Starting phenix.real_space_refine on Tue Aug 26 08:26:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgo_44519/08_2025/9bgo_44519.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgo_44519/08_2025/9bgo_44519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bgo_44519/08_2025/9bgo_44519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgo_44519/08_2025/9bgo_44519.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgo_44519/08_2025/9bgo_44519.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgo_44519/08_2025/9bgo_44519.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 21096 2.51 5 N 6504 2.21 5 O 7296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35028 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2919 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'TRP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 89 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 3.19, per 1000 atoms: 0.09 Number of scatterers: 35028 At special positions: 0 Unit cell: (217.28, 216.16, 108.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 7296 8.00 N 6504 7.00 C 21096 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 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 1.2 microseconds 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8880 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 12 sheets defined 79.7% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 107 through 126 removed outlier: 3.528A pdb=" N GLU A 126 " --> pdb=" O ASP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 163 through 203 removed outlier: 3.575A pdb=" N GLN A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 259 removed outlier: 3.786A pdb=" N GLU A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.756A pdb=" N ALA A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 311 removed outlier: 3.764A pdb=" N GLU A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ARG A 300 " --> pdb=" O PRO A 296 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A 301 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 333 Processing helix chain 'A' and resid 334 through 349 Processing helix chain 'A' and resid 349 through 370 Processing helix chain 'A' and resid 378 through 390 removed outlier: 3.581A pdb=" N SER A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 414 Processing helix chain 'A' and resid 427 through 436 removed outlier: 3.556A pdb=" N LEU A 431 " --> pdb=" O PRO A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 445 through 458 Processing helix chain 'A' and resid 459 through 503 Proline residue: A 470 - end of helix Processing helix chain 'B' and resid 107 through 126 removed outlier: 3.528A pdb=" N GLU B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 163 through 203 removed outlier: 3.575A pdb=" N GLN B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 259 removed outlier: 3.786A pdb=" N GLU B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 288 removed outlier: 3.755A pdb=" N ALA B 280 " --> pdb=" O ASP B 276 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 311 removed outlier: 3.765A pdb=" N GLU B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ARG B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 301 " --> pdb=" O THR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 333 Processing helix chain 'B' and resid 334 through 349 Processing helix chain 'B' and resid 349 through 370 Processing helix chain 'B' and resid 378 through 390 removed outlier: 3.581A pdb=" N SER B 382 " --> pdb=" O ASP B 378 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASN B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 414 Processing helix chain 'B' and resid 427 through 436 removed outlier: 3.555A pdb=" N LEU B 431 " --> pdb=" O PRO B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 445 through 458 Processing helix chain 'B' and resid 459 through 503 Proline residue: B 470 - end of helix Processing helix chain 'C' and resid 107 through 126 removed outlier: 3.528A pdb=" N GLU C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 163 through 203 removed outlier: 3.575A pdb=" N GLN C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 259 removed outlier: 3.786A pdb=" N GLU C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.757A pdb=" N ALA C 280 " --> pdb=" O ASP C 276 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 311 removed outlier: 3.765A pdb=" N GLU C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG C 300 " --> pdb=" O PRO C 296 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN C 301 " --> pdb=" O THR C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 333 Processing helix chain 'C' and resid 334 through 349 Processing helix chain 'C' and resid 349 through 370 Processing helix chain 'C' and resid 378 through 390 removed outlier: 3.582A pdb=" N SER C 382 " --> pdb=" O ASP C 378 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN C 384 " --> pdb=" O LEU C 380 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS C 385 " --> pdb=" O GLY C 381 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE C 386 " --> pdb=" O SER C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 414 Processing helix chain 'C' and resid 427 through 436 removed outlier: 3.556A pdb=" N LEU C 431 " --> pdb=" O PRO C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 443 Processing helix chain 'C' and resid 445 through 458 Processing helix chain 'C' and resid 459 through 503 Proline residue: C 470 - end of helix Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.528A pdb=" N GLU D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 163 through 203 removed outlier: 3.575A pdb=" N GLN D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 259 removed outlier: 3.786A pdb=" N GLU D 242 " --> pdb=" O GLN D 238 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER D 243 " --> pdb=" O ASP D 239 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 288 removed outlier: 3.756A pdb=" N ALA D 280 " --> pdb=" O ASP D 276 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE D 281 " --> pdb=" O GLN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 311 removed outlier: 3.764A pdb=" N GLU D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG D 300 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN D 301 " --> pdb=" O THR D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 333 Processing helix chain 'D' and resid 334 through 349 Processing helix chain 'D' and resid 349 through 370 Processing helix chain 'D' and resid 378 through 390 removed outlier: 3.581A pdb=" N SER D 382 " --> pdb=" O ASP D 378 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS D 385 " --> pdb=" O GLY D 381 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE D 386 " --> pdb=" O SER D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 414 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.555A pdb=" N LEU D 431 " --> pdb=" O PRO D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 445 through 458 Processing helix chain 'D' and resid 459 through 503 Proline residue: D 470 - end of helix Processing helix chain 'E' and resid 107 through 126 removed outlier: 3.528A pdb=" N GLU E 126 " --> pdb=" O ASP E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 163 through 203 removed outlier: 3.575A pdb=" N GLN E 171 " --> pdb=" O LEU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 259 removed outlier: 3.786A pdb=" N GLU E 242 " --> pdb=" O GLN E 238 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER E 243 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 288 removed outlier: 3.755A pdb=" N ALA E 280 " --> pdb=" O ASP E 276 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE E 281 " --> pdb=" O GLN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 311 removed outlier: 3.763A pdb=" N GLU E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG E 300 " --> pdb=" O PRO E 296 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN E 301 " --> pdb=" O THR E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 