333 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 424 " -0.113 2.00e-02 2.50e+03 6.04e-02 7.30e+01 pdb=" CG TYR E 424 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR E 424 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR E 424 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR E 424 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR E 424 " 0.038 2.00e-02 2.50e+03 pdb=" CZ TYR E 424 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 424 " -0.089 2.00e-02 2.50e+03 ... (remaining 2310 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 511 2.75 - 3.29: 13991 3.29 - 3.82: 19980 3.82 - 4.36: 25812 4.36 - 4.90: 42796 Nonbonded interactions: 103090 Sorted by model distance: nonbonded pdb=" O ASP A 250 " pdb=" OD1 ASP A 250 " model vdw 2.209 3.040 nonbonded pdb=" OE1 GLN D 87 " pdb="MG MG D 502 " model vdw 2.248 2.170 nonbonded pdb=" NH1 ARG E 80 " pdb=" OD2 ASP E 85 " model vdw 2.255 3.120 nonbonded pdb=" CE2 PHE C 36 " pdb=" CB LEU C 205 " model vdw 2.267 3.740 nonbonded pdb=" OE1 GLN C 87 " pdb="MG MG C 502 " model vdw 2.275 2.170 ... (remaining 103085 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 2 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 125 or (resid 126 through 128 and ( \ name N or name CA or name C or name O or name CB )) or resid 129 or (resid 130 t \ hrough 132 and (name N or name CA or name C or name O or name CB )) or resid 133 \ through 179 or (resid 180 and (name N or name CA or name C or name O or name CB \ )) or resid 181 through 196 or (resid 197 and (name N or name CA or name C or n \ ame O or name CB )) or resid 198 through 359 or (resid 360 and (name N or name C \ A or name C or name O or name CB )) or resid 361 through 391 or resid 501 throug \ h 502)) selection = (chain 'D' and (resid 2 through 77 or (resid 78 and (name N or name CA or name C \ or name O or name CB )) or resid 79 through 106 or (resid 107 through 108 and ( \ name N or name CA or name C or name O or name CB )) or resid 109 through 111 or \ (resid 112 through 113 and (name N or name CA or name C or name O or name CB )) \ or resid 114 through 120 or (resid 121 and (name N or name CA or name C or name \ O or name CB )) or resid 122 through 124 or (resid 125 through 128 and (name N o \ r name CA or name C or name O or name CB )) or resid 129 through 145 or (resid 1 \ 46 and (name N or name CA or name C or name O or name CB )) or resid 147 through \ 225 or (resid 226 and (name N or name CA or name C or name O or name CB )) or r \ esid 227 through 237 or (resid 238 and (name N or name CA or name C or name O or \ name CB )) or resid 239 through 251 or (resid 252 and (name N or name CA or nam \ e C or name O or name CB )) or resid 253 through 263 or (resid 264 and (name N o \ r name CA or name C or name O or name CB )) or resid 265 through 268 or (resid 2 \ 69 and (name N or name CA or name C or name O or name CB )) or resid 270 through \ 295 or (resid 296 and (name N or name CA or name C or name O or name CB )) or r \ esid 297 or (resid 298 and (name N or name CA or name C or name O or name CB )) \ or resid 299 through 302 or (resid 303 and (name N or name CA or name C or name \ O or name CB )) or resid 304 through 305 or (resid 306 and (name N or name CA or \ name C or name O or name CB )) or resid 307 through 310 or (resid 311 through 3 \ 12 and (name N or name CA or name C or name O or name CB )) or resid 313 through \ 378 or (resid 379 and (name N or name CA or name C or name O or name CB )) or r \ esid 380 through 389 or (resid 390 and (name N or name CA or name C or name O or \ name CB )) or resid 391 or resid 501 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.550 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 30.460 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.012 0.133 13246 Z= 0.817 Angle : 1.773 19.594 18087 Z= 1.214 Chirality : 0.097 0.468 2150 Planarity : 0.012 0.110 2313 Dihedral : 13.068 89.082 4782 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.38 % Allowed : 5.20 % Favored : 94.42 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 3.