333 Processing helix chain 'E' and resid 334 through 349 Processing helix chain 'E' and resid 349 through 370 Processing helix chain 'E' and resid 378 through 390 removed outlier: 3.581A pdb=" N SER E 382 " --> pdb=" O ASP E 378 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN E 384 " --> pdb=" O LEU E 380 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS E 385 " --> pdb=" O GLY E 381 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE E 386 " --> pdb=" O SER E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 414 Processing helix chain 'E' and resid 427 through 436 removed outlier: 3.556A pdb=" N LEU E 431 " --> pdb=" O PRO E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 445 through 458 Processing helix chain 'E' and resid 459 through 503 Proline residue: E 470 - end of helix Processing helix chain 'F' and resid 107 through 126 removed outlier: 3.528A pdb=" N GLU F 126 " --> pdb=" O ASP F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 163 through 203 removed outlier: 3.575A pdb=" N GLN F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 259 removed outlier: 3.787A pdb=" N GLU F 242 " --> pdb=" O GLN F 238 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER F 243 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 288 removed outlier: 3.756A pdb=" N ALA F 280 " --> pdb=" O ASP F 276 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE F 281 " --> pdb=" O GLN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 311 removed outlier: 3.764A pdb=" N GLU F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ARG F 300 " --> pdb=" O PRO F 296 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN F 301 " --> pdb=" O THR F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 333 Processing helix chain 'F' and resid 334 through 349 Processing helix chain 'F' and resid 349 through 370 Processing helix chain 'F' and resid 378 through 390 removed outlier: 3.581A pdb=" N SER F 382 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS F 385 " --> pdb=" O GLY F 381 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE F 386 " --> pdb=" O SER F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 414 Processing helix chain 'F' and resid 427 through 436 removed outlier: 3.556A pdb=" N LEU F 431 " --> pdb=" O PRO F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 445 through 458 Processing helix chain 'F' and resid 459 through 503 Proline residue: F 470 - end of helix Processing helix chain 'G' and resid 107 through 126 removed outlier: 3.528A pdb=" N GLU G 126 " --> pdb=" O ASP G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 163 through 203 removed outlier: 3.574A pdb=" N GLN G 171 " --> pdb=" O LEU G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 259 removed outlier: 3.787A pdb=" N GLU G 242 " --> pdb=" O GLN G 238 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER G 243 " --> pdb=" O ASP G 239 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 288 removed outlier: 3.756A pdb=" N ALA G 280 " --> pdb=" O ASP G 276 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE G 281 " --> pdb=" O GLN G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 311 removed outlier: 3.764A pdb=" N GLU G 298 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG G 300 " --> pdb=" O PRO G 296 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN G 301 " --> pdb=" O THR G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 333 Processing helix chain 'G' and resid 334 through 349 Processing helix chain 'G' and resid 349 through 370 Processing helix chain 'G' and resid 378 through 390 removed outlier: 3.581A pdb=" N SER G 382 " --> pdb=" O ASP G 378 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN G 384 " --> pdb=" O LEU G 380 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS G 385 " --> pdb=" O GLY G 381 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE G 386 " --> pdb=" O SER G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 414 Processing helix chain 'G' and resid 427 through 436 removed outlier: 3.555A pdb=" N LEU G 431 " --> pdb=" O PRO G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 443 Processing helix chain 'G' and resid 445 through 458 Processing helix chain 'G' and resid 459 through 503 Proline residue: G 470 - end of helix Processing helix chain 'H' and resid 107 through 126 removed outlier: 3.527A pdb=" N GLU H 126 " --> pdb=" O ASP H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 163 through 203 removed outlier: 3.575A pdb=" N GLN H 171 " --> pdb=" O LEU H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 259 removed outlier: 3.787A pdb=" N GLU H 242 " --> pdb=" O GLN H 238 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER H 243 " --> pdb=" O ASP H 239 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 288 removed outlier: 3.757A pdb=" N ALA H 280 " --> pdb=" O ASP H 276 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE H 281 " --> pdb=" O GLN H 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 311 removed outlier: 3.764A pdb=" N GLU H 298 " --> pdb=" O THR H 294 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG H 300 " --> pdb=" O PRO H 296 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN H 301 " --> pdb=" O THR H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 333 Processing helix chain 'H' and resid 334 through 349 Processing helix chain 'H' and resid 349 through 370 Processing helix chain 'H' and resid 378 through 390 removed outlier: 3.581A pdb=" N SER H 382 " --> pdb=" O ASP H 378 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASN H 384 " --> pdb=" O LEU H 380 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS H 385 " --> pdb=" O GLY H 381 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE H 386 " --> pdb=" O SER H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 400 through 414 Processing helix chain 'H' and resid 427 through 436 removed outlier: 3.556A pdb=" N LEU H 431 " --> pdb=" O PRO H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 439 through 443 Processing helix chain 'H' and resid 445 through 458 Processing helix chain 'H' and resid 459 through 503 Proline residue: H 470 - end of helix Processing helix chain 'I' and resid 107 through 126 removed outlier: 3.527A pdb=" N GLU I 126 " --> pdb=" O ASP I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 163 through 203 removed outlier: 3.574A pdb=" N GLN I 171 " --> pdb=" O LEU I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 259 removed outlier: 3.786A pdb=" N GLU I 242 " --> pdb=" O GLN I 238 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER I 243 " --> pdb=" O ASP I 239 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE I 250 " --> pdb=" O ALA I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 288 removed outlier: 3.756A pdb=" N ALA I 280 " --> pdb=" O ASP I 276 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE I 281 " --> pdb=" O GLN I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 311 removed outlier: 3.765A pdb=" N GLU I 298 " --> pdb=" O THR I 294 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ARG I 300 " --> pdb=" O PRO I 296 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN I 301 " --> pdb=" O THR I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 333 Processing helix chain 'I' and resid 334 through 349 Processing helix chain 'I' and resid 349 through 370 Processing helix chain 'I' and resid 378 through 390 removed outlier: 3.582A pdb=" N SER I 382 " --> pdb=" O ASP I 378 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASN I 384 " --> pdb=" O LEU I 380 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS I 385 " --> pdb=" O GLY I 381 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE I 386 " --> pdb=" O SER I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 400 through 414 Processing helix chain 'I' and resid 427 through 436 removed outlier: 3.556A pdb=" N LEU I 431 " --> pdb=" O PRO I 427 " (cutoff:3.500A) Processing helix chain 'I' and resid 439 through 443 Processing helix chain 'I' and resid 445 through 458 Processing helix chain 'I' and resid 459 through 503 Proline residue: I 470 - end of helix Processing helix chain 'J' and resid 107 through 126 removed outlier: 3.527A pdb=" N GLU J 126 " --> pdb=" O ASP J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 152 Processing helix chain 'J' and resid 163 through 203 removed outlier: 3.575A pdb=" N GLN J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 259 removed outlier: 3.787A pdb=" N GLU J 242 " --> pdb=" O GLN J 238 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER J 243 " --> pdb=" O ASP J 239 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE J 250 " --> pdb=" O ALA J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 288 removed outlier: 3.756A pdb=" N ALA J 280 " --> pdb=" O ASP J 276 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE J 281 " --> pdb=" O GLN J 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 311 removed outlier: 3.764A pdb=" N GLU J 298 " --> pdb=" O THR J 294 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG J 300 " --> pdb=" O PRO J 296 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN J 301 " --> pdb=" O THR J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 333 Processing helix chain 'J' and resid 334 through 349 Processing helix chain 'J' and resid 349 through 370 Processing helix chain 'J' and resid 378 through 390 removed outlier: 3.581A pdb=" N SER J 382 " --> pdb=" O ASP J 378 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN J 384 " --> pdb=" O LEU J 380 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS J 385 " --> pdb=" O GLY J 381 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE J 386 " --> pdb=" O SER J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 400 through 414 Processing helix chain 'J' and resid 427 through 436 removed outlier: 3.556A pdb=" N LEU J 431 " --> pdb=" O PRO J 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 439 through 443 Processing helix chain 'J' and resid 445 through 458 Processing helix chain 'J' and resid 459 through 503 Proline residue: J 470 - end of helix Processing helix chain 'K' and resid 107 through 126 removed outlier: 3.528A pdb=" N GLU K 126 " --> pdb=" O ASP K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 163 through 203 removed outlier: 3.574A pdb=" N GLN K 171 " --> pdb=" O LEU K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 259 removed outlier: 3.786A pdb=" N GLU K 242 " --> pdb=" O GLN K 238 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER K 243 " --> pdb=" O ASP K 239 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE K 250 " --> pdb=" O ALA K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 274 through 288 removed outlier: 3.757A pdb=" N ALA K 280 " --> pdb=" O ASP K 276 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE K 281 " --> pdb=" O GLN K 277 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 311 removed outlier: 3.763A pdb=" N GLU K 298 " --> pdb=" O THR K 294 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ARG K 300 " --> pdb=" O PRO K 296 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN K 301 " --> pdb=" O THR K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 333 Processing helix chain 'K' and resid 334 through 349 Processing helix chain 'K' and resid 349 through 370 Processing helix chain 'K' and resid 378 through 390 removed outlier: 3.581A pdb=" N SER K 382 " --> pdb=" O ASP K 378 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASN K 384 " --> pdb=" O LEU K 380 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS K 385 " --> pdb=" O GLY K 381 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE K 386 " --> pdb=" O SER K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 400 through 414 Processing helix chain 'K' and resid 427 through 436 removed outlier: 3.555A pdb=" N LEU K 431 " --> pdb=" O PRO K 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 439 through 443 Processing helix chain 'K' and resid 445 through 458 Processing helix chain 'K' and resid 459 through 503 Proline residue: K 470 - end of helix Processing helix chain 'L' and resid 107 through 126 removed outlier: 3.528A pdb=" N GLU L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 163 through 203 removed outlier: 3.574A pdb=" N GLN L 171 " --> pdb=" O LEU L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 259 removed outlier: 3.786A pdb=" N GLU L 242 " --> pdb=" O GLN L 238 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER L 243 " --> pdb=" O ASP L 239 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE L 250 " --> pdb=" O ALA L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 288 removed outlier: 3.757A pdb=" N ALA L 280 " --> pdb=" O ASP L 276 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE L 281 " --> pdb=" O GLN L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 311 removed outlier: 3.764A pdb=" N GLU L 298 " --> pdb=" O THR L 294 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ARG L 300 " --> pdb=" O PRO L 296 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN L 301 " --> pdb=" O THR L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 333 Processing helix chain 'L' and resid 334 through 349 Processing helix chain 'L' and resid 349 through 370 Processing helix chain 'L' and resid 378 through 390 removed outlier: 3.581A pdb=" N SER L 382 " --> pdb=" O ASP L 378 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASN L 384 " --> pdb=" O LEU L 380 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS L 385 " --> pdb=" O GLY L 381 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE L 386 " --> pdb=" O SER L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 414 Processing helix chain 'L' and resid 427 through 436 removed outlier: 3.555A pdb=" N LEU L 431 " --> pdb=" O PRO L 427 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 443 Processing helix chain 'L' and resid 445 through 458 Processing helix chain 'L' and resid 459 through 503 Proline residue: L 470 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 416 through 417 Processing sheet with id=AA2, first strand: chain 'B' and resid 416 through 417 Processing sheet with id=AA3, first strand: chain 'C' and resid 416 through 417 Processing sheet with id=AA4, first strand: chain 'D' and resid 416 through 417 Processing sheet with id=AA5, first strand: chain 'E' and resid 416 through 417 Processing sheet with id=AA6, first strand: chain 'F' and resid 416 through 417 Processing sheet with id=AA7, first strand: chain 'G' and resid 416 through 417 Processing sheet with id=AA8, first strand: chain 'H' and resid 416 through 417 Processing sheet with id=AA9, first strand: chain 'I' and resid 416 through 417 Processing sheet with id=AB1, first strand: chain 'J' and resid 416 through 417 Processing sheet with id=AB2, first strand: chain 'K' and resid 416 through 417 Processing sheet with id=AB3, first strand: chain 'L' and resid 416 through 417 2880 hydrogen bonds defined for protein. 