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.18), residues: 1704 helix: -1.33 (0.15), residues: 824 sheet: 0.53 (0.47), residues: 112 loop : -0.99 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.130 0.020 TRP E 153 HIS 0.012 0.003 HIS C 197 PHE 0.057 0.012 PHE C 234 TYR 0.116 0.018 TYR E 333 ARG 0.007 0.001 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 336 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7567 (mmt90) cc_final: 0.7366 (mmm160) REVERT: A 289 TYR cc_start: 0.7904 (m-10) cc_final: 0.7559 (m-80) REVERT: B 12 TRP cc_start: 0.8446 (t-100) cc_final: 0.8234 (t60) REVERT: B 125 ILE cc_start: 0.8887 (mm) cc_final: 0.8485 (mm) REVERT: C 100 ASN cc_start: 0.8153 (m-40) cc_final: 0.7312 (t0) REVERT: C 220 ILE cc_start: 0.9030 (mt) cc_final: 0.8580 (mp) REVERT: C 260 PHE cc_start: 0.6833 (p90) cc_final: 0.6374 (p90) REVERT: C 308 PHE cc_start: 0.3849 (p90) cc_final: 0.3457 (p90) REVERT: D 36 PHE cc_start: 0.7907 (t80) cc_final: 0.7685 (t80) REVERT: D 84 MET cc_start: 0.8802 (ttt) cc_final: 0.8555 (ttm) REVERT: D 199 GLN cc_start: 0.8361 (pp30) cc_final: 0.8085 (pp30) REVERT: E 54 GLN cc_start: 0.7459 (mt0) cc_final: 0.7090 (mt0) outliers start: 5 outliers final: 3 residues processed: 338 average time/residue: 0.2870 time to fit residues: 135.6503 Evaluate side-chains 228 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 225 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 118 HIS Chi-restraints excluded: chain B residue 238 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 98 optimal weight: 0.0170 chunk 153 optimal weight: 8.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 261 ASN C 99 GLN C 325 HIS E 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13246 Z= 0.208 Angle : 0.696 8.406 18087 Z= 0.370 Chirality : 0.046 0.215 2150 Planarity : 0.005 0.040 2313 Dihedral : 7.530 71.303 1958 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.75 % Allowed : 11.16 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: -0.12 (0.20), residues: 1704 helix: 0.26 (0.17), residues: 853 sheet: 0.03 (0.38), residues: 160 loop : -0.36 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 80 HIS 0.004 0.001 HIS E 359 PHE 0.024 0.002 PHE C 234 TYR 0.026 0.002 TYR E 192 ARG 0.006 0.001 ARG E 418 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 253 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7568 (mmt90) cc_final: 0.7283 (mmm160) REVERT: B 58 LYS cc_start: 0.8896 (ptpt) cc_final: 0.8653 (mtmm) REVERT: B 158 SER cc_start: 0.9352 (t) cc_final: 0.9023 (m) REVERT: B 208 ASN cc_start: 0.7833 (p0) cc_final: 0.7625 (p0) REVERT: C 4 ILE cc_start: 0.8963 (mp) cc_final: 0.8718 (tt) REVERT: C 100 ASN cc_start: 0.7946 (m-40) cc_final: 0.7413 (t0) REVERT: C 219 GLN cc_start: 0.7676 (tp40) cc_final: 0.7360 (tp40) REVERT: C 244 MET cc_start: 0.3893 (ttm) cc_final: 0.3667 (ttp) REVERT: C 260 PHE cc_start: 0.6630 (p90) cc_final: 0.5958 (p90) REVERT: D 158 LYS cc_start: 0.8270 (mttt) cc_final: 0.7519 (tptt) REVERT: D 199 GLN cc_start: 0.8203 (pp30) cc_final: 0.7960 (pp30) REVERT: E 54 GLN cc_start: 0.7225 (mt0) cc_final: 0.6845 (mt0) REVERT: E 263 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7254 (tp30) REVERT: E 378 TYR cc_start: 0.7897 (t80) cc_final: 0.7619 (t80) REVERT: E 461 LYS cc_start: 0.8464 (mmpt) cc_final: 0.7775 (mtpt) outliers start: 36 outliers final: 20 residues processed: 273 average time/residue: 0.2238 time to fit residues: 92.9505 Evaluate side-chains 226 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 155 TYR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 428 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 153 optimal weight: 0.0070 chunk 166 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 152 optimal weight: 0.0470 chunk 52 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN B 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13246 Z= 0.163 Angle : 0.608 9.090 18087 Z= 0.313 Chirality : 0.044 0.172 2150 Planarity : 0.005 0.057 2313 Dihedral : 6.978 69.873 1955 