8532 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.06 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 12924 1.35 - 1.46: 6284 1.46 - 1.58: 15796 1.58 - 1.70: 0 1.70 - 1.82: 264 Bond restraints: 35268 Sorted by residual: bond pdb=" C SER L 295 " pdb=" N PRO L 296 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.63e+00 bond pdb=" C SER B 295 " pdb=" N PRO B 296 " ideal model delta sigma weight residual 1.334 1.364 -0.030 2.34e-02 1.83e+03 1.61e+00 bond pdb=" C SER J 295 " pdb=" N PRO J 296 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.57e+00 bond pdb=" C SER C 295 " pdb=" N PRO C 296 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.57e+00 bond pdb=" C SER I 295 " pdb=" N PRO I 296 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.56e+00 ... (remaining 35263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 46181 1.49 - 2.98: 999 2.98 - 4.47: 244 4.47 - 5.96: 84 5.96 - 7.45: 48 Bond angle restraints: 47556 Sorted by residual: angle pdb=" N GLU B 361 " pdb=" CA GLU B 361 " pdb=" CB GLU B 361 " ideal model delta sigma weight residual 110.12 115.26 -5.14 1.47e+00 4.63e-01 1.22e+01 angle pdb=" N GLU C 361 " pdb=" CA GLU C 361 " pdb=" CB GLU C 361 " ideal model delta sigma weight residual 110.12 115.24 -5.12 1.47e+00 4.63e-01 1.21e+01 angle pdb=" N GLU I 361 " pdb=" CA GLU I 361 " pdb=" CB GLU I 361 " ideal model delta sigma weight residual 110.12 115.24 -5.12 1.47e+00 4.63e-01 1.21e+01 angle pdb=" N GLU G 361 " pdb=" CA GLU G 361 " pdb=" CB GLU G 361 " ideal model delta sigma weight residual 110.12 115.21 -5.09 1.47e+00 4.63e-01 1.20e+01 angle pdb=" N GLU L 361 " pdb=" CA GLU L 361 " pdb=" CB GLU L 361 " ideal model delta sigma weight residual 110.12 115.21 -5.09 1.47e+00 4.63e-01 1.20e+01 ... (remaining 47551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 19514 15.45 - 30.90: 1785 30.90 - 46.35: 541 46.35 - 61.81: 132 61.81 - 77.26: 156 Dihedral angle restraints: 22128 sinusoidal: 8508 harmonic: 13620 Sorted by residual: dihedral pdb=" CA PRO I 296 " pdb=" C PRO I 296 " pdb=" N THR I 297 " pdb=" CA THR I 297 " ideal model delta harmonic sigma weight residual 180.00 163.08 16.92 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA PRO L 296 " pdb=" C PRO L 296 " pdb=" N THR L 297 " pdb=" CA THR L 297 " ideal model delta harmonic sigma weight residual 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA PRO C 296 " pdb=" C PRO C 296 " pdb=" N THR C 297 " pdb=" CA THR C 297 " ideal model delta harmonic sigma weight residual 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 22125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3640 0.029 - 0.059: 1206 0.059 - 0.088: 432 0.088 - 0.118: 146 0.118 - 0.147: 36 Chirality restraints: 5460 Sorted by residual: chirality pdb=" CA GLU F 467 " pdb=" N GLU F 467 " pdb=" C GLU F 467 " pdb=" CB GLU F 467 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA GLU K 467 " pdb=" N GLU K 467 " pdb=" C GLU K 467 " pdb=" CB GLU K 467 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA GLU G 467 " pdb=" N GLU G 467 " pdb=" C GLU G 467 " pdb=" CB GLU G 467 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.32e-01 ... (remaining 5457 not shown) Planarity restraints: 6552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR G 297 " 0.008 2.00e-02 2.50e+03 1.50e-02 2.25e+00 pdb=" C THR G 297 " -0.026 2.00e-02 2.50e+03 pdb=" O THR G 297 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU G 298 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 297 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.24e+00 pdb=" C THR H 297 " 0.026 2.00e-02 2.50e+03 pdb=" O THR H 297 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU H 298 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 297 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C THR I 297 " 0.026 2.00e-02 2.50e+03 pdb=" O THR I 297 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU I 298 " -0.009 2.00e-02 2.50e+03 ... (remaining 6549 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 260 2.54 - 3.13: 30691 3.13 - 3.72: 61360 3.72 - 4.31: 70795 4.31 - 4.90: 115291 Nonbonded interactions: 278397 Sorted by model distance: nonbonded pdb=" O ASP K 263 " pdb=" NZ LYS L 165 " model vdw 1.955 3.120 nonbonded pdb=" NH2 ARG C 252 " pdb=" O LYS D 165 " model vdw 2.165 3.120 nonbonded pdb=" OG1 THR K 262 " pdb=" NZ LYS L 165 " model vdw 2.189 3.120 nonbonded pdb=" O ARG L 357 " pdb=" OG1 THR L 360 " model vdw 2.199 3.040 nonbonded pdb=" O ARG I 357 " pdb=" OG1 THR I 360 " model vdw 2.200 3.040 ... (remaining 278392 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 12.900 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.140 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 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 : 0.002 0.030 35268 Z= 0.120 Angle : 0.603 7.448 47556 Z= 0.327 Chirality : 0.037 0.147 5460 Planarity : 0.003 0.030 6552 Dihedral : 15.259 77.257 13248 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.13), residues: 4668 helix: 2.39 (0.09), residues: 3648 sheet: None (None), residues: 0 loop : -1.93 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 252 TYR 0.005 0.001 TYR F 363 PHE 0.006 0.001 PHE E 411 TRP 0.000 0.000 TRP A 397 HIS 0.001 0.000 HIS G 198 Details of bonding type rmsd covalent geometry : bond 0.00237 (35268) covalent geometry : angle 0.60332 (47556) hydrogen bonds : bond 0.11109 ( 2880) hydrogen bonds : angle 4.68703 ( 8532) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 ASN cc_start: 0.8590 (t0) cc_final: 0.8188 (t0) REVERT: B 122 ASP cc_start: 0.8708 (m-30) cc_final: 0.8447 (t0) REVERT: B 237 PHE cc_start: 0.8490 (t80) cc_final: 0.8230 (t80) REVERT: B 324 MET cc_start: 0.7966 (mmp) cc_final: 0.7726 (mmm) REVERT: B 403 ASP cc_start: 0.7665 (t70) cc_final: 0.7334 (t70) REVERT: C 402 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8383 (tm-30) REVERT: C 403 ASP cc_start: 0.8522 (t70) cc_final: 0.8173 (t70) REVERT: C 405 ASN cc_start: 0.8951 (m-40) cc_final: 0.8514 (m-40) REVERT: D 436 ASN cc_start: 0.8674 (t0) cc_final: 0.8326 (t0) REVERT: E 436 ASN cc_start: 0.8554 (t0) cc_final: 0.8247 (t0) REVERT: F 436 ASN cc_start: 0.8566 (t0) cc_final: 0.8307 (t0) REVERT: G 251 MET cc_start: 0.7561 (mtt) cc_final: 0.6661 (mtt) REVERT: G 436 ASN cc_start: 0.8691 (t0) cc_final: 0.8393 (t0) REVERT: H 436 ASN cc_start: 0.8479 (t0) cc_final: 0.8107 (t0) REVERT: I 436 ASN cc_start: 0.8589 (t0) cc_final: 0.8226 (t0) REVERT: J 436 ASN cc_start: 0.8577 (t0) cc_final: 0.8256 (t0) REVERT: K 122 ASP cc_start: 0.8481 (m-30) cc_final: 0.8113 (t0) REVERT: K 123 MET cc_start: 0.6157 (mmp) cc_final: 0.5904 (mmp) REVERT: K 324 MET cc_start: 0.7720 (mmp) cc_final: 0.7323 (mmm) REVERT: K 345 ILE cc_start: 0.8400 (mm) cc_final: 0.8149 (mm) REVERT: K 402 GLN cc_start: 0.8699 (tp-100) cc_final: 0.8463 (tm-30) REVERT: K 403 ASP cc_start: 0.7836 (t70) cc_final: 0.7573 (t70) REVERT: K 473 ARG cc_start: 0.7316 (ttm110) cc_final: 0.6473 (ttp-170) REVERT: L 436 ASN cc_start: 0.8469 (t0) cc_final: 0.8120 (t0) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.1971 time to fit residues: 121.1002 Evaluate side-chains 291 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 432 optimal weight: 0.0170 chunk 197 optimal weight: 50.0000 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 6.9990 overall best weight: 5.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 GLN B 402 GLN C 405 ASN G 405 ASN H 405 ASN K 277 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.064547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.054463 restraints weight = 378870.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.055205 restraints weight = 291755.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.055718 restraints weight = 241545.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.056098 restraints weight = 210610.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.056363 restraints weight = 189691.177| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 35268 Z= 0.122 Angle : 0.534 8.510 47556 Z= 0.289 Chirality : 0.037 0.136 5460 Planarity : 0.004 0.041 6552 Dihedral : 3.313 15.151 5064 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.14 % Allowed : 5.40 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.78 (0.13), residues: 4668 helix: 2.78 (0.08), residues: 3624 sheet: None (None), residues: 0 loop : -1.82 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 365 TYR 0.008 0.001 TYR K 363 PHE 0.011 0.001 PHE E 411 TRP 0.000 0.000 TRP A 397 HIS 0.001 0.000 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00243 (35268) covalent geometry : angle 0.53390 (47556) hydrogen bonds : bond 0.03648 ( 2880) hydrogen bonds : angle 3.68855 ( 8532) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 334 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.1006 (mmp) cc_final: 0.0764 (mmm) REVERT: A 267 MET cc_start: 0.8693 (tpp) cc_final: 0.8038 (ttt) REVERT: B 237 PHE cc_start: 0.8616 (t80) cc_final: 0.8228 (t80) REVERT: B 324 MET cc_start: 0.8369 (mmp) cc_final: 0.8013 (mmm) REVERT: B 429 LYS cc_start: 0.9113 (pptt) cc_final: 0.8767 (pptt) REVERT: C 267 MET cc_start: 0.8744 (tpp) cc_final: 0.8194 (mmp) REVERT: C 324 MET cc_start: 0.8696 (mmp) cc_final: 0.8378 (mmm) REVERT: C 402 GLN cc_start: 0.8978 (tp-100) cc_final: 0.8599 (tp40) REVERT: C 405 ASN cc_start: 0.9197 (m110) cc_final: 0.8709 (m-40) REVERT: C 462 MET cc_start: 0.8954 (mmm) cc_final: 0.8677 (mmp) REVERT: D 436 ASN cc_start: 0.8769 (t0) cc_final: 0.8405 (t0) REVERT: E 324 MET cc_start: 0.8585 (mmp) cc_final: 0.8299 (mmm) REVERT: E 405 ASN cc_start: 0.8961 (m-40) cc_final: 0.8500 (m-40) REVERT: E 462 MET cc_start: 0.8923 (mmm) cc_final: 0.8354 (mmp) REVERT: F 324 MET cc_start: 0.8804 (mmp) cc_final: 0.8528 (mmm) REVERT: F 436 ASN cc_start: 0.8847 (t0) cc_final: 0.8557 (t0) REVERT: G 260 MET cc_start: 0.0061 (mmp) cc_final: -0.0356 (mmm) REVERT: G 436 ASN cc_start: 0.8784 (t0) cc_final: 0.8576 (t0) REVERT: H 436 ASN cc_start: 0.8355 (t0) cc_final: 0.8123 (t0) REVERT: I 260 MET cc_start: 0.1074 (mmp) cc_final: -0.0041 (mmm) REVERT: I 267 MET cc_start: 0.9009 (tpp) cc_final: 0.8357 (tmm) REVERT: I 436 ASN cc_start: 0.8741 (t0) cc_final: 0.8367 (t0) REVERT: J 267 MET cc_start: 0.9109 (tpp) cc_final: 0.8897 (tmm) REVERT: J 405 ASN cc_start: 0.8931 (m-40) cc_final: 0.8613 (m110) REVERT: J 436 ASN cc_start: 0.8574 (t0) cc_final: 0.8354 (t0) REVERT: K 122 ASP cc_start: 0.8329 (m-30) cc_final: 0.7996 (t0) REVERT: K 260 MET cc_start: 0.3333 (mpp) cc_final: 0.2499 (mpp) REVERT: K 324 MET cc_start: 0.8327 (mmp) cc_final: 0.7860 (mmm) REVERT: K 361 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: K 367 VAL cc_start: 0.8566 (t) cc_final: 0.8243 (t) REVERT: K 429 LYS cc_start: 0.9124 (pptt) cc_final: 0.8826 (pptt) REVERT: K 473 ARG cc_start: 0.8169 (ttm110) cc_final: 0.7827 (ptp-170) REVERT: L 436 ASN cc_start: 0.8402 (t0) cc_final: 0.8201 (t0) outliers start: 5 outliers final: 0 residues processed: 339 average time/residue: 0.1752 time to fit residues: 97.8994 Evaluate side-chains 280 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 454 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 42 optimal weight: 0.0670 chunk 374 optimal weight: 8.9990 chunk 353 optimal weight: 50.0000 chunk 239 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 438 optimal weight: 50.0000 chunk 222 optimal weight: 8.9990 chunk 236 optimal weight: 50.0000 chunk 164 optimal weight: 9.9990 overall best weight: 7.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 ASN B 406 ASN D 405 ASN E 405 ASN F 405 ASN I 405 ASN J 405 ASN K 406 ASN L 405 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.063413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.053349 restraints weight = 379546.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.054086 restraints weight = 290875.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.054599 restraints weight = 240131.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.054951 restraints weight = 208788.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.055211 restraints weight = 189191.996| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35268 Z= 0.126 Angle : 0.541 9.170 47556 Z= 0.295 Chirality : 0.038 0.151 5460 Planarity : 0.004 0.034 6552 Dihedral : 3.342 16.701 5064 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.14 % Allowed : 2.79 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.83 (0.13), residues: 4668 helix: 2.85 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.89 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 365 TYR 0.007 0.001 TYR K 363 PHE 0.019 0.001 PHE C 411 TRP 0.000 0.000 TRP A 397 HIS 0.002 0.001 HIS K 198 Details of bonding type rmsd covalent geometry : bond 0.00258 (35268) covalent geometry : angle 0.54142 (47556) hydrogen bonds : bond 0.03558 ( 2880) hydrogen bonds : angle 3.63468 ( 8532) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 322 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.1250 (mmp) cc_final: 0.0972 (mmm) REVERT: A 267 MET cc_start: 0.8913 (tpp) cc_final: 0.8093 (ttt) REVERT: B 237 PHE cc_start: 0.8676 (t80) cc_final: 0.8316 (t80) REVERT: B 324 MET cc_start: 0.8341 (mmp) cc_final: 0.8017 (mmm) REVERT: B 436 ASN cc_start: 0.8698 (t0) cc_final: 0.8332 (p0) REVERT: C 267 MET cc_start: 0.8777 (tpp) cc_final: 0.8144 (mmp) REVERT: C 324 MET cc_start: 0.8830 (mmp) cc_final: 0.8524 (mmm) REVERT: C 402 GLN cc_start: 0.9044 (tp-100) cc_final: 0.8688 (tp40) REVERT: C 405 ASN cc_start: 0.9152 (m110) cc_final: 0.8550 (m110) REVERT: C 436 ASN cc_start: 0.8765 (t0) cc_final: 0.8536 (t0) REVERT: C 462 MET cc_start: 0.9012 (mmm) cc_final: 0.8745 (mmp) REVERT: D 251 MET cc_start: 0.7336 (mtt) cc_final: 0.7008 (mtt) REVERT: D 436 ASN cc_start: 0.8752 (t0) cc_final: 0.8502 (t0) REVERT: E 202 MET cc_start: 0.7226 (tmm) cc_final: 0.6661 (tmm) REVERT: E 324 MET cc_start: 0.8671 (mmp) cc_final: 0.8392 (mmp) REVERT: F 324 MET cc_start: 0.8963 (mmp) cc_final: 0.8663 (mmp) REVERT: G 251 MET cc_start: 0.7380 (mtt) cc_final: 0.6988 (mtt) REVERT: I 260 MET cc_start: 0.1134 (mmp) cc_final: 0.0361 (mmm) REVERT: J 260 MET cc_start: 0.1602 (mmp) cc_final: 0.0599 (mmm) REVERT: K 324 MET cc_start: 0.8463 (mmp) cc_final: 0.7950 (mmm) REVERT: K 361 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8293 (pm20) REVERT: K 402 GLN cc_start: 0.4087 (tm-30) cc_final: 0.3715 (tm-30) REVERT: L 436 ASN cc_start: 0.8500 (t0) cc_final: 0.8283 (t0) outliers start: 5 outliers final: 0 residues processed: 327 average time/residue: 0.1750 time to fit residues: 93.8786 Evaluate side-chains 265 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 264 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 255 optimal weight: 8.9990 chunk 39 optimal weight: 60.0000 chunk 58 optimal weight: 6.9990 chunk 313 optimal weight: 8.9990 chunk 361 optimal weight: 2.9990 chunk 458 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 3 optimal weight: 40.0000 chunk 211 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.063185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.053201 restraints weight = 376761.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.053966 restraints weight = 287058.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.054458 restraints weight = 234877.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.054823 restraints weight = 204467.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.055066 restraints weight = 184662.197| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35268 Z= 0.112 Angle : 0.532 9.143 47556 Z= 0.284 Chirality : 0.037 0.140 5460 Planarity : 0.004 0.040 6552 Dihedral : 3.326 15.155 5064 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.32 % Allowed : 1.70 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.94 (0.13), residues: 4668 helix: 2.93 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.81 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 488 TYR 0.007 0.001 TYR D 363 PHE 0.028 0.001 PHE A 411 TRP 0.000 0.000 TRP A 397 HIS 0.001 0.000 HIS K 198 Details of bonding type rmsd covalent geometry : bond 0.00230 (35268) covalent geometry : angle 0.53233 (47556) hydrogen bonds : bond 0.03395 ( 2880) hydrogen bonds : angle 3.50283 ( 8532) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 325 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.0920 (mmp) cc_final: 0.0715 (mmm) REVERT: A 267 MET cc_start: 0.8899 (tpp) cc_final: 0.8673 (mmm) REVERT: A 403 ASP cc_start: 0.8899 (t70) cc_final: 0.8671 (t70) REVERT: A 436 ASN cc_start: 0.8759 (t0) cc_final: 0.8498 (t0) REVERT: B 324 MET cc_start: 0.8330 (mmp) cc_final: 0.8081 (mmm) REVERT: C 202 MET cc_start: 0.7192 (tpp) cc_final: 0.6925 (tpp) REVERT: C 267 MET cc_start: 0.8855 (tpp) cc_final: 0.8216 (mmp) REVERT: C 324 MET cc_start: 0.8813 (mmp) cc_final: 0.8467 (mmm) REVERT: C 402 GLN cc_start: 0.9048 (tp-100) cc_final: 0.8671 (tp40) REVERT: C 405 ASN cc_start: 0.9141 (m110) cc_final: 0.8559 (m110) REVERT: C 462 MET cc_start: 0.8953 (mmm) cc_final: 0.8717 (mmp) REVERT: D 436 ASN cc_start: 0.8738 (t0) cc_final: 0.8524 (t0) REVERT: E 324 MET cc_start: 0.8794 (mmp) cc_final: 0.8424 (mmm) REVERT: E 462 MET cc_start: 0.9021 (mmp) cc_final: 0.8718 (mmp) REVERT: F 260 MET cc_start: 0.0835 (mmp) cc_final: 0.0274 (mmm) REVERT: F 324 MET cc_start: 0.8941 (mmp) cc_final: 0.8649 (mmm) REVERT: G 267 MET cc_start: 0.8812 (mmm) cc_final: 0.8570 (ttt) REVERT: G 436 ASN cc_start: 0.8735 (t0) cc_final: 0.8517 (t0) REVERT: I 260 MET cc_start: 0.0807 (mmp) cc_final: 0.0168 (mmm) REVERT: I 267 MET cc_start: 0.9057 (tpp) cc_final: 0.8745 (tmm) REVERT: K 324 MET cc_start: 0.8502 (mmp) cc_final: 0.8029 (mmm) REVERT: K 405 ASN cc_start: 0.8488 (m110) cc_final: 0.8279 (m-40) REVERT: L 267 MET cc_start: 0.8802 (mmp) cc_final: 0.8187 (ttt) REVERT: L 436 ASN cc_start: 0.8505 (t0) cc_final: 0.8294 (t0) outliers start: 11 outliers final: 4 residues processed: 336 average time/residue: 0.1944 time to fit residues: 106.7293 Evaluate side-chains 278 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 274 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 350 optimal weight: 30.0000 chunk 256 optimal weight: 8.9990 chunk 150 optimal weight: 50.0000 chunk 35 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 344 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 272 optimal weight: 20.0000 chunk 320 optimal weight: 30.0000 chunk 45 optimal weight: 8.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 402 GLN K 406 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.062512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.052523 restraints weight = 380195.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.053259 restraints weight = 288583.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.053777 restraints weight = 237081.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.054079 restraints weight = 205419.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.054350 restraints weight = 187941.633| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35268 Z= 0.115 Angle : 0.546 7.266 47556 Z= 0.293 Chirality : 0.037 0.137 5460 Planarity : 0.004 0.048 6552 Dihedral : 3.320 15.591 5064 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.06 % Allowed : 2.44 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.01 (0.13), residues: 4668 helix: 2.95 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.67 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 452 TYR 0.006 0.001 TYR K 363 PHE 0.024 0.001 PHE A 411 TRP 0.000 0.000 TRP A 397 HIS 0.001 0.000 HIS K 198 Details of bonding type rmsd covalent geometry : bond 0.00236 (35268) covalent geometry : angle 0.54565 (47556) hydrogen bonds : bond 0.03439 ( 2880) hydrogen bonds : angle 3.48378 ( 8532) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.0782 (mmp) cc_final: 0.0516 (mmm) REVERT: A 403 ASP cc_start: 0.8910 (t70) cc_final: 0.8700 (t70) REVERT: A 436 ASN cc_start: 0.8733 (t0) cc_final: 0.8477 (t0) REVERT: B 324 MET cc_start: 0.8411 (mmp) cc_final: 0.8096 (mmm) REVERT: B 462 MET cc_start: 0.8884 (mmm) cc_final: 0.8636 (mmm) REVERT: C 267 MET cc_start: 0.8870 (tpp) cc_final: 0.8241 (mmp) REVERT: C 324 MET cc_start: 0.8891 (mmp) cc_final: 0.8512 (mmm) REVERT: C 402 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8623 (tp40) REVERT: C 405 ASN cc_start: 0.9189 (m110) cc_final: 0.8571 (m-40) REVERT: D 251 MET cc_start: 0.7613 (mtm) cc_final: 0.7162 (mtt) REVERT: D 436 ASN cc_start: 0.8784 (t0) cc_final: 0.8558 (t0) REVERT: E 251 MET cc_start: 0.7496 (mtm) cc_final: 0.7090 (mtp) REVERT: E 324 MET cc_start: 0.8907 (mmp) cc_final: 0.8469 (mmm) REVERT: F 324 MET cc_start: 0.9029 (mmp) cc_final: 0.8699 (mmm) REVERT: G 436 ASN cc_start: 0.8691 (t0) cc_final: 0.8478 (t0) REVERT: I 267 MET cc_start: 0.9092 (tpp) cc_final: 0.8808 (tmm) REVERT: I 324 MET cc_start: 0.8685 (mmp) cc_final: 0.8477 (mmm) REVERT: K 405 ASN cc_start: 0.8531 (m110) cc_final: 0.8299 (m-40) REVERT: L 436 ASN cc_start: 0.8490 (t0) cc_final: 0.8280 (t0) outliers start: 2 outliers final: 0 residues processed: 328 average time/residue: 0.1946 time to fit residues: 103.8574 Evaluate side-chains 264 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 118 optimal weight: 6.9990 chunk 418 optimal weight: 50.0000 chunk 14 optimal weight: 20.0000 chunk 67 optimal weight: 40.0000 chunk 219 optimal weight: 9.9990 chunk 351 optimal weight: 220.0000 chunk 119 optimal weight: 30.0000 chunk 71 optimal weight: 10.0000 chunk 202 optimal weight: 50.0000 chunk 385 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 384 ASN J 384 ASN K 402 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.061763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.051871 restraints weight = 380314.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.052591 restraints weight = 287245.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.053091 restraints weight = 235660.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.053383 restraints weight = 204205.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.053633 restraints weight = 187070.455| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 35268 Z= 0.125 Angle : 0.563 7.937 47556 Z= 0.299 Chirality : 0.038 0.145 5460 Planarity : 0.004 0.050 6552 Dihedral : 3.413 17.169 5064 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.05 (0.13), residues: 4668 helix: 2.95 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.53 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 357 TYR 0.006 0.001 TYR J 363 PHE 0.027 0.001 PHE A 411 TRP 0.000 0.000 TRP A 397 HIS 0.001 0.001 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00258 (35268) covalent geometry : angle 0.56332 (47556) hydrogen bonds : bond 0.03589 ( 2880) hydrogen bonds : angle 3.55548 ( 8532) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.7106 (mtm) cc_final: 0.6726 (mtp) REVERT: A 260 MET cc_start: 0.0687 (mmp) cc_final: 0.0409 (mmm) REVERT: A 436 ASN cc_start: 0.8729 (t0) cc_final: 0.8505 (t0) REVERT: B 457 MET cc_start: 0.8540 (ppp) cc_final: 0.8241 (ppp) REVERT: C 267 MET cc_start: 0.8925 (tpp) cc_final: 0.8240 (mmm) REVERT: C 324 MET cc_start: 0.8885 (mmp) cc_final: 0.8623 (mmm) REVERT: C 402 GLN cc_start: 0.9022 (tp-100) cc_final: 0.8669 (tm-30) REVERT: C 405 ASN cc_start: 0.9168 (m110) cc_final: 0.8605 (m-40) REVERT: D 251 MET cc_start: 0.7257 (mtm) cc_final: 0.6855 (mtp) REVERT: D 436 ASN cc_start: 0.8808 (t0) cc_final: 0.8600 (t0) REVERT: E 324 MET cc_start: 0.8991 (mmp) cc_final: 0.8534 (mmm) REVERT: F 324 MET cc_start: 0.8998 (mmp) cc_final: 0.8734 (mmm) REVERT: G 436 ASN cc_start: 0.8764 (t0) cc_final: 0.8563 (t0) REVERT: H 251 MET cc_start: 0.7323 (mtm) cc_final: 0.7108 (mtp) REVERT: H 462 MET cc_start: 0.8969 (mmm) cc_final: 0.8478 (mmp) REVERT: I 267 MET cc_start: 0.9174 (tpp) cc_final: 0.8962 (tmm) REVERT: I 324 MET cc_start: 0.8809 (mmp) cc_final: 0.8571 (mmp) REVERT: K 267 MET cc_start: 0.9008 (mmm) cc_final: 0.8738 (mmm) REVERT: K 324 MET cc_start: 0.9068 (mmm) cc_final: 0.8220 (mmm) REVERT: L 260 MET cc_start: 0.0357 (mmm) cc_final: 0.0091 (mmm) REVERT: L 267 MET cc_start: 0.8837 (mmp) cc_final: 0.8141 (ttt) REVERT: L 436 ASN cc_start: 0.8548 (t0) cc_final: 0.8342 (t0) outliers start: 1 outliers final: 1 residues processed: 321 average time/residue: 0.2061 time to fit residues: 106.4958 Evaluate side-chains 267 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 261 optimal weight: 10.0000 chunk 247 optimal weight: 20.0000 chunk 49 optimal weight: 0.0670 chunk 25 optimal weight: 30.0000 chunk 234 optimal weight: 220.0000 chunk 70 optimal weight: 20.0000 chunk 262 optimal weight: 50.0000 chunk 209 optimal weight: 50.0000 chunk 401 optimal weight: 30.0000 chunk 255 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 overall best weight: 12.0132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN K 149 ASN ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 402 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.060695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.050821 restraints weight = 384296.