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.98 % Allowed : 12.46 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.29 (0.20), residues: 1704 helix: 0.73 (0.18), residues: 851 sheet: -0.06 (0.36), residues: 192 loop : -0.28 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 79 HIS 0.003 0.001 HIS C 197 PHE 0.016 0.001 PHE B 183 TYR 0.032 0.002 TYR E 192 ARG 0.005 0.000 ARG D 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7525 (mmt90) cc_final: 0.7041 (mmm160) REVERT: B 58 LYS cc_start: 0.8917 (ptpt) cc_final: 0.8698 (mtmm) REVERT: C 4 ILE cc_start: 0.8946 (mp) cc_final: 0.8634 (tt) REVERT: C 100 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7293 (t0) REVERT: C 153 ILE cc_start: 0.8175 (mm) cc_final: 0.7915 (tp) REVERT: C 219 GLN cc_start: 0.7609 (tp40) cc_final: 0.7202 (tp40) REVERT: C 244 MET cc_start: 0.3701 (ttm) cc_final: 0.3453 (ttp) REVERT: C 260 PHE cc_start: 0.6698 (p90) cc_final: 0.6063 (p90) REVERT: C 283 ILE cc_start: 0.8671 (mm) cc_final: 0.8209 (pt) REVERT: D 151 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7423 (mtm110) REVERT: D 158 LYS cc_start: 0.8210 (mttt) cc_final: 0.7488 (tppt) REVERT: E 263 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7178 (tp30) REVERT: E 378 TYR cc_start: 0.7922 (t80) cc_final: 0.7679 (t80) outliers start: 39 outliers final: 25 residues processed: 248 average time/residue: 0.2431 time to fit residues: 90.7764 Evaluate side-chains 227 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 0.3980 chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 103 optimal weight: 0.0970 chunk 154 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN C 99 GLN D 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13246 Z= 0.165 Angle : 0.583 7.653 18087 Z= 0.297 Chirality : 0.043 0.195 2150 Planarity : 0.004 0.050 2313 Dihedral : 6.692 69.159 1955 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.21 % Allowed : 13.53 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.51 (0.20), residues: 1704 helix: 0.97 (0.18), residues: 847 sheet: -0.01 (0.36), residues: 192 loop : -0.24 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 80 HIS 0.005 0.001 HIS E 359 PHE 0.014 0.001 PHE C 234 TYR 0.023 0.001 TYR D 89 ARG 0.015 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 220 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8670 (mp) REVERT: A 45 TYR cc_start: 0.8555 (t80) cc_final: 0.8345 (t80) REVERT: A 110 ARG cc_start: 0.7424 (mmt90) cc_final: 0.6973 (mmm160) REVERT: C 4 ILE cc_start: 0.8920 (mp) cc_final: 0.8564 (tt) REVERT: C 100 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7218 (t0) REVERT: C 219 GLN cc_start: 0.7536 (tp40) cc_final: 0.7120 (tp40) REVERT: C 244 MET cc_start: 0.3682 (ttm) cc_final: 0.3426 (ttp) REVERT: C 260 PHE cc_start: 0.6676 (p90) cc_final: 0.6221 (p90) REVERT: C 283 ILE cc_start: 0.8672 (mm) cc_final: 0.8237 (pt) REVERT: D 21 ARG cc_start: 0.6766 (ptt-90) cc_final: 0.6510 (ptt180) REVERT: D 151 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7388 (mtm110) REVERT: D 158 LYS cc_start: 0.8205 (mttt) cc_final: 0.7506 (tppt) REVERT: D 178 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.6582 (mtt180) REVERT: E 263 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7199 (tp30) REVERT: E 378 TYR cc_start: 0.7935 (t80) cc_final: 0.7705 (t80) outliers start: 42 outliers final: 27 residues processed: 243 average time/residue: 0.2315 time to fit residues: 84.4920 Evaluate side-chains 234 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 2 optimal weight: 0.0670 chunk 121 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 367 GLN E 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13246 Z= 0.160 Angle : 0.572 8.479 18087 Z= 0.289 Chirality : 0.043 0.163 2150 Planarity : 0.004 0.047 2313 Dihedral : 6.438 70.281 1955 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.29 % Allowed : 14.30 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.69 (0.20), residues: 1704 helix: 1.20 (0.18), residues: 832 sheet: 0.04 (0.36), residues: 192 loop : -0.25 