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.051536 restraints weight = 287801.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.052035 restraints weight = 235117.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.052372 restraints weight = 203164.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.052610 restraints weight = 183965.344| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35268 Z= 0.163 Angle : 0.623 8.989 47556 Z= 0.335 Chirality : 0.039 0.150 5460 Planarity : 0.004 0.051 6552 Dihedral : 3.668 18.330 5064 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.06 % Allowed : 1.09 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.70 (0.13), residues: 4668 helix: 2.67 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.55 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 369 TYR 0.023 0.001 TYR H 240 PHE 0.028 0.002 PHE C 411 TRP 0.000 0.000 TRP A 397 HIS 0.002 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00339 (35268) covalent geometry : angle 0.62266 (47556) hydrogen bonds : bond 0.04107 ( 2880) hydrogen bonds : angle 3.86058 ( 8532) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 305 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.0770 (mmp) cc_final: 0.0478 (mmm) REVERT: A 267 MET cc_start: 0.8906 (mmm) cc_final: 0.8632 (tpt) REVERT: B 324 MET cc_start: 0.9139 (mmm) cc_final: 0.8373 (mmm) REVERT: C 260 MET cc_start: 0.1573 (mmt) cc_final: 0.1220 (mmm) REVERT: C 267 MET cc_start: 0.8956 (tpp) cc_final: 0.8405 (mmm) REVERT: C 324 MET cc_start: 0.9050 (mmp) cc_final: 0.8676 (mmm) REVERT: C 402 GLN cc_start: 0.9026 (tp-100) cc_final: 0.8650 (tm-30) REVERT: C 405 ASN cc_start: 0.9272 (m110) cc_final: 0.8723 (m110) REVERT: C 457 MET cc_start: 0.8230 (ppp) cc_final: 0.7960 (ppp) REVERT: D 324 MET cc_start: 0.8787 (mmp) cc_final: 0.8535 (mmm) REVERT: D 384 ASN cc_start: 0.8974 (p0) cc_final: 0.8611 (p0) REVERT: D 436 ASN cc_start: 0.8744 (t0) cc_final: 0.8522 (t0) REVERT: E 324 MET cc_start: 0.8927 (mmp) cc_final: 0.8558 (mmm) REVERT: E 462 MET cc_start: 0.9165 (mmm) cc_final: 0.8681 (mmp) REVERT: F 260 MET cc_start: 0.0985 (mmm) cc_final: 0.0768 (mmm) REVERT: F 324 MET cc_start: 0.9007 (mmp) cc_final: 0.8670 (mmm) REVERT: G 324 MET cc_start: 0.8740 (mmp) cc_final: 0.8434 (mmm) REVERT: H 324 MET cc_start: 0.8745 (mmp) cc_final: 0.8508 (mmm) REVERT: H 462 MET cc_start: 0.8996 (mmm) cc_final: 0.8505 (mmp) REVERT: I 260 MET cc_start: 0.0878 (mmm) cc_final: 0.0584 (mmm) REVERT: I 324 MET cc_start: 0.8944 (mmp) cc_final: 0.8632 (mmm) REVERT: K 267 MET cc_start: 0.8961 (mmm) cc_final: 0.8733 (mmm) REVERT: K 324 MET cc_start: 0.9011 (mmm) cc_final: 0.8284 (mmm) REVERT: K 405 ASN cc_start: 0.8823 (m110) cc_final: 0.8608 (m-40) REVERT: L 436 ASN cc_start: 0.8672 (t0) cc_final: 0.8449 (t0) outliers start: 2 outliers final: 2 residues processed: 307 average time/residue: 0.1905 time to fit residues: 96.0780 Evaluate side-chains 257 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 255 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 445 optimal weight: 20.0000 chunk 437 optimal weight: 20.0000 chunk 375 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 464 optimal weight: 9.9990 chunk 364 optimal weight: 50.0000 chunk 231 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 461 optimal weight: 8.9990 chunk 312 optimal weight: 220.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.060885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.051056 restraints weight = 383731.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.051792 restraints weight = 285902.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.052307 restraints weight = 232674.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.052649 restraints weight = 200659.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.052867 restraints weight = 181237.664| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35268 Z= 0.131 Angle : 0.592 8.274 47556 Z= 0.313 Chirality : 0.038 0.153 5460 Planarity : 0.004 0.054 6552 Dihedral : 3.540 16.789 5064 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.13), residues: 4668 helix: 2.77 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.52 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 369 TYR 0.018 0.002 TYR E 240 PHE 0.023 0.001 PHE A 411 TRP 0.000 0.000 TRP A 397 HIS 0.002 0.001 HIS H 198 Details of bonding type rmsd covalent geometry : bond 0.00273 (35268) covalent geometry : angle 0.59180 (47556) hydrogen bonds : bond 0.03813 ( 2880) hydrogen bonds : angle 3.67675 ( 8532) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.0691 (mmp) cc_final: 0.0337 (mmm) REVERT: A 384 ASN cc_start: 0.8996 (p0) cc_final: 0.8681 (p0) REVERT: B 457 MET cc_start: 0.8434 (ppp) cc_final: 0.7931 (ppp) REVERT: C 202 MET cc_start: 0.6903 (tpt) cc_final: 0.6313 (tmm) REVERT: C 267 MET cc_start: 0.8949 (tpp) cc_final: 0.8360 (mmm) REVERT: C 270 MET cc_start: 0.8001 (tpt) cc_final: 0.7202 (mpp) REVERT: C 324 MET cc_start: 0.9045 (mmp) cc_final: 0.8670 (mmm) REVERT: C 402 GLN cc_start: 0.9076 (tp-100) cc_final: 0.8663 (tm-30) REVERT: C 405 ASN cc_start: 0.9244 (m110) cc_final: 0.8709 (m-40) REVERT: C 457 MET cc_start: 0.8210 (ppp) cc_final: 0.7948 (ppp) REVERT: D 267 MET cc_start: 0.9046 (mmm) cc_final: 0.8689 (tpt) REVERT: D 324 MET cc_start: 0.8867 (mmp) cc_final: 0.8590 (mmm) REVERT: E 324 MET cc_start: 0.9033 (mmm) cc_final: 0.8443 (mmm) REVERT: E 405 ASN cc_start: 0.9077 (m110) cc_final: 0.8571 (m110) REVERT: F 202 MET cc_start: 0.7076 (tmm) cc_final: 0.6762 (tmm) REVERT: F 324 MET cc_start: 0.8960 (mmm) cc_final: 0.8573 (mmp) REVERT: G 324 MET cc_start: 0.8814 (mmp) cc_final: 0.8493 (mmm) REVERT: G 436 ASN cc_start: 0.8812 (t0) cc_final: 0.8607 (t0) REVERT: H 324 MET cc_start: 0.8852 (mmp) cc_final: 0.8532 (mmm) REVERT: I 324 MET cc_start: 0.8848 (mmp) cc_final: 0.8630 (mmm) REVERT: K 267 MET cc_start: 0.9025 (mmm) cc_final: 0.8730 (mmm) REVERT: K 324 MET cc_start: 0.9043 (mmm) cc_final: 0.8699 (mmm) REVERT: L 202 MET cc_start: 0.7149 (tmm) cc_final: 0.6667 (tmm) REVERT: L 436 ASN cc_start: 0.8669 (t0) cc_final: 0.8452 (t0) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1880 time to fit residues: 93.8364 Evaluate side-chains 250 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 279 optimal weight: 50.0000 chunk 127 optimal weight: 0.7980 chunk 237 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 270 optimal weight: 6.9990 chunk 284 optimal weight: 50.0000 chunk 240 optimal weight: 6.9990 chunk 202 optimal weight: 50.0000 chunk 172 optimal weight: 30.0000 chunk 113 optimal weight: 6.9990 chunk 234 optimal weight: 220.0000 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 406 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.061018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.051265 restraints weight = 381906.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.051999 restraints weight = 285248.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.052513 restraints weight = 232289.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.052845 restraints weight = 200342.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.053095 restraints weight = 181112.069| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 35268 Z= 0.123 Angle : 0.601 10.578 47556 Z= 0.317 Chirality : 0.038 0.161 5460 Planarity : 0.004 0.055 6552 Dihedral : 3.479 16.132 5064 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.91 (0.13), residues: 4668 helix: 2.82 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.49 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 357 TYR 0.017 0.001 TYR E 240 PHE 0.021 0.001 PHE A 411 TRP 0.000 0.000 TRP A 397 HIS 0.001 0.000 HIS C 198 Details of bonding type rmsd covalent geometry : bond 0.00254 (35268) covalent geometry : angle 0.60134 (47556) hydrogen bonds : bond 0.03718 ( 2880) hydrogen bonds : angle 3.66413 ( 8532) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 MET cc_start: 0.7282 (mtm) cc_final: 0.6764 (mtp) REVERT: A 260 MET cc_start: 0.1369 (mmp) cc_final: 0.0981 (mmm) REVERT: B 202 MET cc_start: 0.6863 (tpt) cc_final: 0.6454 (tpp) REVERT: B 457 MET cc_start: 0.8340 (ppp) cc_final: 0.7855 (ppp) REVERT: C 202 MET cc_start: 0.6870 (tpt) cc_final: 0.6298 (tmm) REVERT: C 267 MET cc_start: 0.8998 (tpp) cc_final: 0.8364 (mmm) REVERT: C 270 MET cc_start: 0.8034 (tpt) cc_final: 0.7198 (mpp) REVERT: C 324 MET cc_start: 0.9109 (mmm) cc_final: 0.8541 (mmm) REVERT: C 402 GLN cc_start: 0.9063 (tp-100) cc_final: 0.8660 (tm-30) REVERT: C 405 ASN cc_start: 0.9234 (m110) cc_final: 0.8692 (m110) REVERT: C 457 MET cc_start: 0.8185 (ppp) cc_final: 0.7916 (ppp) REVERT: D 267 MET cc_start: 0.8979 (mmm) cc_final: 0.8636 (tpt) REVERT: D 324 MET cc_start: 0.8883 (mmp) cc_final: 0.8577 (mmm) REVERT: E 267 MET cc_start: 0.8891 (mmm) cc_final: 0.8589 (tpt) REVERT: E 324 MET cc_start: 0.8989 (mmm) cc_final: 0.8404 (mmm) REVERT: E 405 ASN cc_start: 0.9073 (m110) cc_final: 0.8560 (m110) REVERT: F 260 MET cc_start: 0.0552 (mmm) cc_final: 0.0196 (mmp) REVERT: F 324 MET cc_start: 0.8958 (mmm) cc_final: 0.8550 (mmp) REVERT: F 411 PHE cc_start: 0.8099 (m-10) cc_final: 0.7859 (m-80) REVERT: G 267 MET cc_start: 0.8981 (mmm) cc_final: 0.8758 (tpt) REVERT: G 324 MET cc_start: 0.8852 (mmp) cc_final: 0.8501 (mmm) REVERT: H 251 MET cc_start: 0.7386 (mtm) cc_final: 0.6949 (mtp) REVERT: H 324 MET cc_start: 0.8843 (mmp) cc_final: 0.8539 (mmm) REVERT: H 436 ASN cc_start: 0.8590 (t0) cc_final: 0.8388 (t0) REVERT: I 260 MET cc_start: 0.0469 (mmm) cc_final: 0.0129 (mmm) REVERT: I 267 MET cc_start: 0.9126 (tpp) cc_final: 0.8303 (tpt) REVERT: I 324 MET cc_start: 0.8798 (mmp) cc_final: 0.8592 (mmm) REVERT: K 267 MET cc_start: 0.9113 (mmm) cc_final: 0.8781 (mmm) REVERT: K 324 MET cc_start: 0.9004 (mmm) cc_final: 0.8662 (mmm) REVERT: L 202 MET cc_start: 0.7089 (tmm) cc_final: 0.6575 (tmm) REVERT: L 260 MET cc_start: -0.0509 (mmm) cc_final: -0.0749 (mmm) REVERT: L 267 MET cc_start: 0.8972 (mmm) cc_final: 0.8357 (tpt) REVERT: L 436 ASN cc_start: 0.8657 (t0) cc_final: 0.8448 (t0) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.2041 time to fit residues: 101.0217 Evaluate side-chains 256 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 0 optimal weight: 120.0000 chunk 7 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 142 optimal weight: 1.9990 chunk 434 optimal weight: 50.0000 chunk 285 optimal weight: 50.0000 chunk 440 optimal weight: 50.0000 chunk 266 optimal weight: 8.9990 chunk 288 optimal weight: 0.0470 chunk 89 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 overall best weight: 5.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 384 ASN H 277 GLN ** H 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 277 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.061094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.051369 restraints weight = 382617.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.052114 restraints weight = 285297.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.052634 restraints weight = 231802.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.052986 restraints weight = 199228.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.053233 restraints weight = 179846.939| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 35268 Z= 0.121 Angle : 0.607 10.271 47556 Z= 0.318 Chirality : 0.038 0.159 5460 Planarity : 0.004 0.056 6552 Dihedral : 3.419 15.662 5064 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.99 (0.13), residues: 4668 helix: 2.87 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.42 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 365 TYR 0.010 0.001 TYR E 240 PHE 0.022 0.001 PHE A 411 TRP 0.000 0.000 TRP A 397 HIS 0.001 0.000 HIS J 198 Details of bonding type rmsd covalent geometry : bond 0.00250 (35268) covalent geometry : angle 0.60677 (47556) hydrogen bonds : bond 0.03641 ( 2880) hydrogen bonds : angle 3.61502 ( 8532) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.1256 (mmp) cc_final: 0.0894 (mmm) REVERT: A 436 ASN cc_start: 0.8803 (t0) cc_final: 0.8556 (t0) REVERT: B 202 MET cc_start: 0.6791 (tpt) cc_final: 0.6447 (tpp) REVERT: B 324 MET cc_start: 0.9159 (mmm) cc_final: 0.8468 (mmm) REVERT: B 457 MET cc_start: 0.8334 (ppp) cc_final: 0.7906 (ppp) REVERT: C 202 MET cc_start: 0.6705 (tpt) cc_final: 0.6172 (tmm) REVERT: C 267 MET cc_start: 0.9031 (tpp) cc_final: 0.8437 (mmm) REVERT: C 270 MET cc_start: 0.8121 (tpt) cc_final: 0.7295 (mpp) REVERT: C 324 MET cc_start: 0.9116 (mmm) cc_final: 0.8523 (mmm) REVERT: C 402 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8635 (tm-30) REVERT: C 405 ASN cc_start: 0.9222 (m110) cc_final: 0.8658 (m110) REVERT: C 457 MET cc_start: 0.8151 (ppp) cc_final: 0.7934 (ppp) REVERT: D 267 MET cc_start: 0.8925 (mmm) cc_final: 0.8606 (tpt) REVERT: D 324 MET cc_start: 0.8836 (mmp) cc_final: 0.8493 (mmm) REVERT: D 436 ASN cc_start: 0.8874 (t0) cc_final: 0.8637 (t0) REVERT: E 324 MET cc_start: 0.8981 (mmm) cc_final: 0.8397 (mmm) REVERT: E 405 ASN cc_start: 0.9056 (m110) cc_final: 0.8555 (m110) REVERT: F 260 MET cc_start: 0.0489 (mmm) cc_final: -0.0072 (mmp) REVERT: F 324 MET cc_start: 0.8975 (mmm) cc_final: 0.8505 (mmm) REVERT: G 267 MET cc_start: 0.8985 (mmm) cc_final: 0.8671 (tpt) REVERT: G 324 MET cc_start: 0.8828 (mmp) cc_final: 0.8469 (mmm) REVERT: H 267 MET cc_start: 0.8975 (mmm) cc_final: 0.8552 (tpt) REVERT: H 324 MET cc_start: 0.8794 (mmp) cc_final: 0.8434 (mmp) REVERT: I 260 MET cc_start: 0.0380 (mmm) cc_final: 0.0020 (mmm) REVERT: I 267 MET cc_start: 0.9107 (tpp) cc_final: 0.8363 (tpt) REVERT: I 324 MET cc_start: 0.8803 (mmp) cc_final: 0.8584 (mmm) REVERT: J 324 MET cc_start: 0.8714 (mmp) cc_final: 0.8465 (mmm) REVERT: K 267 MET cc_start: 0.9121 (mmm) cc_final: 0.8764 (mmm) REVERT: K 324 MET cc_start: 0.8988 (mmm) cc_final: 0.8418 (mmm) REVERT: K 457 MET cc_start: 0.8327 (ppp) cc_final: 0.7990 (ppp) REVERT: L 202 MET cc_start: 0.6924 (tmm) cc_final: 0.6413 (tmm) REVERT: L 260 MET cc_start: -0.0183 (mmm) cc_final: -0.0839 (mmm) REVERT: L 267 MET cc_start: 0.8911 (mmm) cc_final: 0.8337 (tpt) REVERT: L 436 ASN cc_start: 0.8645 (t0) cc_final: 0.8411 (t0) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1924 time to fit residues: 98.1054 Evaluate side-chains 256 residues out of total 3852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 5 optimal weight: 50.0000 chunk 84 optimal weight: 4.9990 chunk 166 optimal weight: 50.0000 chunk 272 optimal weight: 50.0000 chunk 113 optimal weight: 8.9990 chunk 357 optimal weight: 7.9990 chunk 258 optimal weight: 9.9990 chunk 209 optimal weight: 20.0000 chunk 429 optimal weight: 220.0000 chunk 163 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 ASN ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.060696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.050962 restraints weight = 382212.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.051703 restraints weight = 286060.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.052219 restraints weight = 232950.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.052569 restraints weight = 200731.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.052812 restraints weight = 180888.023| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35268 Z= 0.130 Angle : 0.605 9.918 47556 Z= 0.320 Chirality : 0.039 0.216 5460 Planarity : 0.004 0.055 6552 Dihedral : 3.463 18.191 5064 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.54 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.13), residues: 4668 helix: 2.84 (0.08), residues: 3612 sheet: None (None), residues: 0 loop : -1.48 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 164 TYR 0.011 0.001 TYR E 240 PHE 0.030 0.001 PHE B 411 TRP 0.000 0.000 TRP A 397 HIS 0.001 0.001 HIS I 198 Details of bonding type rmsd covalent geometry : bond 0.00270 (35268) covalent geometry : angle 0.60507 (47556) hydrogen bonds : bond 0.03742 ( 2880) hydrogen bonds : angle 3.67693 ( 8532) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5077.31 seconds wall clock time: 88 minutes 44.50 seconds (5324.50 seconds total)