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 166 HIS 0.004 0.001 HIS E 359 PHE 0.018 0.001 PHE B 183 TYR 0.024 0.001 TYR D 89 ARG 0.014 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8754 (mp) REVERT: A 45 TYR cc_start: 0.8574 (t80) cc_final: 0.8334 (t80) REVERT: A 110 ARG cc_start: 0.7398 (mmt90) cc_final: 0.6960 (mmm160) REVERT: C 4 ILE cc_start: 0.8911 (mp) cc_final: 0.8504 (tt) REVERT: C 100 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7202 (t0) REVERT: C 219 GLN cc_start: 0.7551 (tp40) cc_final: 0.7126 (tp40) REVERT: C 244 MET cc_start: 0.3578 (ttm) cc_final: 0.3314 (ttp) REVERT: C 260 PHE cc_start: 0.6651 (p90) cc_final: 0.6287 (p90) REVERT: C 283 ILE cc_start: 0.8659 (mm) cc_final: 0.8234 (pt) REVERT: D 151 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7375 (mtm110) REVERT: D 158 LYS cc_start: 0.8194 (mttt) cc_final: 0.7517 (tppt) REVERT: D 178 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7430 (mtt180) REVERT: E 263 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: E 378 TYR cc_start: 0.7948 (t80) cc_final: 0.7714 (t80) outliers start: 43 outliers final: 35 residues processed: 237 average time/residue: 0.2367 time to fit residues: 83.8293 Evaluate side-chains 229 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 135 optimal weight: 0.0000 chunk 75 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 85 optimal weight: 20.0000 chunk 157 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 99 GLN D 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13246 Z= 0.206 Angle : 0.587 8.415 18087 Z= 0.296 Chirality : 0.043 0.178 2150 Planarity : 0.005 0.067 2313 Dihedral : 6.317 72.364 1955 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.52 % Allowed : 14.98 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.77 (0.20), residues: 1704 helix: 1.25 (0.18), residues: 841 sheet: 0.12 (0.36), residues: 196 loop : -0.20 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 129 HIS 0.003 0.001 HIS E 359 PHE 0.018 0.001 PHE B 183 TYR 0.025 0.001 TYR D 89 ARG 0.015 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8808 (mp) REVERT: A 45 TYR cc_start: 0.8579 (t80) cc_final: 0.8375 (t80) REVERT: A 110 ARG cc_start: 0.7403 (mmt90) cc_final: 0.6992 (mmm160) REVERT: A 147 TYR cc_start: 0.8517 (p90) cc_final: 0.8230 (p90) REVERT: B 58 LYS cc_start: 0.9064 (mttt) cc_final: 0.8598 (mtpp) REVERT: B 130 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7617 (mmm-85) REVERT: B 216 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8206 (mp) REVERT: B 240 GLU cc_start: 0.6848 (mp0) cc_final: 0.6591 (mp0) REVERT: C 100 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7334 (t0) REVERT: C 207 ASP cc_start: 0.8179 (t70) cc_final: 0.7864 (m-30) REVERT: C 244 MET cc_start: 0.3598 (ttm) cc_final: 0.3325 (ttp) REVERT: C 283 ILE cc_start: 0.8650 (mm) cc_final: 0.8226 (pt) REVERT: D 151 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7410 (mtm110) REVERT: D 158 LYS cc_start: 0.8147 (mttt) cc_final: 0.7515 (tppt) REVERT: D 178 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7348 (mtt180) REVERT: E 263 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: E 378 TYR cc_start: 0.8012 (t80) cc_final: 0.7762 (t80) outliers start: 46 outliers final: 37 residues processed: 231 average time/residue: 0.2322 time to fit residues: 81.9335 Evaluate side-chains 236 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 119 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 99 optimal weight: 0.3980 chunk 75 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13246 Z= 0.247 Angle : 0.607 8.369 18087 Z= 0.307 Chirality : 0.044 0.180 2150 Planarity : 0.004 0.047 2313 Dihedral : 6.274 75.495 1955 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.05 % Allowed : 15.75 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.75 (0.20), residues: 1704 helix: 1.24 (0.18), residues: 842 sheet: 0.10 (0.34), residues: 219 loop : -0.23 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 129 HIS 0.003 0.001 HIS E 359 PHE 0.011 0.001 PHE A 83 TYR 0.027 0.002 TYR D 89 ARG 0.015 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8847 (mp) REVERT: A 110 ARG cc_start: 0.7410 (mmt90) cc_final: 0.7029 (mmm160) REVERT: A 147 TYR cc_start: 0.8556 (p90) cc_final: 0.8289 (p90) REVERT: B 58 LYS cc_start: 0.9096 (mttt) cc_final: 0.8620 (mtpp) REVERT: B 174 MET cc_start: 0.8289 (mmt) cc_final: 0.7827 (mmt) REVERT: B 216 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8238 (mp) REVERT: B 240 GLU cc_start: 0.7013 (mp0) cc_final: 0.6780 (mp0) REVERT: C 100 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7384 (t0) REVERT: C 207 ASP cc_start: 0.8184 (t70) cc_final: 0.7869 (m-30) REVERT: C 244 MET cc_start: 0.3550 (ttm) cc_final: 0.3297 (ttp) REVERT: C 283 ILE cc_start: 0.8602 (mm) cc_final: 0.8169 (pt) REVERT: D 151 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.7517 (mtm110) REVERT: D 158 LYS cc_start: 0.8195 (mttt) cc_final: 0.7581 (tppt) REVERT: D 178 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7307 (mtt180) REVERT: E 263 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7160 (tp30) REVERT: E 345 THR cc_start: 0.8719 (m) cc_final: 0.8396 (p) REVERT: E 378 TYR cc_start: 0.8027 (t80) cc_final: 0.7817 (t80) outliers start: 53 outliers final: 43 residues processed: 238 average time/residue: 0.2348 time to fit residues: 84.5815 Evaluate side-chains 234 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 51 CYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 0.0970 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 15 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 148 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13246 Z= 0.157 Angle : 0.589 9.108 18087 Z= 0.294 Chirality : 0.042 0.180 2150 Planarity : 0.004 0.046 2313 Dihedral : 6.018 74.175 1955 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.59 % Allowed : 16.51 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.79 (0.20), residues: 1704 helix: 1.30 (0.18), residues: 843 sheet: 0.22 (0.36), residues: 201 loop : -0.29 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 80 HIS 0.004 0.001 HIS E 359 PHE 0.032 0.001 PHE C 234 TYR 0.025 0.001 TYR D 89 ARG 0.013 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7304 (mmt90) cc_final: 0.6925 (mmm160) REVERT: A 147 TYR cc_start: 0.8473 (p90) cc_final: 0.8235 (p90) REVERT: B 58 LYS cc_start: 0.9073 (mttt) cc_final: 0.8579 (mtpp) REVERT: B 216 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8182 (mp) REVERT: C 100 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.7359 (t0) REVERT: C 149 MET cc_start: 0.8876 (tpp) cc_final: 0.8638 (tpp) REVERT: C 207 ASP cc_start: 0.8124 (t70) cc_final: 0.7881 (m-30) REVERT: C 244 MET cc_start: 0.3547 (ttm) cc_final: 0.3308 (ttp) REVERT: D 151 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7452 (mtm110) REVERT: D 158 LYS cc_start: 0.8157 (mttt) cc_final: 0.7560 (tppt) REVERT: E 263 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6634 (tp30) REVERT: E 345 THR cc_start: 0.8632 (m) cc_final: 0.8307 (p) outliers start: 47 outliers final: 30 residues processed: 239 average time/residue: 0.2684 time to fit residues: 95.5756 Evaluate side-chains 223 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 450 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 151 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13246 Z= 0.181 Angle : 0.615 13.277 18087 Z= 0.305 Chirality : 0.043 0.232 2150 Planarity : 0.004 0.046 2313 Dihedral : 5.957 75.537 1955 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.98 % Allowed : 17.43 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.77 (0.20), residues: 1704 helix: 1.29 (0.18), residues: 840 sheet: 0.25 (0.36), residues: 201 loop : -0.30 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 129 HIS 0.003 0.001 HIS E 359 PHE 0.010 0.001 PHE E 59 TYR 0.024 0.001 TYR D 89 ARG 0.011 0.000 ARG D 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ARG cc_start: 0.7349 (mmt90) cc_final: 0.6962 (mmm160) REVERT: A 147 TYR cc_start: 0.8494 (p90) cc_final: 0.8276 (p90) REVERT: B 58 LYS cc_start: 0.9096 (mttt) cc_final: 0.8585 (mtpp) REVERT: B 216 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8165 (mp) REVERT: C 100 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7375 (t0) REVERT: C 207 ASP cc_start: 0.8105 (t70) cc_final: 0.7877 (m-30) REVERT: C 244 MET cc_start: 0.3483 (ttm) cc_final: 0.3240 (ttp) REVERT: D 151 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7454 (mtm110) REVERT: D 158 LYS cc_start: 0.8190 (mttt) cc_final: 0.7600 (tppt) REVERT: E 263 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6950 (tp30) REVERT: E 345 THR cc_start: 0.8638 (m) cc_final: 0.8323 (p) REVERT: E 378 TYR cc_start: 0.8043 (t80) cc_final: 0.7625 (t80) outliers start: 39 outliers final: 32 residues processed: 219 average time/residue: 0.2388 time to fit residues: 79.7927 Evaluate side-chains 223 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 134 optimal weight: 0.0370 chunk 13 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 82 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13246 Z= 0.161 Angle : 0.612 13.244 18087 Z= 0.303 Chirality : 0.043 0.176 2150 Planarity : 0.004 0.056 2313 Dihedral : 5.824 75.142 1955 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.75 % Allowed : 17.74 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.85 (0.20), residues: 1704 helix: 1.32 (0.18), residues: 843 sheet: 0.34 (0.36), residues: 203 loop : -0.25 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 80 HIS 0.004 0.001 HIS E 359 PHE 0.011 0.001 PHE E 59 TYR 0.025 0.001 TYR D 89 ARG 0.008 0.000 ARG D 178 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3408 Ramachandran restraints generated. 1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.9221 (tp) cc_final: 0.8969 (tt) REVERT: A 110 ARG cc_start: 0.7404 (mmt90) cc_final: 0.6974 (mmm160) REVERT: B 216 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8130 (mp) REVERT: C 100 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7366 (t0) REVERT: C 244 MET cc_start: 0.3472 (ttm) cc_final: 0.3222 (ttp) REVERT: D 158 LYS cc_start: 0.8164 (mttt) cc_final: 0.7598 (tppt) REVERT: E 263 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6694 (tp30) REVERT: E 345 THR cc_start: 0.8589 (m) cc_final: 0.8263 (p) REVERT: E 378 TYR cc_start: 0.7956 (t80) cc_final: 0.7628 (t80) outliers start: 36 outliers final: 29 residues processed: 232 average time/residue: 0.2272 time to fit residues: 80.1876 Evaluate side-chains 226 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 60 HIS Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 63 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 203 LEU Chi-restraints excluded: chain E residue 263 GLU Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain E residue 428 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 0.7980 chunk 123 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 134 optimal weight: 0.0040 chunk 56 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 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 = 0.4015 r_free = 0.4015 target = 0.150514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114351 restraints weight = 24282.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.115320 restraints weight = 12823.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117946 restraints weight = 7958.256| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13246 Z= 0.169 Angle : 0.620 12.833 18087 Z= 0.305 Chirality : 0.043 0.353 2150 Planarity : 0.004 0.046 2313 Dihedral : 5.749 76.367 1955 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.68 % Allowed : 18.20 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.16 % 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: 0.90 (0.20), residues: 1704 helix: 1.36 (0.18), residues: 843 sheet: 0.37 (0.36), residues: 203 loop : -0.23 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 129 HIS 0.003 0.001 HIS E 359 PHE 0.010 0.001 PHE E 59 TYR 0.025 0.001 TYR D 89 ARG 0.008 0.000 ARG C 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2783.15 seconds wall clock time: 52 minutes 21.19 seconds (3141.19 seconds total)